Merge pull request #3446 from samsrabin/merge-master-20250822

Merge tag 'ctsm5.3.071' into merge-master-20250822

Author: samsrabin

.gitmodules

@@ -28,7 +28,7 @@
 [submodule "fates"]
 path = src/fates
 url = https://github.com/NGEET/fates
-fxtag = sci.1.84.0_api.40.0.0
+fxtag = sci.1.87.0_api.41.0.0
 fxrequired = AlwaysRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/NGEET/fates
@@ -44,15 +44,15 @@ fxDONOTUSEurl = https://github.com/ESCOMP/CISM-wrapper
 [submodule "rtm"]
 path = components/rtm
 url = https://github.com/ESCOMP/RTM
-fxtag = rtm1_0_88
+fxtag = rtm1_0_89
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/RTM
 
 [submodule "mosart"]
 path = components/mosart
 url = https://github.com/ESCOMP/MOSART
-fxtag = mosart1.1.10
+fxtag = mosart1.1.12
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/MOSART
@@ -76,15 +76,15 @@ fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git
 [submodule "cime"]
 path = cime
 url = https://github.com/ESMCI/cime
-fxtag = cime6.1.107
+fxtag = cime6.1.112
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESMCI/cime
 
 [submodule "cmeps"]
 path = components/cmeps
 url = https://github.com/ESCOMP/CMEPS.git
-fxtag = cmeps1.1.2
+fxtag = cmeps1.1.5
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git

bld/CLMBuildNamelist.pm

@@ -811,7 +811,8 @@ sub setup_cmdl_fates_mode {
                       "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"
+                      "fates_regeneration_model", "fates_hydro_solver", "fates_radiation_model", "fates_electron_transport_model",
+		      "use_fates_managed_fire"
                    );
 
        # dis-allow fates specific namelist items with non-fates runs
@@ -4761,12 +4762,13 @@ sub setup_logic_fates {
 
     if (&value_is_true( $nl_flags->{'use_fates'})  ) {
         add_default($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",
+        my @list  = (  "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",
                        "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"
+                       "fates_regeneration_model", "fates_hydro_solver", "fates_radiation_model", "fates_electron_transport_model",
+		       "use_fates_managed_fire"
                     );
 
         foreach my $var ( @list ) {
@@ -4786,6 +4788,9 @@ sub setup_logic_fates {
         add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_fixed_biogeog', 'use_fates'=>$nl_flags->{'use_fates'},
                     'use_fates_lupft'=>$nl->get_value('use_fates_lupft'),
                     'use_fates_sp'=>$nl_flags->{'use_fates_sp'} );
+        add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fates_spitfire_mode', 'use_fates'=>$nl_flags->{'use_fates'},
+                    'use_fates_managed_fire'=>$nl->get_value('use_fates_managed_fire'),
+                    'use_fates_sp'=>$nl_flags->{'use_fates_sp'} );
 
         my $suplnitro = $nl->get_value('suplnitro');
         my $parteh_mode = $nl->get_value('fates_parteh_mode');
@@ -4807,7 +4812,7 @@ sub setup_logic_fates {
            }
            # spit-fire can't be on with FATES SP mode is active
            if ( $nl->get_value('fates_spitfire_mode') > 0 ) {
-                 $log->fatal_error('fates_spitfire_mode can NOT be set to greater than 0 when use_fates_sp is true');
+                 $log->fatal_error("fates_spitfire_mode can NOT be set to greater than 0 when use_fates_sp is true");
            }
 
            # fates landuse can't be on with FATES SP mode is active
@@ -4920,6 +4925,16 @@ sub setup_logic_fates {
               }
            }
         }
+
+        # Check use_fates_managed_fire mode is running with spitfire on
+        my $var = "use_fates_managed_fire";
+        if ( defined($nl->get_value($var))  ) {
+           if ( &value_is_true($nl->get_value($var)) ) {
+              if ( $nl->get_value('fates_spitfire_mode') == 0 ) {
+                 $log->fatal_error("fates_spitfire_mode must be non-zero when $var is true");
+	      }
+           }
+        }
     }
 }
 

bld/namelist_files/namelist_defaults_ctsm.xml

@@ -152,8 +152,10 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <megan clm_accelerated_spinup="sasu">0</megan>
 <megan configuration="nwp"          >0</megan>
 
-<!-- Setting to TRUE replicates previous ctsm5.3.063 answers, setting to false turns the soil moisture effect off -->
-<megan_use_gamma_sm>.true.</megan_use_gamma_sm>
+<!-- The soil moisture effect was added in ctsm5.2.020 with MEGAN2.1 and was hardcoded on. -->
+<!-- As of ctsm5.3.068 megan_use_gamma_sm became default false, which is closer to MEGAN before 2.1. -->
+<!-- Hence we made megan_use_gamma_sm default off for all CLM physics versions. -->
+<megan_use_gamma_sm>.false.</megan_use_gamma_sm>
 <megan_min_gamma_sm>0.0d00</megan_min_gamma_sm>
 
 <!-- Supplmental Nitrogen mode -->
@@ -553,7 +555,7 @@ 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.40.0.0_14pft_c250512.nc</fates_paramfile>
+<fates_paramfile>lnd/clm2/paramdata/fates_params_api.41.0.0_14pft_c250813.nc</fates_paramfile>
 
 
 <!-- ================================================================== -->
@@ -2434,6 +2436,7 @@ lnd/clm2/surfdata_esmf/NEON/ctsm5.3.0/surfdata_1x1_NEON_TOOL_hist_2000_78pfts_c2
 <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_spitfire_mode            use_fates=".true." use_fates_managed_fire=".true." >1</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>
@@ -2442,6 +2445,7 @@ lnd/clm2/surfdata_esmf/NEON/ctsm5.3.0/surfdata_1x1_NEON_TOOL_hist_2000_78pfts_c2
 <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_managed_fire         use_fates=".true.">.false.</use_fates_managed_fire>
 <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>

bld/namelist_files/namelist_definition_ctsm.xml

@@ -750,6 +750,17 @@ ignitions.
 (Only relevant if FATES is on)
 </entry>
 
+<entry id="use_fates_managed_fire" type="logical" category="physics"
+        group="clm_inparm" valid_values="" value=".false.">
+Enable FATES managed fire mode.  Requires that fates_spitfire_mode is on (in any mode).
+This mode allows the FATES model to conduct fuel-load reduction through managed burns.
+The boundary conditions in which a managed fire is allowed is set via the FATES parameter
+file.  The burned area fraction of a managed burn is defined through the FATES parameter
+file as well.  This mode works in conjunction with the SPITFIRE module to determine
+whether a wildfire or managed fire takes place on a given patch.
+(Only relevant if FATES is on)
+</entry>
+
 <entry id="use_fates_fixed_biogeog" type="logical" category="physics"
         group="clm_inparm" valid_values="" value=".false.">
 Toggle to turn on fixed biogeography mode

bld/unit_testers/build-namelist_test.pl

@@ -163,7 +163,7 @@ sub cat_and_create_namelistinfile {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 3393;
+my $ntests = 3394;
 
 if ( defined($opts{'compare'}) ) {
    $ntests += 2061;
@@ -1118,6 +1118,10 @@ sub cat_and_create_namelistinfile {
                                      namelst=>"fates_spitfire_mode=1,use_fates_sp=.true.",
                                      phys=>"clm5_0",
                                    },
+     "managedfirenospitfire"    =>{ options=>"-envxml_dir . --bgc fates",
+                                     namelst=>"fates_spitfire_mode=0,use_fates_managed_fire=.true.",
+                                     phys=>"clm5_0",
+                                   },
      "usefatesspusefateshydro"   =>{ options=>"-envxml_dir . --bgc fates",
                                      namelst=>"use_fates_sp=.true.,use_fates_planthydro=.true.",
                                      phys=>"clm5_0",

cime

@@ -0,0 +1,100 @@
+"""
+Parent class for CTSM-specific tests that first run the subset_data tool and then ensure
+that CTSM does not fail using the just-generated input files
+"""
+
+import os
+import sys
+import logging
+from CIME.SystemTests.system_tests_common import SystemTestsCommon
+from CIME.user_mod_support import apply_user_mods
+from CIME.XML.standard_module_setup import *
+
+# In case we need to import subset_data later
+_CTSM_PYTHON = os.path.join(
+    os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir, "python"
+)
+sys.path.insert(1, _CTSM_PYTHON)
+
+logger = logging.getLogger(__name__)
+
+
+class SUBSETDATASHARED(SystemTestsCommon):
+    def __init__(self, case, subset_data_cmd):
+        """
+        initialize an object interface to the SMS system test
+        """
+        SystemTestsCommon.__init__(self, case)
+
+        # Check the test setup
+        if not self._case.get_value("LND_GRID") == "CLM_USRDAT":
+            raise RuntimeError("SUBSETDATA tests require resolution CLM_USRDAT")
+        if "serial" not in self._case.get_value("MPILIB"):
+            raise RuntimeError("SUBSETDATA tests require a serial MPILIB")
+        if "BGC-CROP" not in self._case.get_value("COMPSET"):
+            raise RuntimeError("SUBSETDATA tests require a BGC-CROP compset")
+
+        # Add standard subset_data arguments
+        out_dir = os.path.join(self._get_caseroot(), "subset_data_output")
+        self.usermods_dir = os.path.join(out_dir, "user_mods")
+        self.subset_data_cmd = subset_data_cmd + [
+            "--create-user-mods",
+            "--outdir",
+            out_dir,
+            "--user-mods-dir",
+            self.usermods_dir,
+            "--overwrite",
+        ]
+
+        # Run subset_data, if needed.
+        # It's needed during SETUP and/or NLCOMP phases if comparing/generating a baseline because
+        # the namelist comparison will require generating a namelist, and that will fail if we
+        # haven't specified our custom fsurdat and other stuff. By calling self._run_subset_data()
+        # only if the usermods directory doesn't yet exist, we avoid it being called every time the
+        # test class is initialized (which happens, e.g., in RUN phase).
+        # if not os.path.exists(self.usermods_dir):
+        #     self._run_subset_data()
+
+    def build_phase(self, sharedlib_only=False, model_only=False):
+        """
+        Run subset_data and then build the model
+        """
+
+        # Run subset_data.
+        # build_phase gets called twice:
+        # - once with sharedlib_only = True and
+        # - once with model_only = True
+        # Because we only need subset_data run once, we only do it for the sharedlib_only call.
+        # We could also check for the existence of the subset_data outputs, but that might lead to
+        # a situation where the user expects subset_data to be called but it's not. Better to run
+        # unnecessarily (e.g., if you fixed some FORTRAN code and just need to rebuild).
+        # In that same vein, yes we did run subset_data during the first time this test case was
+        # initialized (see __init__() above), but we're doing it again here just to be safe.
+        if sharedlib_only:
+            self._run_subset_data()
+
+        # Do the build
+        self.build_indv(sharedlib_only=sharedlib_only, model_only=model_only)
+
+    def _run_subset_data(self):
+        """
+        Run subset_data
+        """
+        # Import subset_data. Do it here rather than at top because otherwise the import will
+        # be attempted even during RUN phase.
+        # pylint: disable=wrong-import-position,import-outside-toplevel
+        from ctsm.subset_data import main as subset_data
+
+        # Run subset_data
+        sys.argv = self.subset_data_cmd
+        subset_data()
+
+        # Required so that CTSM doesn't fail
+        user_nl_clm_path = os.path.join(self.usermods_dir, "user_nl_clm")
+        with open(user_nl_clm_path, "a", encoding="utf-8") as user_nl_clm:
+            user_nl_clm.write("\ncheck_dynpft_consistency = .false.\n")
+
+        # Apply the user mods
+        self._case.flush(flushall=True)
+        apply_user_mods(self._get_caseroot(), self.usermods_dir)
+        self._case.read_xml()

cime_config/SystemTests/subsetdata.py

@@ -0,0 +1,38 @@
+"""
+CTSM-specific test that first runs the subset_data point tool and then ensures
+that CTSM does not fail using the just-generated input files
+"""
+
+from subsetdata import SUBSETDATASHARED
+
+
+class SUBSETDATAPOINT(SUBSETDATASHARED):
+    def __init__(self, case):
+        """
+        initialize an object interface to the SMS system test
+        """
+
+        lat = 45.402252
+        lon = -92.798085
+
+        # Don't need to include things that are added during SUBSETDATASHARED.__init__()
+        subset_data_cmd = [
+            "tools/site_and_regional/subset_data",
+            "point",
+            "--lat",
+            str(lat),
+            "--lon",
+            str(lon),
+            "--create-surface",
+            "--crop",
+            "--create-landuse",
+            "--surf-year",
+            "1850",
+            "--create-datm",
+            "--datm-syr",
+            "1901",
+            "--datm-eyr",
+            "1901",
+        ]
+
+        super().__init__(case, subset_data_cmd)

cime_config/SystemTests/subsetdatapoint.py

@@ -0,0 +1,41 @@
+"""
+CTSM-specific test that first runs the subset_data region tool and then ensures
+that CTSM does not fail using the just-generated input files
+"""
+
+from subsetdata import SUBSETDATASHARED
+
+
+class SUBSETDATAREGION(SUBSETDATASHARED):
+    def __init__(self, case):
+        """
+        initialize an object interface to the SMS system test
+        """
+
+        lat1 = -9
+        lat2 = -7
+        lon1 = 291
+        lon2 = 293
+
+        # Don't need to include things that are added during SUBSETDATASHARED.__init__()
+        subset_data_cmd = [
+            "tools/site_and_regional/subset_data",
+            "region",
+            "--lat1",
+            str(lat1),
+            "--lat2",
+            str(lat2),
+            "--lon1",
+            str(lon1),
+            "--lon2",
+            str(lon2),
+            "--create-mesh",
+            "--create-domain",
+            "--create-surface",
+            "--crop",
+            "--create-landuse",
+            "--surf-year",
+            "1850",
+        ]
+
+        super().__init__(case, subset_data_cmd)

cime_config/SystemTests/subsetdataregion.py

@@ -9,11 +9,11 @@
     <hist_file_extension>e</hist_file_extension>
     <rest_history_varname>locfnh</rest_history_varname>
     <rpointer>
-      <rpointer_file>rpointer.lnd$NINST_STRING</rpointer_file>
+      <rpointer_file>rpointer.lnd$NINST_STRING.$DATENAME</rpointer_file>
       <rpointer_content>./$CASE.clm2$NINST_STRING.r.$DATENAME.nc</rpointer_content>
     </rpointer>
     <test_file_names>
-      <tfile disposition="copy">rpointer.lnd</tfile>
+      <tfile disposition="copy">rpointer.lnd.1976-01-01-00000</tfile>
       <tfile disposition="copy">rpointer.lnd_9999.1976-01-01-00000</tfile>
       <tfile disposition="copy">casename.clm2.r.1976-01-01-00000.nc</tfile>
       <tfile disposition="copy">casename.clm2.rh4a.1976-01-01-00000.nc</tfile>