Migrate FATES parameter file switches to the namelist

bld/CLMBuildNamelist.pm

@@ -808,7 +808,10 @@ sub setup_cmdl_fates_mode {
                       "use_fates_cohort_age_tracking","use_fates_inventory_init","use_fates_fixed_biogeog",
                       "use_fates_nocomp","use_fates_sp","fates_inventory_ctrl_filename","fates_harvest_mode",
                       "fates_parteh_mode","use_fates_tree_damage","fates_seeddisp_cadence","use_fates_luh","fluh_timeseries",
-                      "flandusepftdat","use_fates_potentialveg","use_fates_lupft","fates_history_dimlevel" );
+                      "flandusepftdat","use_fates_potentialveg","use_fates_lupft","fates_history_dimlevel",
+                      "use_fates_daylength_factor", "use_fates_photosynth_acclimation","fates_stomatal_assimilation",
+                      "fates_cstarvation_model", "fates_regeneration_model", "fates_hydro_solver", "fates_radiation_model"
+                    );
 
        # dis-allow fates specific namelist items with non-fates runs
        foreach my $var ( @list ) {
@@ -4702,7 +4705,10 @@ sub setup_logic_fates {
         add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fates_paramfile', 'phys'=>$nl_flags->{'phys'});
         my @list  = (  "fates_spitfire_mode", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys",
                        "use_fates_inventory_init","fates_seeddisp_cadence","fates_history_dimlevel",
-                       "fates_harvest_mode","fates_parteh_mode", "use_fates_cohort_age_tracking","use_fates_tree_damage" );
+                       "fates_harvest_mode","fates_parteh_mode", "use_fates_cohort_age_tracking","use_fates_tree_damage",
+                       "use_fates_daylength_factor", "use_fates_photosynth_acclimation","fates_stomatal_assimilation",
+                       "fates_cstarvation_model", "fates_regeneration_model", "fates_hydro_solver", "fates_radiation_model"
+                    );
 
         foreach my $var ( @list ) {
            add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'},

bld/namelist_files/namelist_defaults_ctsm.xml

@@ -2386,11 +2386,18 @@ lnd/clm2/surfdata_esmf/NEON/ctsm5.3.0/surfdata_1x1_NEON_TOOL_hist_2000_78pfts_c2
 <use_nitrif_denitrif                           >.true.</use_nitrif_denitrif>
 
 <!-- ===== FATES DEFAULTS =========== -->
+<use_fates_photosynth_acclimation use_fates=".true.">.false.</use_fates_photosynth_acclimation>
 <fates_spitfire_mode           use_fates=".true.">0</fates_spitfire_mode>
 <fates_harvest_mode            use_fates=".true.">no_harvest</fates_harvest_mode>
+<fates_stomatal_assimilation   use_fates=".true.">net</fates_stomatal_assimilation>
+<fates_cstarvation_model       use_fates=".true.">linear</fates_cstarvation_model>
+<fates_regeneration_model      use_fates=".true.">default</fates_regeneration_model>
+<fates_radiation_model         use_fates=".true.">norman</fates_radiation_model>
+<fates_hydro_solver            use_fates=".true.">1D_Taylor</fates_hydro_solver>
 <use_fates_planthydro          use_fates=".true.">.false.</use_fates_planthydro>
 <use_fates_tree_damage         use_fates=".true.">.false.</use_fates_tree_damage>
 <use_fates_cohort_age_tracking use_fates=".true.">.false.</use_fates_cohort_age_tracking>
+<use_fates_daylength_factor    use_fates=".true.">.true.</use_fates_daylength_factor>
 <use_fates_ed_st3              use_fates=".true.">.false.</use_fates_ed_st3>
 <use_fates_ed_prescribed_phys  use_fates=".true.">.false.</use_fates_ed_prescribed_phys>
 <use_fates_inventory_init      use_fates=".true.">.false.</use_fates_inventory_init>

bld/namelist_files/namelist_definition_ctsm.xml

@@ -775,6 +775,47 @@ Allowed values are:
 This option is older than the luhdata options and may be depricated at some point in the future.
 </entry>
 
+<entry id="fates_radiation_model" type="char*256" category="physics"
+        group="clm_inparm" valid_values="norman, twostream" value="norman">
+Set the FATES radiation model
+</entry>
+
+<entry id="fates_hydro_solver" type="char*256" category="physics"
+        group="clm_inparm" valid_values="1D_Taylor, 2D_Picard, 2D_Newton" value="1D_Taylor">
+Set the FATES hydro solver method
+</entry>
+
+<entry id="fates_regeneration_model" type="char*256" category="physics"
+        group="clm_inparm" valid_values="default, trs, trs_no_seed_dyn" value="default">
+Set the FATES seed regeneration model
+Valid values:
+  default: default scheme
+  trs: Tree Recruitment Scheme (Hanbury-Brown et al., 2022)
+  trs_no_seed_dyn: Tree Recruitment Scheme (Hanbury-Brown et al., 2022) without seed dynamics
+</entry>
+
+<entry id="fates_cstarvation_model" type="char*256" category="physics"
+        group="clm_inparm" valid_values="linear, exponential" value="linear">
+Set the FATES carbon starvation model
+</entry>
+
+<entry id="fates_stomatal_assimilation" type="char*256" category="physics"
+        group="clm_inparm" valid_values="net, gross" value="net">
+Set net or gross asslimiation for the FATES stomatal model
+</entry>
+
+<entry id="use_fates_photosynth_acclimation" type="logical" category="physics"
+       group="clm_inparm" valid_values="" value=".false.">
+If TRUE, enable FATES to use a photosynthesis temperature acclimation model.
+(Only relevant if FATES is on)
+</entry>
+
+<entry id="use_fates_daylength_factor" type="logical" category="physics"
+       group="clm_inparm" valid_values="" value=".true.">
+If TRUE, enable FATES to utilize the day length factor from the host land model.
+(Only relevant if FATES is on)
+</entry>
+
 <entry id="use_fates_planthydro" type="logical" category="physics"
        group="clm_inparm" valid_values="" value=".false.">
 Toggle to turn on plant hydraulics

src/biogeophys/PhotosynthesisMod.F90

@@ -79,8 +79,8 @@ module  PhotosynthesisMod
   integer, parameter, public  :: root=4                 ! index for root
   integer, parameter, public  :: veg=vegetation_weibull ! index for vegetation
   integer, parameter, public  :: soil=1                 ! index for soil
-  integer, parameter, private :: stomatalcond_mtd_bb1987     = 1   ! Ball-Berry 1987 method for photosynthesis
-  integer, parameter, private :: stomatalcond_mtd_medlyn2011 = 2   ! Medlyn 2011 method for photosynthesis
+  integer, parameter, public  :: stomatalcond_mtd_bb1987     = 1   ! Ball-Berry 1987 method for photosynthesis
+  integer, parameter, public  :: stomatalcond_mtd_medlyn2011 = 2   ! Medlyn 2011 method for photosynthesis
 
   real(r8), parameter, private :: bbbopt_c3 = 10000._r8            ! Ball-Berry Photosynthesis intercept to use for C3 vegetation
   real(r8), parameter, private :: bbbopt_c4 = 40000._r8            ! Ball-Berry Photosynthesis intercept to use for C4 vegetation

src/main/clm_varctl.F90

@@ -331,13 +331,21 @@ module clm_varctl
                                                                         ! see bld/namelist_files/namelist_definition_clm4_5.xml for details
   logical, public            :: use_fates_tree_damage = .false.         ! true => turn on tree damage module
   character(len=256), public :: fates_harvest_mode = ''                 ! five different harvest modes; see namelist definition
+  character(len=256), public :: fates_stomatal_assimilation = ''        ! net or gross assimilation modes
+  character(len=256), public :: fates_cstarvation_model = ''            ! linear or exponential function
+  character(len=256), public :: fates_regeneration_model = ''           ! default, TRS, or TRS without seed dynamics
+  character(len=256), public :: fates_radiation_model = ''              ! Norman or two-stream radiation model
+  character(len=256), public :: fates_hydro_solver = ''                 ! 1D Taylor, 2D Picard, 2D Newton
   logical, public            :: use_fates_planthydro = .false.          ! true => turn on fates hydro
   logical, public            :: use_fates_cohort_age_tracking = .false. ! true => turn on cohort age tracking
   logical, public            :: use_fates_ed_st3   = .false.            ! true => static stand structure
   logical, public            :: use_fates_ed_prescribed_phys = .false.  ! true => prescribed physiology
   logical, public            :: use_fates_inventory_init = .false.      ! true => initialize fates from inventory
   logical, public            :: use_fates_fixed_biogeog = .false.       ! true => use fixed biogeography mode
   logical, public            :: use_fates_nocomp = .false.              ! true => use no comopetition mode
+  logical, public            :: use_fates_daylength_factor = .false.    ! true => enable fates to use host land model daylength factor
+
+  logical, public            :: use_fates_photosynth_acclimation = .false.    ! true => enable fates to use photosynthetic temperature acclimation
 
   ! FATES history dimension level
   ! fates can produce history at either the daily timescale (dynamics)

src/main/controlMod.F90

@@ -242,9 +242,16 @@ subroutine control_init(dtime)
           fluh_timeseries,                              &
           flandusepftdat,                               &
           fates_inventory_ctrl_filename,                &
+          fates_stomatal_assimilation,                  &
+          fates_cstarvation_model,                      &
+          fates_regeneration_model,                     &
+          fates_radiation_model,                        &
+          fates_hydro_solver,                           &
           fates_parteh_mode,                            &
           fates_seeddisp_cadence,                       &
           use_fates_tree_damage,                        &
+          use_fates_daylength_factor,                   &
+          use_fates_photosynth_acclimation,             &
           fates_history_dimlevel
 
     ! Ozone vegetation stress method
@@ -799,6 +806,11 @@ subroutine control_spmd()
 
     call mpi_bcast (fates_spitfire_mode, 1, MPI_INTEGER, 0, mpicom, ier)
     call mpi_bcast (fates_harvest_mode, len(fates_harvest_mode) , MPI_CHARACTER, 0, mpicom, ier)
+    call mpi_bcast (fates_stomatal_assimilation, len(fates_stomatal_assimilation) , MPI_CHARACTER, 0, mpicom, ier)
+    call mpi_bcast (fates_cstarvation_model, len(fates_cstarvation_model) , MPI_CHARACTER, 0, mpicom, ier)
+    call mpi_bcast (fates_regeneration_model, len(fates_regeneration_model) , MPI_CHARACTER, 0, mpicom, ier)
+    call mpi_bcast (fates_radiation_model, len(fates_radiation_model) , MPI_CHARACTER, 0, mpicom, ier)
+    call mpi_bcast (fates_hydro_solver, len(fates_hydro_solver) , MPI_CHARACTER, 0, mpicom, ier)
     call mpi_bcast (use_fates_planthydro, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (use_fates_tree_damage, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (use_fates_cohort_age_tracking, 1, MPI_LOGICAL, 0, mpicom, ier)
@@ -812,6 +824,8 @@ subroutine control_spmd()
     call mpi_bcast (use_fates_lupft, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (use_fates_potentialveg, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (use_fates_bgc, 1, MPI_LOGICAL, 0, mpicom, ier)
+    call mpi_bcast (use_fates_daylength_factor, 1, MPI_LOGICAL, 0, mpicom, ier)
+    call mpi_bcast (use_fates_photosynth_acclimation, 1, MPI_LOGICAL, 0, mpicom, ier)
     call mpi_bcast (fates_inventory_ctrl_filename, len(fates_inventory_ctrl_filename), MPI_CHARACTER, 0, mpicom, ier)
     call mpi_bcast (fates_paramfile, len(fates_paramfile) , MPI_CHARACTER, 0, mpicom, ier)
     call mpi_bcast (fluh_timeseries, len(fluh_timeseries) , MPI_CHARACTER, 0, mpicom, ier)
@@ -1200,11 +1214,18 @@ subroutine control_print ()
     if (use_fates) then
        write(iulog, *) '    fates_spitfire_mode = ', fates_spitfire_mode
        write(iulog, *) '    fates_harvest_mode = ', fates_harvest_mode
+       write(iulog, *) '    fates_stomatal_assimilation = ', fates_stomatal_assimilation
+       write(iulog, *) '    fates_cstarvation_model = ', fates_cstarvation_model
+       write(iulog, *) '    fates_regeneration_model = ', fates_regeneration_model
+       write(iulog, *) '    fates_radiation_model = ', fates_radiation_model
+       write(iulog, *) '    fates_hydro_solver = ', fates_hydro_solver
        write(iulog, *) '    fates_paramfile = ', fates_paramfile
        write(iulog, *) '    fates_parteh_mode = ', fates_parteh_mode
        write(iulog, *) '    use_fates_planthydro = ', use_fates_planthydro
        write(iulog, *) '    use_fates_tree_damage = ', use_fates_tree_damage
        write(iulog, *) '    use_fates_cohort_age_tracking = ', use_fates_cohort_age_tracking
+       write(iulog, *) '    use_fates_daylength_factor = ', use_fates_daylength_factor
+       write(iulog, *) '    use_fates_photosynth_acclimation = ', use_fates_photosynth_acclimation
        write(iulog, *) '    use_fates_ed_st3 = ',use_fates_ed_st3
        write(iulog, *) '    use_fates_ed_prescribed_phys = ',use_fates_ed_prescribed_phys
        write(iulog, *) '    use_fates_inventory_init = ',use_fates_inventory_init

src/utils/clmfates_interfaceMod.F90

@@ -52,9 +52,15 @@ module CLMFatesInterfaceMod
    use clm_varctl        , only : use_fates_tree_damage
    use clm_varctl        , only : use_fates_planthydro
    use clm_varctl        , only : use_fates_cohort_age_tracking
+   use clm_varctl        , only : use_fates_daylength_factor
+   use clm_varctl        , only : use_fates_photosynth_acclimation
    use clm_varctl        , only : use_fates_ed_st3
    use clm_varctl        , only : use_fates_ed_prescribed_phys
    use clm_varctl        , only : fates_harvest_mode
+   use clm_varctl        , only : fates_stomatal_assimilation
+   use clm_varctl        , only : fates_cstarvation_model
+   use clm_varctl        , only : fates_regeneration_model
+   use clm_varctl        , only : fates_hydro_solver
    use clm_varctl        , only : use_fates_inventory_init
    use clm_varctl        , only : use_fates_fixed_biogeog
    use clm_varctl        , only : use_fates_nocomp
@@ -81,6 +87,10 @@ module CLMFatesInterfaceMod
    use clm_varpar        , only : nlevdecomp_full
    use clm_varpar        , only : nlevsoi
    use PhotosynthesisMod , only : photosyns_type
+   use PhotosynthesisMod , only : leafresp_method
+   use PhotosynthesisMod , only : stomatalcond_method
+   use PhotosynthesisMod , only : stomatalcond_mtd_bb1987
+   use PhotosynthesisMod , only : stomatalcond_mtd_medlyn2011
    use atm2lndType       , only : atm2lnd_type
    use SurfaceAlbedoType , only : surfalb_type
    use SolarAbsorbedType , only : solarabs_type
@@ -399,6 +409,13 @@ subroutine CLMFatesGlobals2()
      integer                                        :: pass_use_potentialveg
      integer                                        :: pass_num_luh_states
      integer                                        :: pass_num_luh_transitions
+     integer                                        :: pass_daylength_factor_switch
+     integer                                        :: pass_stomatal_model
+     integer                                        :: pass_stomatal_assimilation
+     integer                                        :: fates_cstarvation_model
+     integer                                        :: fates_regeneration_model
+     integer                                        :: pass_hydro_solver
+     integer                                        :: pass_radiation_model
 
      call t_startf('fates_globals2')
 
@@ -515,6 +532,68 @@ subroutine CLMFatesGlobals2()
         end if
         call set_fates_ctrlparms('use_cohort_age_tracking',ival=pass_cohort_age_tracking)
 
+        if(use_fates_photosynth_acclimation) then
+           pass_photosynth_acclimation_switch = 1
+        else
+           pass_photosynth_acclimation_switch = 0
+        end if
+        call set_fates_ctrlparms('use_photosynth_acclimation',ival=pass_photosynth_acclimation_switch)
+
+        if(use_fates_daylength_factor) then
+           pass_daylength_factor_switch = 1
+        else
+           pass_daylength_factor_switch = 0
+        end if
+        call set_fates_ctrlparms('use_daylength_factor_switch',ival=pass_daylength_factor_switch)
+
+        if (trim(stomatalcond_method) == 'Ball-Berry1987') then
+           pass_stomatal_model = stomatalcond_mtd_bb1987
+        else if (trim(stomatalcond_method) == 'Medlyn2011') then
+           pass_stomatal_model = stomatalcond_mtd_medlyn2011
+        end if
+        call set_fates_ctrlparms('stomatal_model',ival=pass_stomatal_model)
+
+        if (trim(fates_stomatal_assimilation) == 'net') then
+           pass_stomatal_assimilation = 1
+        else if (trim(fates_stomatal_assimilation) == 'gross') then
+           pass_stomatal_assimilation = 2
+        end if
+        call set_fates_ctrlparms('stomatal_assim_model',ival=pass_stomatal_assimilation)
+
+        call set_fates_ctrlparms('maintresp_leaf_model',ival=leafresp_method)
+
+        if (trim(fates_cstarvation_model) == 'linear') then
+           pass_cstarvation_model = 1
+        else if (trim(fates_cstarvation_model) == 'expontential') then
+           pass_cstarvation_model = 2
+        end if
+        call set_fates_ctrlparms('mort_cstarvation_model',ival=pass_cstarvation_model)
+
+        if (trim(fates_regeneration_model) == 'default') then
+           pass_regeneration_model = 1
+        else if (trim(fates_regeneration_model) == 'trs') then
+           pass_regeneration_model = 2
+        else if (trim(fates_regeneration_model) == 'trs_no_seed_dyn') then
+           pass_regeneration_model = 3
+        end if
+        call set_fates_ctrlparms('regeneration_model',ival=pass_regeneration_model)
+
+        if (trim(fates_hydro_solver) == '1D_Taylor') then
+           pass_hydro_solver = 1
+        else if (trim(fates_hydro_solver) == '2D_Picard') then
+           pass_hydro_solver = 2
+        else if (trim(fates_hydro_solver) == '2D_Taylor') then
+           pass_hydro_solver = 3
+        end if
+        call set_fates_ctrlparms('hydr_solver',ival=pass_hydro_solver)
+
+        if (trim(fates_radiation_model) == 'norman') then
+           pass_radiation_model = 1
+        else if (trim(fates_hydro_solver) == 'twostream') then
+           pass_radiation_model = 2
+        end if
+        call set_fates_ctrlparms('radiation_model',ival=pass_radiation_model)
+
         ! FATES logging and harvest modes
         pass_logging = 0
         pass_lu_harvest = 0