ctsm5.3.059: Various cleanup efforts from the cesm3_0_beta04 tags for testing and usability

.gitmodules

@@ -58,8 +58,8 @@ fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/MOSART
 
 [submodule "mizuRoute"]
-path = components/mizuRoute
-url = https://github.com/ESCOMP/mizuRoute
+	path = components/mizuroute
+	url = https://github.com/ESCOMP/mizuRoute
 fxtag = cesm-coupling.n03_v2.2.0
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed

README

@@ -66,7 +66,7 @@ components/cmeps -------------------- CESM top level driver (for NUOPC driver [w
 components/cdeps -------------------- CESM top level data model shared code (for NUOPC driver).
 components/cism --------------------- CESM Community land Ice Sheet Model.
 components/mosart ------------------- Model for Scale Adaptive River Transport
-components/mizuRoute ---------------- Reached based river transport model for water routing 
+components/mizuroute ---------------- Reached based river transport model for water routing 
                                       (allows both gridded river and Hydrologic Responce Unit river grids)
 components/rtm ---------------------- CESM River Transport Model.
 

bld/CLMBuildNamelist.pm

@@ -4071,7 +4071,16 @@ sub setup_logic_fire_emis {
         if ( &value_is_true( $nl_flags->{'use_fates'} ) ) {
           $log->warning("Fire emission option $var can NOT be on when FATES is also on.\n" .
                       "  DON'T use the '--fire_emis' option when '--bgc fates' is activated");
-       }
+        } elsif ( ! &value_is_true( $nl_flags->{'use_cn'} ) ) {
+          $log->fatal_error("Fire emission option $var can NOT be on when BGC SP (i.e. Satellite Phenology) is also on.\n" .
+                           "  DON'T use the '--fire_emis' option when '--bgc sp' is activated");
+        } elsif ( &value_is_true( $nl_flags->{'use_cn'}) ) {
+          my $fire_method = remove_leading_and_trailing_quotes( $nl->get_value('fire_method') );
+          if ( $fire_method eq "nofire" ) {
+             $log->fatal_error("Fire emission option $var can NOT be on with BGC and fire_method=='nofire'.\n" .
+                              "  DON'T use the '--fire_emis' option when fire_method is nofire");
+          }
+        }
      }
    }
 }
@@ -4235,7 +4244,7 @@ sub setup_logic_lai_streams {
   if ( &value_is_true($nl_flags->{'use_crop'}) && &value_is_true($nl->get_value('use_lai_streams'))  ) {
     $log->fatal_error("turning use_lai_streams on is incompatable with use_crop set to true.");
   }
-  if ( $nl_flags->{'bgc_mode'} eq "sp" || ($nl_flags->{'bgc_mode'} eq "fates" && &value_is_true($nl->get_value('use_fates_sp')) )) {
+  if ( $nl_flags->{'bgc_mode'} eq "sp" || ($nl_flags->{'bgc_mode'} eq "fates" && &value_is_true($nl_flags->{'use_fates_sp'}) )) {
      if ( &value_is_true($nl->get_value('use_lai_streams')) ) {
        add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_lai_streams');
        add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'lai_mapalgo',
@@ -4745,29 +4754,26 @@ sub setup_logic_fates {
         # For FATES SP mode make sure no-competetiion, and fixed-biogeography are also set
         # And also check for other settings that can't be trigged on as well
         #
-        my $var = "use_fates_sp";
-        if ( defined($nl->get_value($var))  ) {
-           if ( &value_is_true($nl->get_value($var)) ) {
-              my @list = ( "use_fates_nocomp", "use_fates_fixed_biogeog" );
-              foreach my $var ( @list ) {
-                 if ( ! &value_is_true($nl->get_value($var)) ) {
-                    $log->fatal_error("$var is required when FATES SP is on (use_fates_sp)" );
-                 }
-              }
-              # spit-fire can't be on with FATES SP mode is active
-              if ( $nl->get_value('fates_spitfire_mode') > 0 ) {
-                    $log->fatal_error('fates_spitfire_mode can NOT be set to greater than 0 when use_fates_sp is true');
-              }
+        if ( &value_is_true($nl_flags->{'use_fates_sp'}) ) {
+           my @list = ( "use_fates_nocomp", "use_fates_fixed_biogeog" );
+           foreach my $var ( @list ) {
+                if ( ! &value_is_true($nl->get_value($var)) ) {
+                   $log->fatal_error("$var is required when FATES SP is on (use_fates_sp)" );
+                }
+           }
+           # 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');
+           }
 
-              # fates landuse can't be on with FATES SP mode is active
-              if ( &value_is_true($nl->get_value('use_fates_luh')) ) {
-                   $log->fatal_error('use_fates_luh can NOT be true when use_fates_sp is true');
-              }
+           # fates landuse can't be on with FATES SP mode is active
+           if ( &value_is_true($nl->get_value('use_fates_luh')) ) {
+                $log->fatal_error('use_fates_luh can NOT be true when use_fates_sp is true');
+           }
 
-              # hydro isn't currently supported to work when FATES SP mode is active
-              if (&value_is_true( $nl->get_value('use_fates_planthydro') )) {
-                    $log->fatal_error('fates sp mode is currently not supported to work with fates hydro');
-              }
+           # hydro isn't currently supported to work when FATES SP mode is active
+           if (&value_is_true( $nl->get_value('use_fates_planthydro') )) {
+                 $log->fatal_error('fates sp mode is currently not supported to work with fates hydro');
            }
         }
         my $var = "use_fates_inventory_init";
@@ -4792,6 +4798,13 @@ sub setup_logic_fates {
             }
           }
         }
+        # Check that both FaTES-SP and FATES ST3 aren't both on
+        my $var = "use_fates_ed_st3";
+        if ( defined($nl->get_value($var))  ) {
+           if ( &value_is_true($nl->get_value($var)) && &value_is_true($nl_flags->{'use_fates_sp'}) ) {
+              $log->fatal_error("$var can NOT also be true with use_fates_sp true" );
+           }
+        }
         # check that fates landuse change mode has the necessary luh2 landuse timeseries data
         # and add the default if not defined.  Do not add default if use_fates_potentialveg is true.
         # If fixed biogeography is on, make sure that flandusepftdat is avilable.

bld/namelist_files/namelist_defaults_ctsm.xml

@@ -1119,6 +1119,12 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 >hgrid=ne0np4.ARCTICGRIS.ne30x8 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
 </init_interp_attributes>
 
+<!-- 2013 IC's - exact match for CONUS grid ... -->
+<init_interp_attributes sim_year="2013" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0"
+			hgrid="ne0np4CONUS.ne30x8" use_cn=".false." maxpft="17"
+>hgrid=ne0np4CONUS.ne30x8 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. use_excess_ice=.false.
+</init_interp_attributes>
+
 <!-- MPAS -->
 <init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false." lnd_tuning_mode="clm5_0_cam6.0"
 			hgrid="mpasa480"
@@ -1667,6 +1673,8 @@ lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_mpasa480_hist_2000_78pfts_c240908.nc</
 <fsurdat hgrid="mpasa120"  sim_year="2000">
 lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_mpasa120_hist_2000_78pfts_c240908.nc</fsurdat>
 
+<fsurdat hgrid="ne3np4"                  sim_year="2000">
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne3np4_hist_2000_78pfts_c240925.nc</fsurdat>
 <fsurdat hgrid="ne3np4.pg3"              sim_year="2000">
 lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne3np4.pg3_hist_2000_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="ne120np4.pg3"             sim_year="2000">
@@ -1721,6 +1729,8 @@ lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne30np4.pg2_hist_1850_78pfts_c240908.n
 lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne30np4.pg3_hist_1850_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="ne3np4.pg3"  sim_year="1850">
 lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne3np4.pg3_hist_1850_78pfts_c240908.nc</fsurdat>
+<fsurdat hgrid="ne3np4"       sim_year="1850">
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne3np4_hist_1850_78pfts_c240925.nc</fsurdat>
 
 <fsurdat hgrid="C96"  sim_year="1850">
 lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_C96_hist_1850_78pfts_c240908.nc</fsurdat>
@@ -1731,8 +1741,6 @@ lnd/clm2/surfdata_esmf/ctsm5.3.0/synthetic/surfdata_1x1_cidadinhoBR_synth_hist_2
 <fsurdat hgrid="1x1_brazil"       sim_year="1850">
 lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_brazil_hist_1850_78pfts_c240912.nc</fsurdat>
 
-<fsurdat hgrid="ne3np4.pg3"               sim_year="1850">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne3np4.pg3_hist_1850_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="ne16np4.pg3"              sim_year="1850">
 lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne16np4.pg3_hist_1850_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="ne120np4.pg3"             sim_year="1850">
@@ -1803,6 +1811,8 @@ lnd/clm2/surfdata_esmf/NEON/ctsm5.3.0/surfdata_1x1_NEON_TOOL_hist_2000_78pfts_c2
 <flanduse_timeseries hgrid="mpasa120"      sim_year_range="1850-2000"
 >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_mpasa120_SSP2-4.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
 
+<flanduse_timeseries hgrid="ne3np4"        sim_year_range="1850-2000"
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_ne3np4_SSP2-4.5_1850-2100_78pfts_c240926.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="ne3np4.pg3"    sim_year_range="1850-2000"
 >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_ne3np4.pg3_SSP2-4.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="ne16np4.pg3"   sim_year_range="1850-2000"
@@ -1849,6 +1859,8 @@ lnd/clm2/surfdata_esmf/NEON/ctsm5.3.0/surfdata_1x1_NEON_TOOL_hist_2000_78pfts_c2
 <flanduse_timeseries hgrid="mpasa120"      sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
 >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_mpasa120_SSP2-4.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
 
+<flanduse_timeseries hgrid="ne3np4"        sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_ne3np4_SSP2-4.5_1850-2100_78pfts_c240926.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="ne3np4.pg3"    sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
 >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_ne3np4.pg3_SSP2-4.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="ne16np4.pg3"   sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"

bld/unit_testers/build-namelist_test.pl

@@ -163,10 +163,10 @@ sub cat_and_create_namelistinfile {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 3276;
+my $ntests = 3285;
 
 if ( defined($opts{'compare'}) ) {
-   $ntests += 1987;
+   $ntests += 2161;
 }
 plan( tests=>$ntests );
 
@@ -288,7 +288,7 @@ sub cat_and_create_namelistinfile {
 &make_config_cache($phys);
 my @mfiles = ( "lnd_in", "drv_flds_in", $tempfile );
 my $mfiles = NMLTest::CompFiles->new( $cwd, @mfiles );
-foreach my $options ( "-drydep", "-megan", "-drydep -megan", "-fire_emis", "-drydep -megan -fire_emis" ) {
+foreach my $options ( "-drydep --bgc sp", "-megan --bgc sp", "-drydep -megan --bgc bgc", "-fire_emis --bgc bgc", "-drydep -megan -fire_emis --bgc bgc" ) {
    &make_env_run();
    eval{ system( "$bldnml -envxml_dir . $options > $tempfile 2>&1 " ); };
    is( $@, '', "options: $options" );
@@ -576,8 +576,8 @@ sub cat_and_create_namelistinfile {
                       "--res 1.9x2.5 --bgc bgc --use_case 1850-2100_SSP2-4.5_transient --namelist '&a start_ymd=19101023/'",
                       "-namelist \"&a dust_emis_method='Zender_2003', zender_soil_erod_source='lnd' /'\"",
                       "-bgc bgc -use_case 2000_control -namelist \"&a fire_method='nofire'/\" -crop",
-                      "-res 0.9x1.25 -bgc sp -use_case 1850_noanthro_control -drydep -fire_emis",
-                      "-res 0.9x1.25 -bgc bgc -use_case 1850_noanthro_control -drydep -fire_emis -light_res 360x720",
+                      "-res 0.9x1.25 -bgc sp -use_case 1850_noanthro_control -drydep",
+                      "-res 0.9x1.25 -bgc bgc -use_case 1850_noanthro_control -drydep -fire_emis -megan -light_res 360x720",
                       "--bgc bgc --light_res none --namelist \"&a fire_method='nofire'/\"",
                       "--bgc fates --light_res 360x720 --no-megan --namelist \"&a fates_spitfire_mode=2/\"",
                       "--bgc fates --light_res none --no-megan --namelist \"&a fates_spitfire_mode=1/\"",
@@ -1093,6 +1093,10 @@ sub cat_and_create_namelistinfile {
                                      namelst=>"suplnitro='NONE'",
                                      phys=>"clm6_0",
                                    },
+     "FATESwBothSpST3"           =>{ options=>"--bgc fates --envxml_dir . --no-megan",
+                                     namelst=>"use_fates_sp = TRUE, use_fates_ed_st3 = TRUE",
+                                     phys=>"clm6_0",
+                                   },
      "FireNoneButBGCfireon"    =>{ options=>"-bgc bgc -envxml_dir . -light_res none",
                                      namelst=>"fire_method='li2021gswpfrc'",
                                      phys=>"clm6_0",
@@ -1145,6 +1149,14 @@ sub cat_and_create_namelistinfile {
                                     namelst=>"",
                                     phys=>"clm4_5",
                                  },
+     "useFIREEMISwithNOFIRE"     =>{ options=>"--bgc bgc --envxml_dir . --fire_emis",
+                                    namelst=>"fire_method='nofire'",
+                                    phys=>"clm6_0",
+                                 },
+     "useFIREEMISwithSP"         =>{ options=>"--bgc sp --envxml_dir . --fire_emis",
+                                    namelst=>"",
+                                    phys=>"clm6_0",
+                                 },
      "useDRYDEPwithFATES"        =>{ options=>"--bgc fates --envxml_dir . --no-megan --drydep",
                                      namelst=>"",
                                      phys=>"clm4_5",
@@ -1494,7 +1506,7 @@ sub cat_and_create_namelistinfile {
 print "========================================================================\n";
 
 # Check for ALL resolutions with CLM50SP
-my @resolutions = ( "360x720cru", "10x15", "4x5", "0.9x1.25", "1.9x2.5", "ne3np4.pg3", "ne16np4.pg3", "ne30np4", "ne30np4.pg2", "ne30np4.pg3", "ne120np4.pg3", "ne0np4CONUS.ne30x8", "ne0np4.ARCTIC.ne30x4", "ne0np4.ARCTICGRIS.ne30x8", "C96", "mpasa480", "mpasa120" );
+my @resolutions = ( "360x720cru", "10x15", "4x5", "0.9x1.25", "1.9x2.5", "ne3np4", "ne3np4.pg3", "ne16np4.pg3", "ne30np4", "ne30np4.pg2", "ne30np4.pg3", "ne120np4.pg3", "ne0np4CONUS.ne30x8", "ne0np4.ARCTIC.ne30x4", "ne0np4.ARCTICGRIS.ne30x8", "C96", "mpasa480", "mpasa120" );
 my @only2000_resolutions = ( "1x1_numaIA", "1x1_brazil", "1x1_mexicocityMEX", "1x1_vancouverCAN", "1x1_urbanc_alpha", "5x5_amazon", "0.125nldas2", "mpasa60", "mpasa15", "mpasa3p75" );
 my @regional;
 foreach my $res ( @resolutions ) {
@@ -1531,7 +1543,7 @@ sub cat_and_create_namelistinfile {
 print " Test important resolutions for BGC and historical\n";
 print "==================================================\n";
 
-my @resolutions = ( "4x5", "10x15", "360x720cru", "ne30np4.pg3", "ne3np4.pg3", "1.9x2.5", "0.9x1.25", "C96", "mpasa120" );
+my @resolutions = ( "4x5", "10x15", "360x720cru", "ne30np4.pg3", "ne3np4", "ne3np4.pg3", "1.9x2.5", "0.9x1.25", "C96", "mpasa120" );
 my @regional;
 my $nlbgcmode = "bgc";
 my $mode = "$phys-$nlbgcmode";
@@ -1758,7 +1770,7 @@ sub cat_and_create_namelistinfile {
    &cleanup();
 }
 
-my @crop_res = ( "1x1_numaIA", "4x5", "10x15", "0.9x1.25", "1.9x2.5", "ne3np4.pg3", "ne30np4", "ne30np4.pg3", "C96", "mpasa120" );
+my @crop_res = ( "1x1_numaIA", "4x5", "10x15", "0.9x1.25", "1.9x2.5", "ne3np4", "ne3np4.pg3", "ne30np4", "ne30np4.pg3", "C96", "mpasa120" );
 foreach my $res ( @crop_res ) {
    $options = "-bgc bgc -crop -res $res -envxml_dir .";
    &make_env_run();
@@ -1847,7 +1859,7 @@ sub cat_and_create_namelistinfile {
    &cleanup();
 }
 # Transient ssp_rcp scenarios that work
-my @tran_res = ( "4x5", "0.9x1.25", "1.9x2.5", "10x15", "360x720cru", "ne3np4.pg3", "ne16np4.pg3", "ne30np4.pg3", "C96", "mpasa120" );
+my @tran_res = ( "4x5", "0.9x1.25", "1.9x2.5", "10x15", "360x720cru", "ne3np4", "ne3np4.pg3", "ne16np4.pg3", "ne30np4.pg3", "C96", "mpasa120" );
 foreach my $usecase ( "1850-2100_SSP2-4.5_transient" ) {
    my $startymd = 20150101;
    foreach my $res ( @tran_res ) {
@@ -1884,7 +1896,7 @@ sub cat_and_create_namelistinfile {
                      "-bgc bgc -clm_demand flanduse_timeseries -sim_year 1850-2000 -namelist '&a start_ymd=18500101/'",
                      "-bgc bgc -envxml_dir . -namelist '&a use_c13=.true.,use_c14=.true.,use_c14_bombspike=.true./'" );
   foreach my $clmopts ( @clmoptions ) {
-     my @clmres = ( "10x15", "4x5", "360x720cru", "0.9x1.25", "1.9x2.5", "ne3np4.pg3", "ne16np4.pg3", "ne30np4.pg3", "C96", "mpasa120" );
+     my @clmres = ( "10x15", "4x5", "360x720cru", "0.9x1.25", "1.9x2.5", "ne3np4", "ne3np4.pg3", "ne16np4.pg3", "ne30np4.pg3", "C96", "mpasa120" );
      foreach my $res ( @clmres ) {
         $options = "-res $res -envxml_dir . ";
         &make_env_run( );

cime_config/config_component.xml

@@ -241,12 +241,24 @@
     <type>char</type>
     <default_value></default_value>
     <values>
-      <!--- All versions -->
-      <value compset="_CLM[^_]*%SP"       >-bgc sp</value>
-      <value compset="_CLM[^_]*BGC"       >-bgc bgc</value>
-      <value compset="_CLM[^_]*BGC-CROP"  >-bgc bgc -crop</value>
-      <value compset="_CLM[^_]*FATES"     >-bgc fates -no-megan</value>
-      <value compset="_CLM[^_]*FATES-SP"  >-bgc fates -no-megan</value>
+      <!--- All versions with DATM -->
+      <value compset="DATM[^_]*_CLM[^_]*%SP"       >-bgc sp</value>
+      <value compset="DATM[^_]*_CLM[^_]*BGC"       >-bgc bgc</value>
+      <value compset="DATM[^_]*_CLM[^_]*BGC-CROP"  >-bgc bgc -crop</value>
+
+      <!-- FATES currently can't use MEGAN, drydep, or fire-emission whether coupled to CAM or NOT-->
+      <value compset="CLM[^_]*FATES" >--bgc fates --no-megan --no-drydep --no-fire_emis</value>
+
+      <!-- ======================================= Coupled to CAM Options ======================================
+        All versions with CAM - turn off sending test drv_flds_in namelists from CTSM
+
+        When coupled to CAM - expect CAM to determine these drv_flds settings
+        See issue #2713 for more information on this.
+      -->
+      <value compset="CAM[^_]*_CLM[^_]*%SP"       >--bgc sp --no-megan --no-drydep --no-fire_emis</value>
+      <value compset="CAM[^_]*_CLM[^_]*BGC"       >--bgc bgc --no-megan --no-drydep --no-fire_emis</value>
+      <value compset="CAM[^_]*_CLM[^_]*BGC-CROP"  >--bgc bgc --crop --no-megan --no-drydep --no-fire_emis</value>
+      <!-- ======================================= End of Coupled to CAM Options ===============================  -->
 
       <!-- Options specific for CLM4.5 -->
       <value compset="_CLM45%[^_]*BGCDV"	 >-bgc bgc -dynamic_vegetation</value>