alpha-ctsm5.4.CMIP7.19.ctsm5.3.085: Update ctsm5.4 alpha branch to ctsm5.3.085

.github/workflows/docs-build-and-deploy.yml

@@ -33,6 +33,10 @@ concurrency:
 jobs:
 
   build-and-deploy:
+
+    # Only run on upstream repository
+    if: ${{ github.repository == 'ESCOMP/CTSM' }}
+
     environment:
       name: github-pages
       url: ${{ steps.deployment.outputs.page_url }}

.gitmodules

@@ -28,7 +28,7 @@
 [submodule "fates"]
 path = src/fates
 url = https://github.com/NGEET/fates
-fxtag = sci.1.87.2_api.41.0.0
+fxtag = sci.1.88.0_api.42.0.0
 fxrequired = AlwaysRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/NGEET/fates
@@ -100,7 +100,7 @@ fxDONOTUSEurl = https://github.com/ESCOMP/CDEPS.git
 [submodule "share"]
 path = share
 url = https://github.com/ESCOMP/CESM_share
-fxtag = share1.1.9
+fxtag = share1.1.15
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/CESM_share

bld/CLMBuildNamelist.pm

@@ -3770,48 +3770,94 @@ sub setup_logic_c_isotope {
         $log->warning("use_c14 is ONLY scientifically validated with the bgc=BGC configuration" );
       }
     }
+    my $use_c14_bombspike = $nl->get_value('use_c14_bombspike');
+    my $stream_fldfilename_atm_c14 = $nl->get_value('stream_fldfilename_atm_c14');
+    my $atm_c14_filename = $nl->get_value('atm_c14_filename');
     if ( &value_is_true($use_c14) ) {
       add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_c14_bombspike', 'use_c14'=>$use_c14 );
-      my $use_c14_bombspike = $nl->get_value('use_c14_bombspike');
+      $use_c14_bombspike = $nl->get_value('use_c14_bombspike');
       if ( &value_is_true($use_c14_bombspike) ) {
-         add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'atm_c14_filename',
-                 'use_c14'=>$use_c14, 'use_cn'=>$nl_flags->{'use_cn'}, 'use_c14_bombspike'=>$nl->get_value('use_c14_bombspike'),
-                 'ssp_rcp'=>$nl_flags->{'ssp_rcp'} );
+         if ( defined($stream_fldfilename_atm_c14) ) {
+            setup_logic_c14_streams($opts, $nl_flags, $definition, $defaults, $nl);
+         } else {
+            add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'atm_c14_filename',
+                    'use_c14'=>$use_c14, 'use_cn'=>$nl_flags->{'use_cn'}, 'use_c14_bombspike'=>$nl->get_value('use_c14_bombspike'),
+                    'ssp_rcp'=>$nl_flags->{'ssp_rcp'} );
+         }
+         $stream_fldfilename_atm_c14 = $nl->get_value('stream_fldfilename_atm_c14');
+         $atm_c14_filename = $nl->get_value('atm_c14_filename');
+         if ( defined($stream_fldfilename_atm_c14) && defined($atm_c14_filename) ) {
+           $log->fatal_error("Both stream_fldfilename_atm_c14 and atm_c14_filename set, only one should be set");
+         }
       }
     } else {
-      if ( defined($nl->get_value('use_c14_bombspike')) ||
-           defined($nl->get_value('atm_c14_filename')) ) {
-        $log->fatal_error("use_c14 is FALSE and use_c14_bombspike or atm_c14_filename set");
+      if ( defined($use_c14_bombspike) ||
+           defined($stream_fldfilename_atm_c14) ||
+           defined($atm_c14_filename) ) {
+        $log->fatal_error("use_c14 is FALSE and use_c14_bombspike, stream_fldfilename_atm_c14 or atm_c14_filename set");
       }
     }
+    my $use_c13_timeseries = $nl->get_value('use_c13_timeseries');
+    my $stream_fldfilename_atm_c13 = $nl->get_value('stream_fldfilename_atm_c13');
+    my $atm_c13_filename = $nl->get_value('atm_c13_filename');
     if ( &value_is_true($use_c13) ) {
       add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_c13_timeseries', 'use_c13'=>$use_c13 );
-      my $use_c13_timeseries = $nl->get_value('use_c13_timeseries');
+      $use_c13_timeseries = $nl->get_value('use_c13_timeseries');
       if ( &value_is_true($use_c13_timeseries) ) {
-         add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'atm_c13_filename',
-                 'use_c13'=>$use_c13, 'use_cn'=>$nl_flags->{'use_cn'}, 'use_c13_timeseries'=>$nl->get_value('use_c13_timeseries'),
-                 'ssp_rcp'=>$nl_flags->{'ssp_rcp'} );
+         if ( defined($stream_fldfilename_atm_c13) ) {
+            setup_logic_c13_streams($opts, $nl_flags, $definition, $defaults, $nl);
+         } else {
+            add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'atm_c13_filename',
+                    'use_c13'=>$use_c13, 'use_cn'=>$nl_flags->{'use_cn'}, 'use_c13_timeseries'=>$nl->get_value('use_c13_timeseries'),
+                    'ssp_rcp'=>$nl_flags->{'ssp_rcp'} );
+         }
+         $stream_fldfilename_atm_c13 = $nl->get_value('stream_fldfilename_atm_c13');
+         $atm_c13_filename = $nl->get_value('atm_c13_filename');
+         if ( defined($stream_fldfilename_atm_c13) && defined($atm_c13_filename) ) {
+           $log->fatal_error("Both stream_fldfilename_atm_c13 and atm_c13_filename set, only one should be set");
+         }
       }
     } else {
       if ( defined($nl->get_value('use_c13_timeseries')) ||
+           defined($nl->get_value('stream_fldfilename_atm_c13')) ||
            defined($nl->get_value('atm_c13_filename')) ) {
-        $log->fatal_error("use_c13 is FALSE and use_c13_timeseries or atm_c13_filename set");
+        $log->fatal_error("use_c13 is FALSE and use_c13_timeseries, stream_fldfilename_atm_c13 or atm_c13_filename set");
       }
     }
   } else {
     if ( &value_is_true($use_c13) ||
          &value_is_true($use_c14) ||
          &value_is_true($nl->get_value('use_c14_bombspike')) ||
          defined($nl->get_value('atm_c14_filename'))  ||
+         defined($nl->get_value('stream_fldfilename_atm_c14'))  ||
          &value_is_true($nl->get_value('use_c13_timeseries')) ||
-         defined($nl->get_value('atm_c13_filename')) ) {
+         defined($nl->get_value('atm_c13_filename')) ||
+         defined($nl->get_value('stream_fldfilename_atm_c13')) ) {
            $log->fatal_error("bgc=sp and C isotope  namelist variables were set, both can't be used at the same time");
     }
   }
 }
 
 #-------------------------------------------------------------------------------
 
+sub setup_logic_c13_streams {
+  my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
+  #
+  # C13 stream file settings
+  #
+}
+
+#-------------------------------------------------------------------------------
+
+sub setup_logic_c14_streams {
+  my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
+  #
+  # C14 stream file settings
+  #
+}
+
+#-------------------------------------------------------------------------------
+
 sub setup_logic_nitrogen_deposition {
   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
 
@@ -5334,6 +5380,9 @@ sub write_output_files {
   push @groups, "clm_canopy_inparm";
   push @groups, "prigentroughness";
   push @groups, "zendersoilerod";
+  if ( &value_is_true($nl_flags->{'use_cn'}) ) {
+    push @groups, "carbon_isotope_streams";
+  }
   if (remove_leading_and_trailing_quotes($nl->get_value('snow_cover_fraction_method')) eq 'SwensonLawrence2012') {
      push @groups, "scf_swenson_lawrence_2012_inparm";
   }

bld/namelist_files/namelist_definition_ctsm.xml

@@ -1806,6 +1806,51 @@ Mapping method from Nitrogen deposition input file to the model resolution
     none     = no interpolation
 </entry>
 
+<!-- ======================================================================================== 
+     Carbon isotope streams Namelist (only used when use_c13/use_c14 is on and bgc=cn or bgc)
+     (Atmospheric C13 and C14 ratios in terms of a delta)
+     ========================================================================================  -->
+
+<entry id="stream_year_first_atm_c14" type="integer" category="datasets"
+       group="carbon_isotope_streams" valid_values="" >
+First year to loop over for atmospheric C14 isotope delta data
+</entry>
+
+<entry id="stream_year_last_atm_c14" type="integer" category="datasets"
+       group="carbon_isotope_streams" valid_values="" >
+Last year to loop over for data atmospheric C14 isotope delta data
+</entry>
+
+<entry id="stream_model_year_align_atm_c14" type="integer" category="datasets"
+       group="carbon_isotope_streams" valid_values="" >
+Simulation year that aligns with stream_year_first_atm_c14 value
+</entry>
+
+<entry id="stream_fldfilename_atm_c14" type="char*512" category="datasets"
+       input_pathname="abs" group="carbon_isotope_streams" valid_values="" >
+Filename of input stream data for atmospheric C14 isotope delta data
+</entry>
+
+<entry id="stream_year_first_atm_c13" type="integer" category="datasets"
+       group="carbon_isotope_streams" valid_values="" >
+First year to loop over for atmospheric C13 isotope delta data
+</entry>
+
+<entry id="stream_year_last_atm_c13" type="integer" category="datasets"
+       group="carbon_isotope_streams" valid_values="" >
+Last year to loop over for data atmospheric C13 isotope delta data
+</entry>
+
+<entry id="stream_model_year_align_atm_c13" type="integer" category="datasets"
+       group="carbon_isotope_streams" valid_values="" >
+Simulation year that aligns with stream_year_first_atm_c13 value
+</entry>
+
+<entry id="stream_fldfilename_atm_c13" type="char*512" category="datasets"
+       input_pathname="abs" group="carbon_isotope_streams" valid_values="" >
+Filename of input stream data for atmospheric C13 isotope delta data
+</entry>
+
 <!-- ========================================================================================  -->
 <!-- Prigent roughness stream -->
 <!-- ========================================================================================  -->

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 = 3396;
+my $ntests = 3402;
 
 if ( defined($opts{'compare'}) ) {
    $ntests += 2061;
@@ -821,6 +821,30 @@ sub cat_and_create_namelistinfile {
                                      namelst=>"use_c14_bombspike=.true.",
                                      phys=>"clm5_0",
                                    },
+     "bombspike file and stream" =>{ options=>"-bgc bgc -envxml_dir .",
+                                     namelst=>"use_c14=TRUE use_c14_bombspike=.true. stream_fldfilename_atm_c14='/dev/null', atm_c14_filename='/dev/null'",
+                                     phys=>"clm6_0",
+                                   },
+     "c13 file and stream"       =>{ options=>"-bgc bgc -envxml_dir .",
+                                     namelst=>"use_c13_timeseries=.true. stream_fldfilename_atm_c13='/dev/null', atm_c13_filename='/dev/null'",
+                                     phys=>"clm6_0",
+                                   },
+     "c13 off, but stream"       =>{ options=>"-bgc bgc -envxml_dir .",
+                                     namelst=>"use_c13=.false. stream_fldfilename_atm_c13='/dev/null'",
+                                     phys=>"clm6_0",
+                                   },
+     "c14 off, but stream"       =>{ options=>"-bgc bgc -envxml_dir .",
+                                     namelst=>"use_c14=.false. stream_fldfilename_atm_c14='/dev/null'",
+                                     phys=>"clm6_0",
+                                   },
+     "sp,  but c13 stream"       =>{ options=>"-bgc sp -envxml_dir .",
+                                     namelst=>"stream_fldfilename_atm_c13='/dev/null'",
+                                     phys=>"clm6_0",
+                                   },
+     "sp,  but c14 stream"       =>{ options=>"-bgc sp -envxml_dir .",
+                                     namelst=>"stream_fldfilename_atm_c14='/dev/null'",
+                                     phys=>"clm6_0",
+                                   },
      "lightres no cn"            =>{ options=>"-bgc sp -envxml_dir . -light_res 360x720",
                                      namelst=>"",
                                      phys=>"clm5_0",

cime_config/testdefs/ExpectedTestFails.xml

@@ -247,6 +247,15 @@
 
   <!-- fates test suite failures -->
 
+  <!-- This is commented out because cime currently does NOT allow longnames in the XML in the XSD for this file
+  <test name="ERS_D_Ld30.f45_f45_mg37.HIST_DATM%CRUv7_CLM50%FATES_SICE_SOCN_SROF_SGLC_SWAV_SESP.izumi_nag.clm-FatesColdLandUse">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#3500</issue>
+    </phase>
+  </test>
+  -->
+
   <test name="ERS_D_Ld30.f45_f45_mg37.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesColdLUH2">
     <phase name="RUN">
       <status>FAIL</status>

cime_config/testdefs/testlist_clm.xml

@@ -195,6 +195,25 @@
       <option name="comment">Testing that a initial condition file with an missing urban landunit will be filled with another urban landunit</option>
     </options>
   </test>
+
+  <test name="SMS_Ly3" grid="f10_f10_mt232" compset="IHistClm60BgcCropCrujra" testmods="clm-ciso_monthly_2013Start">
+    <machines>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">01:40:00</option>
+      <option name="comment">Testing a few years with CMIP6 carbon isotopes</option>
+    </options>
+  </test>
+  <test name="SMS_Ly3" grid="f10_f10_mt232" compset="IHistClm60BgcCropCrujra" testmods="clm-ciso_cmip7_monthly_2013Start">
+    <machines>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">01:40:00</option>
+      <option name="comment">Testing a few years with CMIP7 carbon isotopes</option>
+    </options>
+  </test>
   <test name="ERS_D_Ld9" grid="ne30pg3_t232" compset="I1850Clm60BgcCropG" testmods="clm/clm60cam7LndTuningMode">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -4445,6 +4464,7 @@
   <test name="FUNITCTSM_P1x1" grid="f10_f10_mg37" compset="I2000Clm50Sp">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="prealpha"/>
       <machine name="izumi" compiler="intel" category="aux_clm"/>
     </machines>
     <options>

cime_config/testdefs/testmods_dirs/clm/ciso_cmip7_monthly_2013Start/include_user_mods

@@ -0,0 +1 @@
+../ciso_monthly_2013Start

cime_config/testdefs/testmods_dirs/clm/ciso_cmip7_monthly_2013Start/user_nl_clm

@@ -0,0 +1,6 @@
+ stream_fldfilename_atm_c13 = '$DIN_LOC_ROOT/lnd/clm2/isotopes/ctsmforc.Graven.atm_delta_C13_CMIP7_global_1700-2023_yearly_v3.0_c251013.nc'
+ stream_fldfilename_atm_c14 = '$DIN_LOC_ROOT/lnd/clm2/isotopes/ctsmforc.Graven.atm_delta_C14_CMIP7_4x1_global_1700-2023_yearly_v3.0_c251013.nc'
+ stream_year_first_atm_c14 = 2013
+ stream_model_year_align_atm_c14 = 2013
+ stream_year_first_atm_c13 = 2013
+ stream_model_year_align_atm_c13 = 2013

cime_config/testdefs/testmods_dirs/clm/ciso_monthly_2013Start/include_user_mods

@@ -0,0 +1 @@
+../ciso_monthly

cime_config/testdefs/testmods_dirs/clm/ciso_monthly_2013Start/shell_commands

@@ -0,0 +1 @@
+./xmlchange RUN_STARTDATE=2013-01-01

cime_config/testdefs/testmods_dirs/clm/ciso_monthly_2013Start/user_nl_clm

@@ -0,0 +1,3 @@
+! Add C13/C14 output to validate the incoming data
+hist_fincl1 += 'RC13_CANAIR', 'RC14_CANAIR'
+hist_fincl2 = 'RC13_CANAIR', 'RC14_CANAIR'