Merge pull request #2883 from ekluzek/beta05_cleanup_2_5313

Update branch to latest master ctsm5.3.012
ESCOMP · Nov 17, 2024 · 8e31637 · 8e31637
2 parents 3d811ca + 8402d31
commit 8e31637
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Showing 28 changed files with 527 additions and 235 deletions.
diff --git a/.gitmodules b/.gitmodules
@@ -28,7 +28,7 @@
 [submodule "fates"]
 path = src/fates
 url = https://github.com/NGEET/fates
-fxtag = sci.1.78.3_api.36.1.0
+fxtag = sci.1.79.3_api.37.0.0
 fxrequired = AlwaysRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/NCAR/fates-release

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
@@ -2593,12 +2593,9 @@ sub setup_logic_initial_conditions {
   my $finidat = $nl->get_value($var);
   $nl_flags->{'excess_ice_on_finidat'} = "unknown";
   if ( $nl_flags->{'clm_start_type'} =~ /cold/ ) {
-    if (defined $finidat ) {
-      $log->warning("setting $var (either explicitly in your user_nl_clm or by doing a hybrid or branch RUN_TYPE)\n is incomptable with using a cold start" .
+    if (defined $finidat && !&value_is_true(($nl->get_value('use_fates')))) {
+      $log->fatal_error("setting $var (either explicitly in your user_nl_clm or by doing a hybrid or branch RUN_TYPE)\n is incompatible with using a cold start" .
               " (by setting CLM_FORCE_COLDSTART=on)." );
-      $log->warning("Overridding input $var file with one specifying that this is a cold start from arbitrary initial conditions." );
-      my $group = $definition->get_group_name($var);
-      $nl->set_variable_value($group, $var, "' '" );
     }
     add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl,
                 $var, 'val'=>"' '", 'no_abspath'=>1);
@@ -3607,17 +3604,6 @@ sub setup_logic_luna {
   if ( &value_is_true($nl->get_value('lnc_opt') ) && not &value_is_true( $nl_flags->{'use_cn'}) ) {
      $log->fatal_error("Cannot turn lnc_opt to true when bgc=sp" );
   }
-  my $var = "jmaxb1";
-  if ( &value_is_true( $nl_flags->{'use_luna'} ) ) {
-     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var,
-                 'use_luna'=>$nl_flags->{'use_luna'} );
-  }
-  my $val = $nl->get_value($var);
-  if ( ! &value_is_true( $nl_flags->{'use_luna'} ) ) {
-     if ( defined($val) ) {
-        $log->fatal_error("Cannot set $var when use_luna is NOT on" );
-     }
-  }
 }
 
 #-------------------------------------------------------------------------------
@@ -4531,8 +4517,6 @@ sub setup_logic_canopyhydrology {
   #
   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
 
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'interception_fraction' );
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'maximum_leaf_wetted_fraction' );
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_clm5_fpi' );
 }
 
@@ -4551,7 +4535,6 @@ sub setup_logic_snowpack {
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'wind_dependent_snow_density');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snow_overburden_compaction_method');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'lotmp_snowdensity_method');
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'upplim_destruct_metamorph');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'reset_snow');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'reset_snow_glc');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'reset_snow_glc_ela');

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -394,11 +394,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- Canopy hydrology namelist defaults -->
 <use_clm5_fpi                               >.true.</use_clm5_fpi>
-<interception_fraction                      >1.0</interception_fraction>
-<maximum_leaf_wetted_fraction               >0.05</maximum_leaf_wetted_fraction>
 <use_clm5_fpi                 phys="clm4_5" >.false.</use_clm5_fpi>
-<interception_fraction        phys="clm4_5" >0.25</interception_fraction>
-<maximum_leaf_wetted_fraction phys="clm4_5" >1.0</maximum_leaf_wetted_fraction>
 
 <!-- Soilwater movement namelist defaults -->
 <soilwater_movement_method               >1</soilwater_movement_method>
@@ -474,9 +470,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <lotmp_snowdensity_method               >'Slater2017'</lotmp_snowdensity_method>
 <lotmp_snowdensity_method phys="clm4_5" >'TruncatedAnderson1976'</lotmp_snowdensity_method>
 
-<upplim_destruct_metamorph                 >175.d00</upplim_destruct_metamorph>
-<upplim_destruct_metamorph   phys="clm4_5" >100.d00</upplim_destruct_metamorph>
-
 <overburden_compress_tfactor>0.08d00</overburden_compress_tfactor>
 
 <reset_snow>.false.</reset_snow>
@@ -531,9 +524,10 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- The default filenames are given relative to the root directory
      for the CLM2 data in the CESM distribution -->
 <!-- Plant function types (relative to {csmdata}) -->
-<paramfile phys="clm6_0" >lnd/clm2/paramdata/ctsm60_params.c240822.nc</paramfile>
-<paramfile phys="clm5_0" >lnd/clm2/paramdata/clm50_params.c240814.nc</paramfile>
-<paramfile phys="clm4_5" >lnd/clm2/paramdata/clm45_params.c240814.nc</paramfile>
+<paramfile phys="clm6_0" >lnd/clm2/paramdata/ctsm60_params.c241017.nc</paramfile>
+<paramfile phys="clm5_1" >lnd/clm2/paramdata/ctsm51_params.c241017.nc</paramfile>
+<paramfile phys="clm5_0" >lnd/clm2/paramdata/clm50_params.c241017.nc</paramfile>
+<paramfile phys="clm4_5" >lnd/clm2/paramdata/clm45_params.c241017.nc</paramfile>
 
 <!-- ================================================================== -->
 <!-- FATES default parameter file                                       -->
@@ -584,9 +578,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <use_fertilizer                   >.false.</use_fertilizer>
 <use_fertilizer use_crop=".true." >.true.</use_fertilizer>
 
-<!-- Could depend on physics version -->
-<jmaxb1 use_luna=".true." >0.17</jmaxb1>
-
 <!-- o3_veg_stress_method-->
 <o3_veg_stress_method>unset</o3_veg_stress_method>
 

diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -404,21 +404,11 @@ Max number of iterations used in subr. CanopyFluxes. For many years, 40 was the
 <default>Default: 40</default>
 </entry>
 
-<entry id="interception_fraction" type="real" category="clm_physics"
-       group="clm_canopyhydrology_inparm" valid_values="" >
-Fraction of intercepted precipitation
-</entry>
-
 <entry id="use_clm5_fpi" type="logical" category="clm_physics"
        group="clm_canopyhydrology_inparm" valid_values="" >
 If TRUE use clm5 equation for fraction of intercepted precipitation
 </entry>
 
-<entry id="maximum_leaf_wetted_fraction" type="real" category="clm_physics"
-       group="clm_canopyhydrology_inparm" valid_values="" >
-Maximum fraction of leaf that may be wet prior to drip occuring
-</entry>
-
 <entry id="baseflow_scalar" type="real" category="clm_physics"
        group="soilhydrology_inparm" valid_values="" >
 Scalar multiplier for base flow rate
@@ -712,11 +702,6 @@ Scalar of leaf respiration to vcmax
 The maximum value to use for zeta under stable conditions
 </entry>
 
-<entry id="Jmaxb1" type="real" category="clm_physics"
-       group="luna" >
-baseline proportion of nitrogen allocated for electron transport (J)
-</entry>
-
 <entry id="use_fates" type="logical" category="physics"
         group="clm_inparm" valid_values="" value=".false.">
 Toggle to turn on the FATES model
@@ -2844,11 +2829,6 @@ TruncatedAnderson1976 -- Truncate the Anderson-1976 equation at the value for -1
 Slater2017 ------------- Use equation from Slater that increases snow density for very cold temperatures  (Arctic, Antarctic)
 </entry>
 
-<entry id="upplim_destruct_metamorph" type="real" category="clm_physics"
-       group="clm_snowhydrology_inparm"   >
-Upper Limit on Destructive Metamorphism Compaction [kg/m3]
-</entry>
-
 <entry id="overburden_compress_Tfactor" type="real" category="clm_physics"
        group="clm_snowhydrology_inparm"   >
 Snow compaction overburden exponential factor (1/K)

diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
@@ -1265,10 +1265,6 @@ sub cat_and_create_namelistinfile {
                                      namelst=>"use_luna=.true., lnc_opt=.true.",
                                      phys=>"clm5_0",
                                    },
-     "NOlunabutsetJmaxb1"        =>{ options=>"-envxml_dir . -bgc sp",
-                                     namelst=>"use_luna=.false., jmaxb1=1.0",
-                                     phys=>"clm5_0",
-                                   },
      "envxml_not_dir"            =>{ options=>"-envxml_dir myuser_nl_clm",
                                      namelst=>"",
                                      phys=>"clm5_0",
@@ -1348,10 +1344,6 @@ sub cat_and_create_namelistinfile {
 
 my %warntest = (
      # Warnings without the -ignore_warnings option given
-     "coldwfinidat"              =>{ options=>"-envxml_dir . -clm_start_type cold",
-                                     namelst=>"finidat = 'testfile.nc'",
-                                     phys=>"clm5_0",
-                                   },
      "bgcspin_w_suplnitro"       =>{ options=>"-envxml_dir . -bgc bgc -clm_accelerated_spinup on",
                                      namelst=>"suplnitro='ALL'",
                                      phys=>"clm5_0",
@@ -1432,6 +1424,56 @@ sub cat_and_create_namelistinfile {
    system( "cat $tempfile" );
 }
 
+print "\n===============================================================================\n";
+print "Ensure cold starts with finidat are handled properly \n";
+print "=================================================================================\n";
+
+my %coldwfinidat = (
+     "bgc"   => { options=>"-envxml_dir . -clm_start_type cold",
+                  namelst=>"finidat = 'testfile.nc'",
+                  phys=>"clm5_0",
+                  expected_fail=>1,
+                },
+     "fates" => { options=>"-envxml_dir . -clm_start_type cold -bgc fates -no-megan",
+                  namelst=>"finidat = 'testfile.nc', use_fates = .true.",
+                  phys=>"clm5_0",
+                  expected_fail=>0,
+                },
+);
+my $finidat;
+foreach my $key ( keys(%coldwfinidat) ) {
+   print( "$key\n" );
+
+   my $var;
+   foreach $var ( "phys" , "options", "namelst", "expected_fail" ) {
+      if ( not exists $coldwfinidat{$key}{$var} ) {
+         die  "ERROR: Subkey $var does not exist for coldwfinidat $key\nERROR:Check if you spelled $var correctly\n"
+      }
+   }
+
+   &make_config_cache($coldwfinidat{$key}{"phys"});
+   my $options  = $coldwfinidat{$key}{"options"};
+   my $namelist = $coldwfinidat{$key}{"namelst"};
+   my $expected_fail = $coldwfinidat{$key}{"expected_fail"};
+   my %settings;
+   &make_env_run( %settings );
+
+   # Should fail if expected to, pass otherwise
+   eval{ system( "$bldnml $options -namelist \"&clmexp $namelist /\" > $tempfile 2>&1 " ); };
+   is( $? eq 0, $expected_fail eq 0, "coldwfinidat $key run");
+
+   if ( $expected_fail ) {
+      # Now run with -ignore_warnings and make sure it still doesn't work
+      $options .= " -ignore_warnings";
+      eval{ system( "$bldnml $options -namelist \"&clmexp $namelist /\" > $tempfile 2>&1 " ); };
+      isnt( $?, 0, "coldwfinidat $key run -ignore_warnings" );
+   } else {
+      # Check that finidat was correctly set
+      $finidat = `grep finidat lnd_in`;
+      ok ( $finidat =~ "testfile.nc", "coldwfinidat $key finidat? $finidat" );
+   }
+}
+
 #
 # Loop over all physics versions
 #

diff --git a/cime_config/buildnml b/cime_config/buildnml
@@ -52,16 +52,8 @@ def buildnml(case, caseroot, compname):
     clm_accelerated_spinup = case.get_value("CLM_ACCELERATED_SPINUP")
     comp_interface = case.get_value("COMP_INTERFACE")
     lilac_mode = case.get_value("LILAC_MODE")
-    if comp_interface == "nuopc":
-        yr_start = case.get_value("DATM_YR_START")
-        yr_end = case.get_value("DATM_YR_END")
-    else:
-        yr_start = case.get_value("DATM_CLMNCEP_YR_START")
-        yr_end = case.get_value("DATM_CLMNCEP_YR_END")
-
-    if yr_start != None and yr_start < 0:
-        yr_start = case.get_value("DATM_CPLHIST_YR_START")
-        yr_end = case.get_value("DATM_CPLHIST_YR_END")
+    yr_start = case.get_value("DATM_YR_START")
+    yr_end = case.get_value("DATM_YR_END")
 
     # For LILAC
     if yr_start == None or lilac_mode == "on":

diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
@@ -183,6 +183,10 @@
       <status>FAIL</status>
       <issue>#2454</issue>
     </phase>
+    <phase name="COMPARE_base_rest">
+      <status>FAIL</status>
+      <issue>#2325</issue>
+    </phase>
   </test>
 
   <test name="SMS_Lm3_D_Mmpi-serial.1x1_brazil.I2000Clm50FatesCruRsGs.izumi_intel.clm-FatesColdHydro">
@@ -191,6 +195,13 @@
       <issue>#2454</issue>
     </phase>
   </test>
+
+  <test name="ERS_Ld60.f45_f45_mg37.I2000Clm50FatesCruRsGs.derecho_intel.clm-FatesColdST3">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2867</issue>
+    </phase>
+  </test>
 
   <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Fates.izumi_nag.clm-FatesFireLightningPopDens--clm-NEON-FATES-NIWO">
     <phase name="SHAREDLIB_BUILD">
@@ -273,17 +284,75 @@
     </phase>
   </test>
 
-  <test name="ERS_D_Ld15.f45_f45_mg37.I2000Clm50FatesRs.izumi_nag.clm-FatesColdTwoStream">
+  <test name="ERS_D_Ld15.f45_f45_mg37.I2000Clm50FatesRs.derecho_gnu.clm-FatesColdTwoStreamNoCompFixedBioGeo">
     <phase name="COMPARE_base_rest">
       <status>FAIL</status>
       <issue>#2325</issue>
     </phase>
   </test>
+
+  <!-- izumi nag failures -->
 
-  <test name="ERS_D_Ld15.f45_f45_mg37.I2000Clm50FatesRs.derecho_gnu.clm-FatesColdTwoStreamNoCompFixedBioGeo">
-    <phase name="COMPARE_base_rest">
+  <test name="SMS_D.f10_f10_mg37.I1850Clm60BgcCrop.izumi_nag.clm-ciso_soil_matrixcn_only">
+    <phase name="RUN">
       <status>FAIL</status>
-      <issue>#2325</issue>
+      <issue>#2861</issue>
+    </phase>
+  </test>
+
+  <test name="ERS_D_Ld5_Mmpi-serial.1x1_vancouverCAN.I1PtClm50SpRs.izumi_nag.clm-CLM1PTStartDate">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2861</issue>
+    </phase>
+  </test>
+
+  <test name="ERS_D_Mmpi-serial_Ld5.1x1_brazil.I2000Clm50FatesRs.izumi_nag.clm-FatesCold">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2861</issue>
+    </phase>
+  </test>
+
+  <test name="SMS_D_Ld1_Mmpi-serial.f45_f45_mg37.I2000Clm50SpRs.izumi_nag.clm-ptsRLA">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2861</issue>
+    </phase>
+  </test>
+
+  <test name="SMS_D_Mmpi-serial_Ld5.5x5_amazon.I2000Clm60FatesRs.izumi_nag.clm-FatesCold">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2861</issue>
+    </phase>
+  </test>
+
+  <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Bgc.izumi_nag.clm-default--clm-NEON-HARV">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2861</issue>
+    </phase>
+  </test>
+
+  <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60SpRs.izumi_nag.clm-default--clm-NEON-TOOL">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2861</issue>
+    </phase>
+  </test>
+
+  <test name="ERP_D_Ld5_P48x1.f10_f10_mg37.I1850Clm60Bgc.izumi_nag.clm-ciso">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2861</issue>
+    </phase>
+  </test>
+
+  <test name="SMS_Lm3_D_Mmpi-serial.1x1_brazil.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesColdHydro">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2861</issue>
     </phase>
   </test>
 
@@ -300,6 +369,29 @@
       <issue>#2810</issue>
     </phase>
   </test>
+
+  <test name="ERS_D_Mmpi-serial_Ld5.1x1_brazil.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesCold">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2861</issue>
+    </phase>
+  </test>
+
+
+  <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Fates.izumi_nag.clm-FatesPRISM--clm-NEON-FATES-YELLO">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2861</issue>
+    </phase>
+  </test>
+
+
+  <test name="ERS_D_Ld30.f45_f45_mg37.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesColdLandUse">
+    <phase name="SHAREDLIB_BUILD">
+      <status>FAIL</status>
+      <issue>#2810</issue>
+    </phase>
+  </test>
 
   <!-- Other submodule test list failures (MOSART, RTM, etc. -->