Get single point surface datasets from subset_data rather than mksurfdata

Externals.cfg

@@ -23,7 +23,7 @@ required = True
 local_path = components/mosart
 protocol = git
 repo_url = https://github.com/ESCOMP/MOSART
-tag = mosart1_0_47
+tag = mosart1_0_48
 required = True
 
 [mizuRoute]

bld/CLMBuildNamelist.pm

@@ -1687,11 +1687,6 @@ sub process_namelist_inline_logic {
   #############################################
   setup_logic_rooting_profile($opts,  $nl_flags, $definition, $defaults, $nl);
 
-  #############################################
-  # namelist group: friction_velocity         #
-  #############################################
-  setup_logic_friction_vel($opts,  $nl_flags, $definition, $defaults, $nl);
-
   #############################
   # namelist group: cngeneral #
   #############################
@@ -1711,6 +1706,11 @@ sub process_namelist_inline_logic {
   #############################################
   setup_logic_canopyfluxes($opts,  $nl_flags, $definition, $defaults, $nl);
 
+  ##########################################################
+  # namelist group: friction_velocity (after canopyfluxes) #
+  ##########################################################
+  setup_logic_friction_vel($opts,  $nl_flags, $definition, $defaults, $nl);
+
   #############################################
   # namelist group: canopyhydrology_inparm #
   #############################################
@@ -3898,10 +3898,11 @@ sub setup_logic_rooting_profile {
 #-------------------------------------------------------------------------------
 
 sub setup_logic_friction_vel {
-  #
+  # Must be after canopyfluxes so that use_biomass_heat_storage will be set
   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
 
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'zetamaxstable' );
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'zetamaxstable',
+     'use_biomass_heat_storage'=>$nl_flags->{'use_biomass_heat_storage'}, 'phys'=>$nl_flags->{'phys'} );
 }
 
 #-------------------------------------------------------------------------------
@@ -3926,6 +3927,11 @@ sub setup_logic_canopyfluxes {
   if ( &value_is_true($nl->get_value('use_biomass_heat_storage') ) && &value_is_true( $nl_flags->{'use_fates'}) ) {
      $log->fatal_error('use_biomass_heat_storage can NOT be set to true when fates is on');
   }
+  if ( &value_is_true($nl->get_value('use_biomass_heat_storage')) ) {
+     $nl_flags->{'use_biomass_heat_storage'} = ".true.";
+  } else {
+     $nl_flags->{'use_biomass_heat_storage'} = ".false.";
+  }
 }
 
 #-------------------------------------------------------------------------------

bld/namelist_files/namelist_defaults_ctsm.xml

@@ -210,9 +210,10 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <baseflow_scalar phys="clm4_5"  lower_boundary_condition="2">1.d-2</baseflow_scalar>
 
 <!-- Friction velocity -->
-<zetamaxstable phys="clm4_5" >2.0d00</zetamaxstable>
-<zetamaxstable phys="clm5_0" >0.5d00</zetamaxstable>
-<zetamaxstable phys="clm5_1" >0.5d00</zetamaxstable>
+<zetamaxstable               use_biomass_heat_storage=".true." >2.0d00</zetamaxstable>
+<zetamaxstable phys="clm4_5"                                   >2.0d00</zetamaxstable>
+<zetamaxstable phys="clm5_0"                                   >0.5d00</zetamaxstable>
+<zetamaxstable phys="clm5_1"                                   >0.5d00</zetamaxstable>
 
 <!-- atm2lnd defaults -->
 <repartition_rain_snow phys="clm5_1" >.true.</repartition_rain_snow>
@@ -1055,10 +1056,11 @@ lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_ne16np4_hist_16pfts_Irrig_CMIP6
 <fsurdat hgrid="0.125nldas2" sim_year="2000" use_crop=".false." irrigate=".true.">
 lnd/clm2/surfdata_map/surfdata_0.125nldas2_hist_16pfts_Irrig_CMIP6_simyr2005_c190412.nc</fsurdat>
 
+<fsurdat hgrid="1x1_brazil"    sim_year="2000">
+lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_brazil_hist_78pfts_CMIP6_simyr2000_c230123.nc</fsurdat>
+
 <fsurdat hgrid="5x5_amazon"    sim_year="2000" use_crop=".false." irrigate=".true.">
 lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_5x5_amazon_hist_16pfts_Irrig_CMIP6_simyr2000_c190214.nc</fsurdat>
-<fsurdat hgrid="1x1_brazil"    sim_year="2000" use_crop=".false." irrigate=".true.">
-lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_1x1_brazil_hist_16pfts_Irrig_CMIP6_simyr2000_c190214.nc</fsurdat>
 
 <!-- Needed for SCAM (Single Column Atmosphere Model) -->
 <fsurdat hgrid="64x128"      sim_year="2000" use_crop=".false." irrigate=".true."
@@ -1085,10 +1087,10 @@ lnd/clm2/surfdata_map/release-clm5.0.24/surfdata_0.125x0.125_hist_78pfts_CMIP6_s
 lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_10x15_hist_78pfts_CMIP6_simyr2000_c190214.nc</fsurdat>
 <fsurdat hgrid="4x5"       sim_year="2000" use_crop=".true." >
 lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_4x5_hist_78pfts_CMIP6_simyr2000_c190214.nc</fsurdat>
-<fsurdat hgrid="1x1_numaIA"       sim_year="2000" use_crop=".true." >
-lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_1x1_numaIA_hist_78pfts_CMIP6_simyr2000_c190214.nc</fsurdat>
-<fsurdat hgrid="1x1_smallvilleIA" sim_year="2000" use_crop=".true." >
-lnd/clm2/surfdata_map/ctsm1.0.dev094-2-g633be0eb/surfdata_1x1_smallvilleIA_hist_78pfts_CMIP6_simyr2000_c200521.nc</fsurdat>
+<fsurdat hgrid="1x1_numaIA"       sim_year="2000" >
+lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_numaIA_hist_78pfts_CMIP6_simyr2000_c230123.nc</fsurdat>
+<fsurdat hgrid="1x1_smallvilleIA" sim_year="2000" >
+lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_smallvilleIA_hist_78pfts_CMIP6_simyr2000_c230123.nc</fsurdat>
 
 <fsurdat hgrid="ne16np4"                  sim_year="2000" use_crop=".true.">
 lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_ne16np4_hist_78pfts_CMIP6_simyr2000_c190214.nc</fsurdat>
@@ -1112,12 +1114,12 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.ARCTIC.ne30x4_hist_78pft
 lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts_CMIP6_simyr2000_c200426.nc</fsurdat>
 
 <!-- 100% Urban single-point datasets (only for sim-year=2000) -->
-<fsurdat hgrid="1x1_vancouverCAN"    sim_year="2000" use_crop=".false." irrigate=".true.">
-lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_1x1_vancouverCAN_hist_16pfts_Irrig_CMIP6_simyr2000_c190214.nc</fsurdat>
-<fsurdat hgrid="1x1_mexicocityMEX"   sim_year="2000" use_crop=".false." irrigate=".true.">
-lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c190214.nc</fsurdat>
-<fsurdat hgrid="1x1_urbanc_alpha"    sim_year="2000" use_crop=".false." irrigate=".true.">
-lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_1x1_urbanc_alpha_hist_16pfts_Irrig_CMIP6_simyr2000_c190214.nc</fsurdat>
+<fsurdat hgrid="1x1_vancouverCAN"    sim_year="2000" >
+lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_vancouverCAN_hist_78pfts_CMIP6_simyr2000_c230123.nc</fsurdat>
+<fsurdat hgrid="1x1_mexicocityMEX"   sim_year="2000" >
+lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_mexicocityMEX_hist_78pfts_CMIP6_simyr2000_c230123.nc</fsurdat>
+<fsurdat hgrid="1x1_urbanc_alpha"    sim_year="2000" >
+lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_urbanc_alpha_hist_78pfts_CMIP6_simyr2000_c230123.nc</fsurdat>
 
 <!-- for pre-industrial simulations - year 1850 without crop -->
 <fsurdat hgrid="48x96"        sim_year="1850" use_crop=".false." irrigate=".true.">
@@ -1132,9 +1134,6 @@ lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_10x15_hist_16pfts_Irrig_CMIP6_s
 <fsurdat hgrid="4x5"          sim_year="1850" use_crop=".false." irrigate=".true.">
 lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_4x5_hist_16pfts_Irrig_CMIP6_simyr1850_c190214.nc</fsurdat>
 
-<fsurdat hgrid="1x1_brazil"    sim_year="1850" use_crop=".false." irrigate=".true.">
-lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_1x1_brazil_hist_16pfts_Irrig_CMIP6_simyr1850_c190214.nc</fsurdat>
-
 <fsurdat hgrid="ne30np4"      sim_year="1850" use_crop=".false." irrigate=".true.">
 lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_ne30np4_hist_16pfts_Irrig_CMIP6_simyr1850_c190303.nc</fsurdat>
 
@@ -1160,13 +1159,13 @@ lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_1.9x2.5_hist_78pfts_CMIP6_simyr
 lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_10x15_hist_78pfts_CMIP6_simyr1850_c190214.nc</fsurdat>
 <fsurdat hgrid="4x5"       sim_year="1850" use_crop=".true." >
 lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_4x5_hist_78pfts_CMIP6_simyr1850_c190214.nc</fsurdat>
-<fsurdat hgrid="1x1_smallvilleIA" sim_year="1850" use_crop=".true." >
-lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_1x1_smallvilleIA_hist_78pfts_CMIP6_simyr1850_c190214.nc</fsurdat>
-<fsurdat hgrid="1x1_numaIA"       sim_year="1850" use_crop=".true." >
-lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_1x1_numaIA_hist_78pfts_CMIP6_simyr1850_c190214.nc</fsurdat>
+<fsurdat hgrid="1x1_smallvilleIA" sim_year="1850" >
+lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_smallvilleIA_hist_78pfts_CMIP6_simyr1850_c230123.nc</fsurdat>
+<fsurdat hgrid="1x1_numaIA"       sim_year="1850" >
+lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_numaIA_hist_78pfts_CMIP6_simyr1850_c230123.nc</fsurdat>
 
-<fsurdat hgrid="1x1_brazil"    sim_year="1850" use_crop=".true." >
-lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_1x1_brazil_hist_78pfts_CMIP6_simyr1850_c190214.nc</fsurdat>
+<fsurdat hgrid="1x1_brazil"               sim_year="1850">
+lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_brazil_hist_78pfts_CMIP6_simyr1850_c230123.nc</fsurdat>
 
 <fsurdat hgrid="ne30np4"                  sim_year="1850" use_crop=".true.">
 lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne30np4_hist_78pfts_CMIP6_simyr1850_c200426.nc</fsurdat>
@@ -1210,8 +1209,6 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts
 <flanduse_timeseries hgrid="48x96"         sim_year_range="1850-2000" irrigate=".true."
  use_crop=".false."  >lnd/clm2/surfdata_map/release-clm5.0.18/landuse.timeseries_48x96_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c190214.nc</flanduse_timeseries>
 
-<flanduse_timeseries hgrid="1x1_brazil"    sim_year_range="1850-2000" irrigate=".true."
- use_crop=".false."  >lnd/clm2/surfdata_map/landuse.timeseries_1x1_brazil_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 
 <flanduse_timeseries hgrid="ne30np4"       sim_year_range="1850-2000"  irrigate=".true."
  use_crop=".false."  >lnd/clm2/surfdata_map/landuse.timeseries_ne30np4_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
@@ -1232,7 +1229,7 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts
  use_crop=".true."  >lnd/clm2/surfdata_map/landuse.timeseries_48x96_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
 
 <flanduse_timeseries hgrid="1x1_brazil"    sim_year_range="1850-2000"
- use_crop=".true."  >lnd/clm2/surfdata_map/landuse.timeseries_1x1_brazil_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc</flanduse_timeseries>
+>lnd/clm2/surfdata_map/ctsm5.1.dev116/landuse.timeseries_1x1_brazil_hist_78pfts_CMIP6_simyr1850-2015_c230123.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="1x1_numaIA"    sim_year_range="1850-2000"
  use_crop=".true."   >lnd/clm2/surfdata_map/landuse.timeseries_1x1_numaIA_hist_78pfts_CMIP6_simyr1850-2015_c170917.nc</flanduse_timeseries>
 

bld/unit_testers/build-namelist_test.pl

@@ -319,22 +319,22 @@ sub cat_and_create_namelistinfile {
 foreach my $driver ( "mct", "nuopc" ) {
    print "   For $driver driver\n\n";
    # configuration, structure, irrigate, verbose, clm_demand, ssp_rcp, test, sim_year, use_case
-   foreach my $options ( "-configuration nwp",
-                         "-structure fast",
-                         "-namelist '&a irrigate=.true./'", "-verbose", "-ssp_rcp SSP1-2.6", "-test", "-sim_year 1850",
-                         "-namelist '&a use_lai_streams=.true.,use_soil_moisture_streams=.true./'",
-                         "-use_case 1850_control",
+   foreach my $options ( "-res 0.9x1.25 -configuration nwp",
+                         "-res 0.9x1.25 -structure fast",
+                         "-res 0.9x1.25 -namelist '&a irrigate=.true./'", "-res 0.9x1.25 -verbose", "-res 0.9x1.25 -ssp_rcp SSP1-2.6", "-res 0.9x1.25 -test", "-res 0.9x1.25 -sim_year 1850",
+                         "-res 0.9x1.25 -namelist '&a use_lai_streams=.true.,use_soil_moisture_streams=.true./'",
+                         "-res 0.9x1.25 -use_case 1850_control",
                          "-res 1x1pt_US-UMB -clm_usr_name 1x1pt_US-UMB -namelist '&a fsurdat=\"/dev/null\"/'",
                          "-res 1x1_brazil",
-                         "-clm_start_type startup", "-namelist '&a irrigate=.false./' -crop -bgc bgc",
-                         "-envxml_dir . -infile myuser_nl_clm",
-                         "-ignore_ic_date -clm_start_type branch -namelist '&a nrevsn=\"thing.nc\"/' -bgc bgc -crop",
-                         "-clm_start_type branch -namelist '&a nrevsn=\"thing.nc\",use_init_interp=T/'",
-                         "-ignore_ic_date -clm_start_type startup -namelist '&a finidat=\"thing.nc\"/' -bgc bgc -crop",
+                         "-res 0.9x1.25 -clm_start_type startup", "-namelist '&a irrigate=.false./' -crop -bgc bgc",
+                         "-res 0.9x1.25 -infile myuser_nl_clm",
+                         "-res 0.9x1.25 -ignore_ic_date -clm_start_type branch -namelist '&a nrevsn=\"thing.nc\"/' -bgc bgc -crop",
+                         "-res 0.9x1.25 -clm_start_type branch -namelist '&a nrevsn=\"thing.nc\",use_init_interp=T/'",
+                         "-res 0.9x1.25 -ignore_ic_date -clm_start_type startup -namelist '&a finidat=\"thing.nc\"/' -bgc bgc -crop",
                         ) {
       my $file = $startfile;
       &make_env_run();
-      my $base_options = "-res 0.9x1.25 -envxml_dir . -driver $driver";
+      my $base_options = "-envxml_dir . -driver $driver";
       if ( $driver eq "mct" ) {
          $base_options = "$base_options -lnd_frac $DOMFILE";
       } else {

cime_config/SystemTests/fsurdatmodifyctsm.py

@@ -40,8 +40,11 @@ def __init__(self, case):
             self._cfg_file_path = os.path.join(self._get_caseroot(),
                                                'modify_fsurdat.cfg')
 
+            logger.info("  create config file to modify")
             self._create_config_file()
+            logger.info("  run modify_fsurdat")
             self._run_modify_fsurdat()
+            logger.info("  modify user_nl files")
             self._modify_user_nl()
             with open('done_FSURDATMODIFYCTSM_setup.txt', 'w') as fp:
                 pass
@@ -68,7 +71,7 @@ def _run_modify_fsurdat(self):
         # Need to specify a specific python version that has the required
         # dependencies
         python_path = _get_python_path()
-        subprocess.check_call([python_path, tool_path, self._cfg_file_path])
+        subprocess.check_call([python_path, tool_path, self._cfg_file_path, "--verbose", "--overwrite", "--allow_ideal_and_include_non_veg"])
 
     def _modify_user_nl(self):
         append_to_user_nl_files(caseroot = self._get_caseroot(),