Merge branch 'b4b-dev' into fix_hh_vector_units

swensosc · Apr 16, 2024 · 08a8468 · 08a8468
2 parents cad8d42 + 074b4df
commit 08a8468
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Showing 5 changed files with 29 additions and 17 deletions.
diff --git a/cime_config/usermods_dirs/NEON/defaults/shell_commands b/cime_config/usermods_dirs/NEON/defaults/shell_commands
@@ -19,6 +19,7 @@ TEST=`./xmlquery TEST --value`
 
 # For a transient case run the whole length and don't cycle
 if  [[ $compset =~ ^HIST ]]; then
+  ./xmlchange CALENDAR=GREGORIAN
   ./xmlchange DATM_YR_END=2022
   ./xmlchange RUN_STARTDATE=2018-01-01
   # Number of months that can be run for the full transient case
@@ -29,6 +30,7 @@ if  [[ $compset =~ ^HIST ]]; then
   ./xmlchange CLM_NML_USE_CASE="2018-PD_transient"
 else
   ./xmlchange CLM_NML_USE_CASE="2018_control"
+  ./xmlchange CALENDAR=NO_LEAP
 fi
 
 # If needed for SP simulations: & set history file variables

diff --git a/cime_config/usermods_dirs/NEON/defaults/user_nl_clm b/cime_config/usermods_dirs/NEON/defaults/user_nl_clm
@@ -18,9 +18,6 @@
 ! Set glc_do_dynglacier  with GLC_TWO_WAY_COUPLING               env variable
 !----------------------------------------------------------------------------------
 
-flanduse_timeseries = ' '   ! This isn't needed for a non transient case, but will be once we start using transient compsets
-fsurdat = "$DIN_LOC_ROOT/lnd/clm2/surfdata_map/NEON/surfdata_1x1_NEON_${NEONSITE}_hist_78pfts_CMIP6_simyr2000_c230601.nc"
-
 ! h1 output stream 
 hist_fincl2 = 'AR','ELAI','FCEV','FCTR','FGEV','FIRA','FSA','FSH','GPP','H2OSOI',
              'HR','SNOW_DEPTH','TBOT','TSOI','SOILC_vr','FV','NET_NMIN_vr'

diff --git a/python/ctsm/site_and_regional/neon_site.py b/python/ctsm/site_and_regional/neon_site.py
@@ -47,8 +47,6 @@ def build_base_case(
             user_mods_dirs = [
                 os.path.join(self.cesmroot, "cime_config", "usermods_dirs", "NEON", self.name)
             ]
-            print("in neonsite adding usermodsdirs")
-        print("usermodsdirs: {}".format(user_mods_dirs))
         case_path = super().build_base_case(cesmroot, output_root, res, compset, user_mods_dirs)
 
         return case_path
@@ -99,8 +97,20 @@ def run_case(
             os.path.join(self.cesmroot, "cime_config", "usermods_dirs", "NEON", self.name)
         ]
         tower_type = "NEON"
+
         super().run_case(
-            base_case_root, run_type, prism, run_length, user_version, tower_type, user_mods_dirs
+            base_case_root,
+            run_type,
+            prism,
+            run_length,
+            user_version,
+            tower_type,
+            user_mods_dirs,
+            overwrite,
+            setup_only,
+            no_batch,
+            rerun,
+            experiment,
         )
 
     def modify_user_nl(self, case_root, run_type, rundir, site_lines=None):

diff --git a/python/ctsm/site_and_regional/run_neon.py b/python/ctsm/site_and_regional/run_neon.py
@@ -228,15 +228,16 @@ def main(description):
                 )
             logger.info("-----------------------------------")
             logger.info("Running CTSM for neon site : %s", neon_site.name)
+
             neon_site.run_case(
                 base_case_root,
                 run_type,
                 prism,
                 run_length,
                 user_version,
-                overwrite,
-                setup_only,
-                no_batch,
-                rerun,
-                experiment,
+                overwrite=overwrite,
+                setup_only=setup_only,
+                no_batch=no_batch,
+                rerun=rerun,
+                experiment=experiment,
             )
diff --git a/python/ctsm/site_and_regional/tower_site.py b/python/ctsm/site_and_regional/tower_site.py
@@ -257,11 +257,11 @@ def run_case(
         user_version,
         tower_type,
         user_mods_dirs,
-        overwrite=False,
-        setup_only=False,
-        no_batch=False,
-        rerun=False,
-        experiment=False,
+        overwrite,
+        setup_only,
+        no_batch,
+        rerun,
+        experiment,
     ):
         """
         Run case.
@@ -301,7 +301,7 @@ def run_case(
 
         print("using this version:", version)
 
-        if experiment is not False:
+        if (experiment is not False) and (experiment is not None):
             self.name = self.name + "." + experiment
         case_root = os.path.abspath(os.path.join(base_case_root, "..", self.name + "." + run_type))
 
@@ -391,11 +391,13 @@ def run_case(
                 case.set_value("RUN_TYPE", "hybrid")
 
             if run_type == "postad":
+                case.case_setup()
                 self.set_ref_case(case)
                 case.set_value("STOP_N", run_length)
 
             # For transient cases STOP will be set in the user_mod_directory
             if run_type == "transient":
+                case.case_setup()
                 if self.finidat:
                     case.set_value("RUN_TYPE", "startup")
                 else: