Merge pull request #3464 from ekluzek/ctsm5.4_update5.3.071

Update the ctsm5.4 alpha branch to ctsm5.3.071

Author: slevis-lmwg

.git-blame-ignore-revs

@@ -70,3 +70,8 @@ cdf40d265cc82775607a1bf25f5f527bacc97405
 4ad46f46de7dde753b4653c15f05326f55116b73
 75db098206b064b8b7b2a0604d3f0bf8fdb950cc
 84609494b54ea9732f64add43b2f1dd035632b4c
+7eb17f3ef0b9829fb55e0e3d7f02e157b0e41cfb
+62d7711506a0fb9a3ad138ceceffbac1b79a6caa
+49ad0f7ebe0b07459abc00a5c33c55a646f1e7e0
+ac03492012837799b7111607188acff9f739044a
+d858665d799690d73b56bcb961684382551193f4

.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
@@ -76,7 +76,7 @@ fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git
 [submodule "cime"]
 path = cime
 url = https://github.com/ESMCI/cime
-fxtag = cime6.1.111
+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

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
@@ -4762,12 +4763,13 @@ 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 $var ( @list ) {
@@ -4787,6 +4789,9 @@ sub setup_logic_fates {
         add_default($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');
@@ -4808,7 +4813,7 @@ 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
@@ -4921,6 +4926,16 @@ 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

@@ -555,7 +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>
 
 
 <!-- ================================================================== -->
@@ -2438,6 +2438,7 @@ 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>
@@ -2446,6 +2447,7 @@ 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 +1,95 @@
+"""
+CTSM-specific test that first runs the set_paramfile tool and then ensures that CTSM does not fail
+using the just-generated parameter file
+"""
+
+import os
+import sys
+import logging
+import re
+from CIME.SystemTests.system_tests_common import SystemTestsCommon
+
+# In case we need to import set_paramfile 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 SETPARAMFILE(SystemTestsCommon):
+    def __init__(self, case):
+        """
+        initialize an object interface to the SMS system test
+        """
+        SystemTestsCommon.__init__(self, case)
+
+        # Create out-of-the-box lnd_in to obtain paramfile
+        case.create_namelists(component="lnd")
+
+        # Find the paramfile to modify
+        lnd_in_path = os.path.join(self._get_caseroot(), "CaseDocs", "lnd_in")
+        self._paramfile_in = None
+        with open(lnd_in_path, "r", encoding="utf-8") as lnd_in:
+            for line in lnd_in:
+                paramfile_in = re.match(r" *paramfile *= *'(.*)'", line)
+                if paramfile_in:
+                    self._paramfile_in = paramfile_in.group(1)
+                    break
+        if not self._paramfile_in:
+            raise RuntimeError(f"paramfile not found in {lnd_in_path}")
+
+        # Get the output file
+        self.paramfile_out = os.path.join(self._get_caseroot(), "paramfile.nc")
+
+        # Define set_paramfile command
+        self.set_paramfile_cmd = [
+            "set_paramfile",
+            "-i",
+            self._paramfile_in,
+            "-o",
+            self.paramfile_out,
+            # Change two parameters for one PFT
+            "-p",
+            "needleleaf_deciduous_boreal_tree",
+            "rswf_min=0.35",
+            "rswf_max=0.7",
+        ]
+
+    def build_phase(self, sharedlib_only=False, model_only=False):
+        """
+        Run set_paramfile and then build the model
+        """
+
+        # Run set_paramfile.
+        # build_phase gets called twice:
+        # - once with sharedlib_only = True and
+        # - once with model_only = True
+        # Because we only need set_paramfile run once, we only do it for the sharedlib_only call.
+        # We could also check for the existence of the set_paramfile outputs, but that might lead to
+        # a situation where the user expects set_paramfile to be called but it's not. Better to run
+        # unnecessarily (e.g., if you fixed some FORTRAN code and just need to rebuild).
+        if sharedlib_only:
+            self._run_set_paramfile()
+
+        # Do the build
+        self.build_indv(sharedlib_only=sharedlib_only, model_only=model_only)
+
+    def _run_set_paramfile(self):
+        """
+        Run set_paramfile
+        """
+        # Import set_paramfile. 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.param_utils.set_paramfile import main as set_paramfile
+
+        # Run set_paramfile
+        sys.argv = self.set_paramfile_cmd
+        set_paramfile()
+
+        # Append
+        user_nl_clm_path = os.path.join(self._get_caseroot(), "user_nl_clm")
+        with open(user_nl_clm_path, "a", encoding="utf-8") as user_nl_clm:
+            user_nl_clm.write(f"paramfile = '{self.paramfile_out}'\n")

cime_config/SystemTests/setparamfile.py

@@ -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)