Merge pull request #2904 from glemieux/fates-switch-migration

ctsm5.3.027: Migrate FATES parameter file switches to the namelist

.gitmodules

@@ -28,7 +28,7 @@
 [submodule "fates"]
 path = src/fates
 url = https://github.com/NGEET/fates
-fxtag = sci.1.81.0_api.37.1.0
+fxtag = sci.1.81.1_api.38.0.0
 fxrequired = AlwaysRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/NCAR/fates-release

bld/CLMBuildNamelist.pm

@@ -808,7 +808,11 @@ 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", "fates_photosynth_acclimation", "fates_stomatal_model",
+                      "fates_stomatal_assimilation", "fates_leafresp_model", "fates_cstarvation_model",
+                      "fates_regeneration_model", "fates_hydro_solver", "fates_radiation_model", "fates_electron_transport_model"
+                   );
 
        # dis-allow fates specific namelist items with non-fates runs
        foreach my $var ( @list ) {
@@ -4707,7 +4711,11 @@ sub setup_logic_fates {
         add_default($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", "fates_photosynth_acclimation", "fates_stomatal_model",
+                       "fates_stomatal_assimilation", "fates_leafresp_model", "fates_cstarvation_model",
+                       "fates_regeneration_model", "fates_hydro_solver", "fates_radiation_model", "fates_electron_transport_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

@@ -532,7 +532,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- FATES default parameter file                                       -->
 <!-- ================================================================== -->
 
-<fates_paramfile>lnd/clm2/paramdata/fates_params_api.37.1.0_14pft_c250214.nc</fates_paramfile>
+<fates_paramfile>lnd/clm2/paramdata/fates_params_api.38.0.0_14pft_c250226.nc</fates_paramfile>
 
 
 <!-- ================================================================== -->
@@ -2387,31 +2387,41 @@ 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 =========== -->
-<fates_spitfire_mode           use_fates=".true.">0</fates_spitfire_mode>
-<fates_harvest_mode            use_fates=".true.">no_harvest</fates_harvest_mode>
-<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_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>
-<use_fates_sp                  use_fates=".true.">.false.</use_fates_sp>
-<use_fates_lupft               use_fates=".true.">.false.</use_fates_lupft>
-<use_fates_potentialveg        use_fates=".true.">.false.</use_fates_potentialveg>
-<use_fates_luh                 use_fates=".true." fates_harvest_mode="luhdata_area"  >.true.</use_fates_luh>
-<use_fates_luh                 use_fates=".true." fates_harvest_mode="luhdata_mass"  >.true.</use_fates_luh>
-<use_fates_luh                 use_fates=".true." use_fates_lupft=".true.">.true.</use_fates_luh>
-<use_fates_luh                 use_fates=".true." use_fates_potentialveg=".true.">.true.</use_fates_luh>
-<use_fates_luh                 use_fates=".true."                                >.false.</use_fates_luh>
-<fates_parteh_mode             use_fates=".true.">1</fates_parteh_mode>
-<fates_seeddisp_cadence        use_fates=".true.">0</fates_seeddisp_cadence>
-<use_fates_nocomp              use_fates=".true." use_fates_sp=".true."   >.true.</use_fates_nocomp>
-<use_fates_nocomp              use_fates=".true." use_fates_lupft=".true.">.true.</use_fates_nocomp>
-<use_fates_nocomp              use_fates=".true."                         >.false.</use_fates_nocomp>
-<use_fates_fixed_biogeog       use_fates=".true." use_fates_sp=".true."   >.true.</use_fates_fixed_biogeog>
-<use_fates_fixed_biogeog       use_fates=".true." use_fates_lupft=".true.">.true.</use_fates_fixed_biogeog>
-<use_fates_fixed_biogeog       use_fates=".true."                         >.false.</use_fates_fixed_biogeog>
-<fates_history_dimlevel        use_fates=".true.">2,2</fates_history_dimlevel>
+<fates_electron_transport_model use_fates=".true.">FvCB1980</fates_electron_transport_model>
+<fates_photosynth_acclimation   use_fates=".true.">nonacclimating</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_model           use_fates=".true.">ballberry1987</fates_stomatal_model>
+<fates_stomatal_assimilation    use_fates=".true.">net</fates_stomatal_assimilation>
+<fates_leafresp_model           use_fates=".true.">ryan1991</fates_leafresp_model>
+<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.">2D_Picard</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>
+<use_fates_sp                   use_fates=".true.">.false.</use_fates_sp>
+<use_fates_lupft                use_fates=".true.">.false.</use_fates_lupft>
+<use_fates_potentialveg         use_fates=".true.">.false.</use_fates_potentialveg>
+<use_fates_luh                  use_fates=".true." fates_harvest_mode="luhdata_area"  >.true.</use_fates_luh>
+<use_fates_luh                  use_fates=".true." fates_harvest_mode="luhdata_mass"  >.true.</use_fates_luh>
+<use_fates_luh                  use_fates=".true." use_fates_lupft=".true.">.true.</use_fates_luh>
+<use_fates_luh                  use_fates=".true." use_fates_potentialveg=".true.">.true.</use_fates_luh>
+<use_fates_luh                  use_fates=".true."                                >.false.</use_fates_luh>
+<fates_parteh_mode              use_fates=".true.">1</fates_parteh_mode>
+<fates_seeddisp_cadence         use_fates=".true.">0</fates_seeddisp_cadence>
+<use_fates_nocomp               use_fates=".true." use_fates_sp=".true."   >.true.</use_fates_nocomp>
+<use_fates_nocomp               use_fates=".true." use_fates_lupft=".true.">.true.</use_fates_nocomp>
+<use_fates_nocomp               use_fates=".true."                         >.false.</use_fates_nocomp>
+<use_fates_fixed_biogeog        use_fates=".true." use_fates_sp=".true."   >.true.</use_fates_fixed_biogeog>
+<use_fates_fixed_biogeog        use_fates=".true." use_fates_lupft=".true.">.true.</use_fates_fixed_biogeog>
+<use_fates_fixed_biogeog        use_fates=".true."                         >.false.</use_fates_fixed_biogeog>
+<fates_history_dimlevel         use_fates=".true.">2,2</fates_history_dimlevel>
 
 
 <!-- =========================================  -->

bld/namelist_files/namelist_definition_ctsm.xml

@@ -780,6 +780,64 @@ 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_electron_transport_model" type="char*256" category="physics"
+        group="elm_inparm" valid_values="FvCB1980,JohnsonBerry2021" value="FvCB1980">
+Set the FATES electron transport model to either Johnson-Berry 2021 or
+  Farquhar von Caemmerer and Berry 1980 (FvCB1980).
+
+</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_leafresp_model" type="char*256" category="physics"
+        group="clm_inparm" valid_values="ryan1991,atkin2017" value="ryan1991">
+Set the FATES leaf maintenance respiration 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="fates_stomatal_model" type="char*256" category="physics"
+        group="clm_inparm" valid_values="ballberry1987,medlyn2011" value="ballberry1987">
+Set the FATES stomatal conductance model
+</entry>
+
+<entry id="fates_photosynth_acclimation" type="char*256" category="physics"
+       group="clm_inparm" valid_values="nonacclimating,kumarathunge2019" value="nonacclimating">
+Set the FATES 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

cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStream/user_nl_clm

@@ -1 +1 @@
-fates_paramfile = '$CASEROOT/fates_params_twostream.nc'
+fates_radiation_model = 'twostream'

cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStreamNoCompFixedBioGeo/user_nl_clm

@@ -1,2 +1,2 @@
-fates_paramfile = '$CASEROOT/fates_params_twostream.nc'
-use_fates_fixed_biogeog=.true.
+use_fates_fixed_biogeog=.true.
+fates_radiation_model = 'twostream'

doc/ChangeLog

@@ -1,4 +1,95 @@
 ===============================================================
+Tag name: ctsm5.3.027
+Originator(s): glemieux (Gregory Lemieux, LBNL, [email protected])
+Date: Sun Mar  2 15:27:01 PST 2025
+One-line Summary: FATES parameter file switch migration
+
+Purpose and description of changes
+----------------------------------
+
+Move global FATES switches from the FATES parameter file to the namelist.
+
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm6_0
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+Notes of particular relevance for users
+---------------------------------------
+
+Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables):
+
+The following FATES namelist options are now available:
+   - use_fates_daylength_factor
+   - fates_photosynth_acclimation
+   - fates_stomatal_model
+   - fates_stomatal_assimilation
+   - fates_leafresp_model
+   - fates_cstarvation_model
+   - fates_regeneration_model
+   - fates_hydro_solver
+   - fates_radiation_model
+
+The following FATES namelist option is available, but not yet implemented in FATES:
+   - fates_electron_transport_model
+
+Notes of particular relevance for developers:
+---------------------------------------------
+Changes to tests or testing:
+
+The FATES two stream tests no longer generation a FATES NetCDF parameter file on-the-fly.
+The need to do so is removed as the fates_radiation_model option is controlled by the
+namelist.
+
+
+Testing summary:
+----------------
+
+  build-namelist tests (if CLMBuildNamelist.pm has changed):
+
+    derecho - PASS
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+  fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates-<FATES TAG>-<CTSM TAG>)
+    derecho ----- OK
+    izumi ------- OK
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: No
+
+Other details
+-------------
+
+List any git submodules updated (cime, rtm, mosart, cism, fates, etc.):
+   fates: sci.1.81.0_api.37.1.0 -> sci.1.81.1_api.38.0.0
+
+Pull Requests that document the changes (include PR ids):
+(https://github.com/ESCOMP/ctsm/pull)
+https://github.com/ESCOMP/CTSM/pull/2904
+https://github.com/NGEET/fates/pull/1300
+https://github.com/NGEET/fates/pull/1344
+
+===============================================================
+===============================================================
 Tag name: ctsm5.3.026
 Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)
 Date: Wed 26 Feb 2025 09:55:48 AM MST
@@ -138,8 +229,8 @@ Testing summary:
 
   regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
 
-    derecho -----
-    izumi -------
+    derecho ----- OK
+    izumi ------- OK
 
   fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates-<FATES TAG>-<CTSM TAG>)
     derecho ----- OK

doc/ChangeSum

@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.3.027 glemieux 03/02/2025 FATES parameter file switch migration
        ctsm5.3.026 samrabin 02/26/2025 Merge b4b-dev to master: run_tower updates, reduce log noise
        ctsm5.3.025 glemieux 02/20/2025 FATES default parameter file update
        ctsm5.3.024 xinchang 02/11/2025 Change choice of pressure in CLMU building energy model

src/main/clm_varctl.F90

@@ -331,13 +331,24 @@ 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_model = ''               ! stomatal conductance model, Ball-berry or Medlyn
+  character(len=256), public :: fates_stomatal_assimilation = ''        ! net or gross assimilation modes
+  character(len=256), public :: fates_leafresp_model = ''               ! Leaf maintenance respiration model, Ryan or Atkin
+  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
+  character(len=256), public :: fates_photosynth_acclimation = ''       ! nonacclimating, kumarathunge2019
+  character(len=256), public :: fates_electron_transport_model = ''     ! Johnson-Berry 2021 or Farquhar von Caemmerer and Berry 1980
   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
+
 
   ! FATES history dimension level
   ! fates can produce history at either the daily timescale (dynamics)