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Megan fates pr follow up #100

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Megan fates pr follow up #100

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24dcb11
Add default for fates since BGC one can change.
mvdebolskiy Dec 3, 2024
618b838
refactor how pft indeces and intercellular CO2 is passed to VOCemissions
mvdebolskiy Dec 3, 2024
c34ed10
fix ci passing
mvdebolskiy Dec 3, 2024
f4af14e
fix isoprene
mvdebolskiy Dec 3, 2024
56cceed
Fix typos.
mvdebolskiy Dec 3, 2024
7f42386
revert check for sp, add patch type in the endrun.
mvdebolskiy Dec 3, 2024
b9e4b4f
add checks for bareground and fix canopy fluxes
mvdebolskiy Dec 6, 2024
4ec97f2
Add cisun and cisha to history
mvdebolskiy Dec 6, 2024
6b7fdc9
add extra fields to FatesColdMeganSatPhen test
mvdebolskiy Dec 6, 2024
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1 change: 1 addition & 0 deletions bld/namelist_files/namelist_defaults_drydep.xml
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Expand Up @@ -25,6 +25,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).

<megan_specifier>'ISOP = isoprene', 'C10H16 = pinene_a + carene_3 + thujene_a', 'CH3OH = methanol', 'C2H5OH = ethanol', 'CH2O = formaldehyde', 'CH3CHO = acetaldehyde', 'CH3COOH = acetic_acid', 'CH3COCH3 = acetone'</megan_specifier>

<megan_factors_file phys="clm6_0" use_fates=".true." >atm/cam/chem/trop_mozart/emis/megan21_emis_factors_78pft_c20161108.nc</megan_factors_file>
<megan_factors_file phys="clm6_0" >atm/cam/chem/trop_mozart/emis/megan21_emis_factors_78pft_c20161108.nc</megan_factors_file>
<megan_factors_file phys="clm5_1" >atm/cam/chem/trop_mozart/emis/megan21_emis_factors_78pft_c20161108.nc</megan_factors_file>
<megan_factors_file phys="clm5_0" >atm/cam/chem/trop_mozart/emis/megan21_emis_factors_78pft_c20161108.nc</megan_factors_file>
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58 changes: 36 additions & 22 deletions src/biogeochem/VOCEmissionMod.F90
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Expand Up @@ -85,14 +85,14 @@ module VOCEmissionMod
!------------------------------------------------------------------------
subroutine Init(this, bounds)

use clm_varctl, only : use_fates, use_fates_nocomp
use clm_varctl, only : use_fates, use_fates_nocomp, use_fates_sp
class(vocemis_type) :: this
type(bounds_type), intent(in) :: bounds


if ( shr_megan_mechcomps_n > 0) then
if (use_fates) then
if (.not. use_fates_nocomp) then
if (.not. (use_fates_nocomp .or. use_fates_sp)) then
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call endrun( msg='ERROR: MEGAN currently only works with when FATES is in SP and/or NOCOMP mode '//&
errMsg(sourcefile, __LINE__))
end if
Expand Down Expand Up @@ -417,6 +417,8 @@ subroutine VOCEmission (bounds, num_soilp, filter_soilp, &
! !USES:
use subgridAveMod , only : p2g
use clm_varctl , only : use_fates
use clm_varcon , only : smallValue
use decompMod , only : subgrid_level_patch
!
! !ARGUMENTS:
type(bounds_type) , intent(in) :: bounds
Expand Down Expand Up @@ -452,7 +454,9 @@ subroutine VOCEmission (bounds, num_soilp, filter_soilp, &
real(r8) :: par240_sha ! temporary

integer :: class_num, n_meg_comps, imech, imeg, ii
integer :: patchpft ! to transfer FATES PFT space into CLM PFT space.
integer :: l_pft_itype(bounds%begp:bounds%endp) ! local index of pft type
! that corresponds to pfts on megan factors
! for BGC it will be 1 to 1 with pftcon%itype(p)
character(len=16) :: mech_name
type(shr_megan_megcomp_t), pointer :: meg_cmp
real(r8) :: cp, alpha, Eopt, topt ! for history output
Expand Down Expand Up @@ -499,7 +503,6 @@ subroutine VOCEmission (bounds, num_soilp, filter_soilp, &
fsun240 => canopystate_inst%fsun240_patch , & ! Input: [real(r8) (:) ] sunlit fraction of canopy last 240 hrs
elai => canopystate_inst%elai_patch , & ! Input: [real(r8) (:) ] one-sided leaf area index with burying by snow
elai240 => canopystate_inst%elai240_patch , & ! Input: [real(r8) (:) ] one-sided leaf area index with burying by snow last 240 hrs
ci_fates => canopystate_inst%ci_patch , & !Input: [real(r8) (:) ] FATES-calculated internalleaf ci
cisun_z => photosyns_inst%cisun_z_patch , & ! Input: [real(r8) (:,:) ] sunlit intracellular CO2 (Pa)
cisha_z => photosyns_inst%cisha_z_patch , & ! Input: [real(r8) (:,:) ] shaded intracellular CO2 (Pa)

Expand Down Expand Up @@ -531,11 +534,27 @@ subroutine VOCEmission (bounds, num_soilp, filter_soilp, &
! initialize variables which get passed to the atmosphere
vocflx(bounds%begp:bounds%endp,:) = 0._r8
vocflx_tot(bounds%begp:bounds%endp) = 0._r8

do imeg=1,shr_megan_megcomps_n
meg_out(imeg)%flux_out(bounds%begp:bounds%endp) = 0._r8
enddo


! Get local pft types:
! this has to be done earlier, so if use_fates, we locally know what is not bare ground
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Oh right, yes, good point...

! voc_pft_index comes from fates-internal mapping between pft's in megan_factors_file and fates pfts
l_pft_itype(bounds%begp:bounds%endp) = 0
if (use_fates) then
do fp = 1,num_soilp
p = filter_soilp(fp)
l_pft_itype(p) = canopystate_inst%voc_pftindex_patch(p)
end do
else
do fp = 1,num_soilp
p = filter_soilp(fp)
l_pft_itype(p) = patch%itype(p)
end do
end if

! Begin loop over points
!_______________________________________________________________________________
do fp = 1,num_soilp
Expand All @@ -551,7 +570,7 @@ subroutine VOCEmission (bounds, num_soilp, filter_soilp, &
vocflx_meg(:) = 0._r8

! calculate VOC emissions for non-bare ground Patches
if (patch%itype(p) > 0) then
if (l_pft_itype(p) > 0) then
gamma=0._r8

! Calculate PAR: multiply w/m2 by 4.6 to get umol/m2/s for par (added 8/14/02)
Expand Down Expand Up @@ -583,16 +602,10 @@ subroutine VOCEmission (bounds, num_soilp, filter_soilp, &

! set emis factor
! if specified, set EF for isoprene with mapped values
if(use_fates)then
patchpft = canopystate_inst%voc_pftindex_patch(p)
else
patchpft = patch%itype(p)
endif

if ( trim(meg_cmp%name) == 'isoprene' .and. shr_megan_mapped_emisfctrs) then
epsilon = get_map_EF(patchpft,g, vocemis_inst)
epsilon = get_map_EF(l_pft_itype(p),g, vocemis_inst)
else
epsilon = meg_cmp%emis_factors(patchpft)
epsilon = meg_cmp%emis_factors(l_pft_itype(p))
end if


Expand All @@ -604,19 +617,20 @@ subroutine VOCEmission (bounds, num_soilp, filter_soilp, &

! Activity factor for T
gamma_t = get_gamma_T(t_veg240(p), t_veg24(p),t_veg(p), ct1(class_num), ct2(class_num),&
betaT(class_num),LDF(class_num), Ceo(class_num), Eopt, topt, patchpft)
betaT(class_num),LDF(class_num), Ceo(class_num), Eopt, topt, l_pft_itype(p))

! Activity factor for Leaf Age
gamma_a = get_gamma_A(patchpft, elai240(p),elai(p),class_num)
gamma_a = get_gamma_A(l_pft_itype(p), elai240(p),elai(p),class_num)

! Activity factor for CO2 (only for isoprene)
if (trim(meg_cmp%name) == 'isoprene') then
co2_ppmv = 1.e6_r8*forc_pco2(g)/forc_pbot(c)
if(use_fates)then
gamma_c = get_gamma_C(ci_fates(p),ci_fates(p),forc_pbot(c),fsun(p), co2_ppmv)
else
gamma_c = get_gamma_C(cisun_z(p,1),cisha_z(p,1),forc_pbot(c),fsun(p), co2_ppmv)
! Check of valid intercellular co2 pressure values.
if (cisha_z(p,nlevcan) < smallValue .or. cisun_z(p,nlevcan) < smallValue) then
write(iulog,*) 'Invalid intercellular co2 pressure (sunlit, shaded): ',cisun_z(p,nlevcan),cisha_z(p,nlevcan)
call endrun(subgrid_index=p, subgrid_level=subgrid_level_patch, msg=errMsg(sourcefile, __LINE__))
endif
co2_ppmv = 1.e6_r8*forc_pco2(g)/forc_pbot(c)
gamma_c = get_gamma_C(cisun_z(p,nlevcan),cisha_z(p,nlevcan),forc_pbot(c),fsun(p), co2_ppmv)

else
gamma_c = 1._r8
Expand Down
4 changes: 3 additions & 1 deletion src/biogeophys/CanopyFluxesMod.F90
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Expand Up @@ -1113,7 +1113,9 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp,
end do

if ( use_fates ) then

! zeroed out here for megan isoprene calculations, in case patches are not transfered properly.
photosyns_inst%cisha_z_patch(begp:endp,:) = -999._r8
photosyns_inst$cisun_z_patch(begp:endp,:) = -999._r8
call clm_fates%wrap_photosynthesis(nc, bounds, fn, filterp(1:fn), &
svpts(begp:endp), eah(begp:endp), o2(begp:endp), &
co2(begp:endp), rb(begp:endp), dayl_factor(begp:endp), &
Expand Down
2 changes: 0 additions & 2 deletions src/biogeophys/CanopyStateType.F90
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Expand Up @@ -46,7 +46,6 @@ module CanopyStateType
real(r8) , pointer :: hbot_patch (:) ! patch canopy bottom (m)
real(r8) , pointer :: z0m_patch (:) ! patch momentum roughness length (m)
real(r8) , pointer :: displa_patch (:) ! patch displacement height (m)
real(r8) , pointer :: ci_patch (:) ! Internal leaf CO2 concentration for MEGAN
real(r8) , pointer :: fsun_patch (:) ! patch sunlit fraction of canopy
real(r8) , pointer :: fsun24_patch (:) ! patch 24hr average of sunlit fraction of canopy
real(r8) , pointer :: fsun240_patch (:) ! patch 240hr average of sunlit fraction of canopy
Expand Down Expand Up @@ -141,7 +140,6 @@ subroutine InitAllocate(this, bounds)
allocate(this%hbot_patch (begp:endp)) ; this%hbot_patch (:) = nan
allocate(this%z0m_patch (begp:endp)) ; this%z0m_patch (:) = nan
allocate(this%displa_patch (begp:endp)) ; this%displa_patch (:) = nan
allocate(this%ci_patch (begp:endp)) ; this%ci_patch (:) = nan
allocate(this%fsun_patch (begp:endp)) ; this%fsun_patch (:) = nan
allocate(this%fsun24_patch (begp:endp)) ; this%fsun24_patch (:) = nan
allocate(this%fsun240_patch (begp:endp)) ; this%fsun240_patch (:) = nan
Expand Down
8 changes: 6 additions & 2 deletions src/utils/clmfates_interfaceMod.F90
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Expand Up @@ -2578,7 +2578,9 @@ subroutine wrap_photosynthesis(this, nc, bounds, fn, filterp, &
rssha => photosyns_inst%rssha_patch, &
psnsun => photosyns_inst%psnsun_patch, &
psnsha => photosyns_inst%psnsha_patch, &
ci => canopystate_inst%ci_patch)
cisun_z => photosyns_inst%cisun_z_patch, &
cisha_z => photosyns_inst%cisha_z_patch, &
)
do s = 1, this%fates(nc)%nsites

c = this%f2hmap(nc)%fcolumn(s)
Expand Down Expand Up @@ -2645,7 +2647,9 @@ subroutine wrap_photosynthesis(this, nc, bounds, fn, filterp, &
this%fates(nc)%bc_in(s)%filter_photo_pa(ifp) = 3
rssun(p) = this%fates(nc)%bc_out(s)%rssun_pa(ifp)
rssha(p) = this%fates(nc)%bc_out(s)%rssha_pa(ifp)
ci(p) = this%fates(nc)%bc_out(s)%ci_pa(ifp)
! this is needed for MEGAN to work with FATES
cisun_z(p,:) = this%fates(nc)%bc_out(s)%ci_pa(ifp)
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cisha_z(p,:) = this%fates(nc)%bc_out(s)%ci_pa(ifp)
! These fields are marked with a bad-value flag
photosyns_inst%psnsun_patch(p) = spval
photosyns_inst%psnsha_patch(p) = spval
Expand Down