Prescribed sowing date and maturity requirements

.git-blame-ignore-revs

@@ -7,3 +7,7 @@ e44dc469439e02e9ee582dab274d890ebdfab104
 b88e1cd1b28e3609684c79a2ec0e88f26cfc362b
 51c102c5df2e0ef971b5f8eeeb477567899af63a
 7dacad70e74e2ec97f6492d4e7a3cb5dd498bcd7
+b771971e3299c4fa56534b93421f7a2b9c7282fd
+9de88bb57ea9855da408cbec1dc8acb9079eda47
+# Ran SystemTests and python/ctsm through black python formatter
+5364ad66eaceb55dde2d3d598fe4ce37ac83a93c

.gitignore

@@ -120,3 +120,4 @@ core.*
 *.log !run.log
 *.pyc
 Depends
+ts_generate_gdds.py

Externals.cfg

@@ -44,7 +44,7 @@ required = True
 local_path = cime
 protocol = git
 repo_url = https://github.com/ESMCI/cime
-tag = cime6.0.108
+tag = cime6.0.118
 required = True
 
 [cmeps]

bld/CLMBuildNamelist.pm

@@ -1625,9 +1625,9 @@ sub process_namelist_inline_logic {
   setup_logic_urban($opts,  $nl_flags, $definition, $defaults, $nl);
 
   ###############################
-  # namelist group: crop        #
+  # namelist group: crop_inparm #
   ###############################
-  setup_logic_crop($opts,  $nl_flags, $definition, $defaults, $nl);
+  setup_logic_crop_inparm($opts,  $nl_flags, $definition, $defaults, $nl);
 
   ###############################
   # namelist group: ch4par_in   #
@@ -1695,6 +1695,11 @@ sub process_namelist_inline_logic {
   ##################################
   setup_logic_lai_streams($opts,  $nl_flags, $definition, $defaults, $nl);
 
+  ##################################
+  # namelist group: cropcal_streams  #
+  ##################################
+  setup_logic_cropcal_streams($opts,  $nl_flags, $definition, $defaults, $nl);
+
   ##########################################
   # namelist group: soil_moisture_streams  #
   ##########################################
@@ -2149,7 +2154,7 @@ sub setup_logic_urban {
 
 #-------------------------------------------------------------------------------
 
-sub setup_logic_crop {
+sub setup_logic_crop_inparm {
   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
 
   if ( &value_is_true($nl->get_value('use_crop')) ) {
@@ -3920,6 +3925,39 @@ sub setup_logic_lai_streams {
 
 #-------------------------------------------------------------------------------
 
+sub setup_logic_cropcal_streams {
+  my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
+
+  # Set first and last stream years
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_first_cropcal',
+              'sim_year'=>$nl_flags->{'sim_year'},
+              'sim_year_range'=>$nl_flags->{'sim_year_range'});
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_last_cropcal',
+              'sim_year'=>$nl_flags->{'sim_year'},
+              'sim_year_range'=>$nl_flags->{'sim_year_range'});
+
+  # Set align year, if first and last years are different
+  if ( $nl->get_value('stream_year_first_cropcal') !=
+      $nl->get_value('stream_year_last_cropcal') ) {
+    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl,
+                'model_year_align_cropcal', 'sim_year'=>$nl_flags->{'sim_year'},
+                'sim_year_range'=>$nl_flags->{'sim_year_range'});
+  }
+
+  # Set up other crop calendar parameters
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'generate_crop_gdds');
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_mxmat');
+
+  # Consistency checking: Do not generate_crop_gdds without use_mxmat false
+  my $generate_crop_gdds = $nl->get_value('generate_crop_gdds') ;
+  my $use_mxmat = $nl->get_value('use_mxmat') ;
+  if ( $generate_crop_gdds eq '.true.' and $use_mxmat eq '.true.' ) {
+     $log->fatal_error("If generate_crop_gdds is true, you must also set use_mxmat to false" );
+  }
+}
+
+#-------------------------------------------------------------------------------
+
 sub setup_logic_soilwater_movement {
   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
 
@@ -4297,14 +4335,15 @@ sub write_output_files {
   my @groups;
   @groups = qw(clm_inparm ndepdyn_nml popd_streams urbantv_streams light_streams
                soil_moisture_streams lai_streams atm2lnd_inparm lnd2atm_inparm clm_canopyhydrology_inparm cnphenology
+               cropcal_streams
                clm_soilhydrology_inparm dynamic_subgrid cnvegcarbonstate
                finidat_consistency_checks dynpft_consistency_checks
                clm_initinterp_inparm century_soilbgcdecompcascade
                soilhydrology_inparm luna friction_velocity mineral_nitrogen_dynamics
                soilwater_movement_inparm rooting_profile_inparm
                soil_resis_inparm  bgc_shared canopyfluxes_inparm aerosol
                clmu_inparm clm_soilstate_inparm clm_nitrogen clm_snowhydrology_inparm
-               cnprecision_inparm clm_glacier_behavior crop irrigation_inparm
+               cnprecision_inparm clm_glacier_behavior crop_inparm irrigation_inparm
                surfacealbedo_inparm water_tracers_inparm);
 
   #@groups = qw(clm_inparm clm_canopyhydrology_inparm clm_soilhydrology_inparm

bld/namelist_files/namelist_defaults_ctsm.xml

@@ -562,6 +562,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <min_critical_dayl_method         use_cn=".true." phys="clm5_1" >DependsOnLat</min_critical_dayl_method>
 <onset_thresh_depends_on_veg                                    >.false.</onset_thresh_depends_on_veg>
 <min_critical_dayl_method                                       >Constant</min_critical_dayl_method>
+<generate_crop_gdds                                             >.false.</generate_crop_gdds>
+<use_mxmat                                                      >.true.</use_mxmat>
 
 <!-- use additional stress deciduous onset trigger    -->
 <constrain_stress_deciduous_onset phys="clm4_5" >.false.</constrain_stress_deciduous_onset>
@@ -1665,6 +1667,11 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1
 <lai_mapalgo  hgrid="1x1_asphaltjungleNJ" >nn</lai_mapalgo>
 <lai_mapalgo  hgrid="5x5_amazon"          >nn</lai_mapalgo>
 
+<!-- crop calendar streams namelist defaults -->
+<stream_year_first_cropcal  >1850</stream_year_first_cropcal>
+<stream_year_last_cropcal   >2100</stream_year_last_cropcal>
+<model_year_align_cropcal   >1850</model_year_align_cropcal>
+
 <!-- lightning streams namelist defaults -->
 
 <light_res    use_cn=".false."                     >none</light_res>

bld/namelist_files/namelist_definition_ctsm.xml

@@ -1090,20 +1090,20 @@ Toggle to turn on the 1-year grain product pool in the crop model
 </entry>
 
 <entry id="baset_mapping" type="char*20" category="physics"
-       group="crop" valid_values="constant,varytropicsbylat" value="constant">
+       group="crop_inparm" valid_values="constant,varytropicsbylat" value="constant">
 Type of mapping to use for base temperature for prognostic crop model
 constant = Just use baset from the PFT parameter file
 varytropicsbylat = Vary the tropics by latitude 
 </entry>
 
 <entry id="baset_latvary_slope" type="real" category="physics"
-       group="crop" valid_values="" value="0.4d00">
+       group="crop_inparm" valid_values="" value="0.4d00">
 Only used when baset_mapping == varytropicsbylat
 Slope with latitude in degrees to vary tropical baset by
 </entry>
 
 <entry id="baset_latvary_intercept" type="real" category="physics"
-       group="crop" valid_values="" value="12.0d00">
+       group="crop_inparm" valid_values="" value="12.0d00">
 Only used when baset_mapping == varytropicsbylat
 Intercept at zero latitude to add to baset from the PFT parameter file
 </entry>
@@ -1129,6 +1129,16 @@ Phenology onset depends on the vegetation type
 (only used when CN is on)
 </entry>
 
+<entry id="generate_crop_gdds" type="logical" category="physics"
+        group="cnphenology" valid_values="" value=".false.">
+Set to .true. in order to override crop harvesting logic and to instead harvest the day before the next sowing date. Used to generate growing-degree day outputs that can be used with an external script to generate new GDD requirement ("cultivar") files.
+</entry>
+
+<entry id="use_mxmat" type="logical" category="physics"
+        group="cnphenology" valid_values="" value=".true.">
+Set to .false. in order to ignore crop PFT parameter for maximum growing season length (mxmat). Must be set to .false. when generate_crop_gdds is .true.
+</entry>
+
 <entry id="min_critical_dayl_method" type="char*25" category="physics"
        group="cnphenology" valid_values="Constant,DependsOnLat,DependsOnVeg,DependsOnLatAndVeg">
 Method for determining what the minimum critical day length for seasonal decidious leaf offset depends on
@@ -1805,6 +1815,41 @@ Mapping method from LAI input file to the model resolution
     copy     = copy using the same indices
 </entry>
 
+<!-- ========================================================================================  -->
+<!-- cropcal_streams streams Namelist                                                          -->
+<!-- ========================================================================================  -->
+
+<!-- Crop calendars -->
+<entry id="stream_year_first_cropcal" type="integer" category="datasets"
+       group="cropcal_streams" valid_values="" >
+First year to loop over for crop calendar data
+</entry>
+
+<entry id="stream_year_last_cropcal" type="integer" category="datasets"
+       group="cropcal_streams" valid_values="" >
+Last year to loop over for crop calendar data
+</entry>
+
+<entry id="model_year_align_cropcal" type="integer" category="datasets"
+       group="cropcal_streams" valid_values="" >
+Simulation year that aligns with stream_year_first_cropcal value
+</entry>
+
+<entry id="stream_fldfilename_sdate" type="char*256(30)" category="datasets"
+       input_pathname="abs" group="cropcal_streams" valid_values="" >
+Filename of input stream data for sowing dates
+</entry>
+
+<entry id="stream_fldfilename_cultivar_gdds" type="char*256(30)" category="datasets"
+       input_pathname="abs" group="cropcal_streams" valid_values="" >
+Filename of input stream data for cultivar growing degree-day targets
+</entry>
+
+<entry id="stream_meshfile_cropcal" type="char*256" category="datasets"
+       input_pathname="abs" group="cropcal_streams" valid_values="" >
+Filename of input stream data for crop calendar inputs
+</entry>
+
 <!-- ========================================================================================  -->
 <!-- light_streams streams Namelist (when CN an CLM4_5 is active)                              -->
 <!-- ========================================================================================  -->

cime_config/SystemTests/fsurdatmodifyctsm.py

@@ -5,7 +5,7 @@
 
 import os
 import re
-import subprocess
+import systemtest_utils as stu
 from CIME.SystemTests.system_tests_common import SystemTestsCommon
 from CIME.XML.standard_module_setup import *
 from CIME.SystemTests.test_utils.user_nl_utils import append_to_user_nl_files
@@ -69,58 +69,17 @@ def _run_modify_fsurdat(self):
         tool_path = os.path.join(self._ctsm_root, "tools/modify_input_files/fsurdat_modifier")
 
         self._case.load_env(reset=True)
-        conda_env = ". " + self._get_caseroot() + "/.env_mach_specific.sh; "
-        # Preprend the commands to get the conda environment for python first
-        conda_env += self._get_conda_env()
-        # Source the env
-        try:
-            subprocess.run(
-                conda_env + "python3 " + tool_path + " " + self._cfg_file_path,
-                shell=True,
-                check=True,
-            )
-        except subprocess.CalledProcessError as error:
-            print("ERROR while getting the conda environment and/or ")
-            print("running the fsurdat_modifier tool: ")
-            print("(1) If your ctsm_pylib environment is out of date or you ")
-            print("have not created the ctsm_pylib environment, yet, you may ")
-            print("get past this error by running ./py_env_create ")
-            print("in your ctsm directory and trying this test again. ")
-            print("(2) If conda is not available, install and load conda, ")
-            print("run ./py_env_create, and then try this test again. ")
-            print("(3) If (1) and (2) are not the issue, then you may be ")
-            print("getting an error within the fsurdat_modifier tool itself. ")
-            print("Default error message: ")
-            print(error.output)
-            raise
-        except:
-            print("ERROR trying to run fsurdat_modifier tool.")
-            raise
+        command = f"python3 {tool_path} {self._cfg_file_path}"
+        stu.run_python_script(
+            self._get_caseroot(),
+            "ctsm_pylib",
+            command,
+            tool_path,
+        )
 
     def _modify_user_nl(self):
         append_to_user_nl_files(
             caseroot=self._get_caseroot(),
             component="clm",
             contents="fsurdat = '{}'".format(self._fsurdat_out),
         )
-
-    def _get_conda_env(self):
-        #
-        # Add specific commands needed on different machines to get conda available
-        # Use semicolon here since it's OK to fail
-        #
-        # Execute the module unload/load when "which conda" fails
-        # eg on cheyenne
-        try:
-            subprocess.run("which conda", shell=True, check=True)
-            conda_env = " "
-        except subprocess.CalledProcessError:
-            # Remove python and add conda to environment for cheyennne
-            conda_env = "module unload python; module load conda;"
-
-        # Activate the python environment
-        conda_env += " conda activate ctsm_pylib"
-        # End above to get to actual command
-        conda_env += " && "
-
-        return conda_env

cime_config/SystemTests/lreprstruct.py

@@ -49,6 +49,20 @@ def _case_one_setup(self):
             contents="for_testing_use_repr_structure_pool=.true.",
         )
 
+        # Replace any GRAIN outputs with the same outputs for REPRODUCTIVE1 and REPRODUCTIVE2
+        user_nl_clm_path = os.path.join(self._get_caseroot(), "user_nl_clm")
+        with open(user_nl_clm_path) as f:
+            user_nl_clm_text = f.read()
+        for grain_output in re.findall("GRAIN\w*", user_nl_clm_text):
+            user_nl_clm_text = user_nl_clm_text.replace(
+                grain_output,
+                grain_output.replace("GRAIN", "REPRODUCTIVE1")
+                + "', '"
+                + grain_output.replace("GRAIN", "REPRODUCTIVE2"),
+            )
+        with open(user_nl_clm_path, "w") as f:
+            f.write(user_nl_clm_text)
+
     def _case_two_setup(self):
         # This is needed in the nearly-standard case to prevent grain from being used to
         # replenish crop seed deficits, thus making grain act like the reproductive