ctsm5.3.051: Update submodules to cesm3_0_beta06 + MEGAN namelist (answer change)

.gitmodules

@@ -36,7 +36,7 @@ fxDONOTUSEurl = https://github.com/NGEET/fates
 [submodule "cism"]
 path = components/cism
 url = https://github.com/ESCOMP/CISM-wrapper
-fxtag = cismwrap_2_2_005
+fxtag = cismwrap_2_2_006
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/CISM-wrapper
@@ -68,31 +68,31 @@ fxDONOTUSEurl = https://github.com/ESCOMP/mizuRoute
 [submodule "ccs_config"]
 path = ccs_config
 url = https://github.com/ESMCI/ccs_config_cesm.git
-fxtag = ccs_config_cesm1.0.23
+fxtag = ccs_config_cesm1.0.43
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git
 
 [submodule "cime"]
 path = cime
 url = https://github.com/ESMCI/cime
-fxtag = cime6.1.72
+fxtag = cime6.1.102
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESMCI/cime
 
 [submodule "cmeps"]
 path = components/cmeps
 url = https://github.com/ESCOMP/CMEPS.git
-fxtag = cmeps1.0.39
+fxtag = cmeps1.0.47
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git
 
 [submodule "cdeps"]
 path = components/cdeps
 url = https://github.com/ESCOMP/CDEPS.git
-fxtag = cdeps1.0.70
+fxtag = cdeps1.0.73
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/CDEPS.git
@@ -108,15 +108,15 @@ fxDONOTUSEurl = https://github.com/ESCOMP/CESM_share
 [submodule "parallelio"]
 path = libraries/parallelio
 url = https://github.com/NCAR/ParallelIO
-fxtag = pio2_6_3
+fxtag = pio2_6_4
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/NCAR/ParallelIO
 
 [submodule "mpi-serial"]
 path = libraries/mpi-serial
 url = https://github.com/ESMCI/mpi-serial
-fxtag = MPIserial_2.5.1
+fxtag = MPIserial_2.5.4
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial
@@ -128,3 +128,13 @@ fxtag = v2.2.6
 fxrequired = ToplevelOptional
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESMCI/doc-builder
+
+# FTorch is an optional library useful for AI and Machine Learning
+# In order to use it -- it must be checked out with git-fleximod
+[submodule "FTorch"]
+path = libraries/FTorch
+url = https://github.com/ESCOMP/FTorch_interface
+fxtag = v0.0.5
+fxrequired = ToplevelOptional
+# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
+fxDONOTUSEurl = https://github.com/ESCOMP/FTorch_interface

bld/CLMBuildNamelist.pm

@@ -4043,6 +4043,7 @@ sub setup_logic_dry_deposition {
   if ($opts->{'drydep'} ) {
     add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'drydep_list');
     add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'dep_data_file');
+    &remove_newlines( $nl, $definition, "drydep_list" );
   }
   if ( &value_is_true( $nl_flags->{'use_fates'}) ) {
      foreach my $var ( @list ) {
@@ -4174,6 +4175,7 @@ sub setup_logic_megan {
 	$log->fatal_error("MEGAN can NOT be on when FATES is also on.\n" .
 			  "   Use the '-no-megan' option when '-bgc fates' is activated");
     }
+    &remove_newlines( $nl, $definition, "megan_specifier" );
   }
 }
 
@@ -5743,7 +5745,21 @@ sub quote_string {
       $str = "\'$str\'";
    }
    return $str;
- }
+}
+
+#-------------------------------------------------------------------------------
+
+sub remove_newlines {
+    # Check for and remove line returns in the string, so that it will validate later
+    my ($nl, $definition, $var) = @_;
+
+    my $value =  $nl->get_value($var);
+    if ( $value =~ /\n/) {
+       $value =~ s/\n//g;
+       my $group = $definition->get_group_name($var);
+       $nl->set_variable_value($group, $var, $value);
+    }
+}
 
 #-------------------------------------------------------------------------------
 

bld/namelist_files/namelist_defaults_drydep.xml

@@ -15,15 +15,51 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- Defaults for drydep_inparm namelist namelists to test standalone CTSM with  -->
 
-<drydep_list>'O3','NO2','HNO3','NO','HO2NO2','CH3OOH','CH2O','CO','H2O2','CH3COOOH','PAN','MPAN','C2H5OOH','ONIT','POOH','C3H7OOH','ROOH','CH3COCHO','CH3COCH3','Pb','ONITR','MACROOH','XOOH','ISOPOOH','CH3OH','C2H5OH','CH3CHO','GLYALD','HYAC','HYDRALD','ALKOOH','MEKOOH','TOLOOH','TERPOOH','CH3COOH','CB1','CB2','OC1','OC2','SOA','SO2','SO4','NH3','NH4NO3'
+<drydep_list>'BIGALK','C2H4','C2H5OH','C2H5OOH','C2H6','C3H6',
+      'C3H7OOH','C3H8','CH2O','CH3CHO','CH3COCH3','CH3COCHO','CH3COOH',
+      'CH3COOOH','CH3OH','CH3OOH','CO','DMS','EOOH','GLYALD','GLYOXAL',
+      'H2O2','H2SO4','HNO3','HO2NO2','HYAC','HYDRALD','ISOP','ISOPOOH',
+      'MACR','MACROOH','MPAN','MVK','N2O5','NH3','NH4','NO','NO2',
+      'NOA','O3','O3S','ONITR','PAN','POOH','ROOH','SO2','SOAG','XOOH'
 </drydep_list>
 
 <!-- effective Henry's coef data for wet and dry deposition -->
-<dep_data_file>atm/cam/chem/trop_mozart/dvel/dep_data_c201019.nc</dep_data_file>
+<dep_data_file>atm/cam/chem/trop_mozart/dvel/dep_data_c20221208.nc</dep_data_file>
 
-<!-- Defaults for megan_emis_nl namelists to test standalone CTSM with -->
+<!-- 
+     Defaults for megan_emis_nl namelists to test standalone CTSM with 
+     This is from the CAM FHISTC_MTt4s compset namelist from 04/25/2025 EBK
+-->
 
-<megan_specifier>'ISOP = isoprene', 'C10H16 = pinene_a + carene_3 + thujene_a', 'CH3OH = methanol', 'C2H5OH = ethanol', 'CH2O = formaldehyde', 'CH3CHO = acetaldehyde', 'CH3COOH = acetic_acid', 'CH3COCH3 = acetone'</megan_specifier>
+<megan_specifier>
+'ISOP = isoprene',
+'TERP = carene_3 + pinene_a + thujene_a + bornene + terpineol_4 + terpineol_a + terpinyl_ACT_a +',
+        ' myrtenal + sabinene + pinene_b + camphene + fenchene_a + limonene + phellandrene_a + terpinene_a +',
+        ' terpinene_g + terpinolene + phellandrene_b + linalool + ionone_b + geranyl_acetone + neryl_acetone +',
+        ' jasmone + verbenene + ipsenol + myrcene + ocimene_t_b + ocimene_al + ocimene_c_b + 2met_nonatriene +',
+        ' farnescene_a + caryophyllene_b + acoradiene + aromadendrene + bergamotene_a + bergamotene_b +',
+        ' bisabolene_a + bisabolene_b + bourbonene_b + cadinene_d + cadinene_g + cedrene_a + copaene_a +',
+        ' cubebene_a + cubebene_b + elemene_b + farnescene_b + germacrene_B + germacrene_D + gurjunene_b +',
+        ' humulene_a + humulene_g + isolongifolene + longifolene + longipinene + muurolene_a + muurolene_g +',
+        ' selinene_b + selinene_d + nerolidol_c + nerolidol_t',
+'BIGALK = tricyclene + camphor + fenchone + thujone_a + thujone_b + cineole_1_8 + borneol + bornyl_ACT +',
+        ' cedrol + decanal + heptanal + heptane + hexane + nonanal + octanal + octanol + oxopentanal + pentane +',
+        ' hexanal + hexanol_1 + pentanal + heptanone',
+'CH3OH = methanol', 'CH3COCH3 = acetone', 'CH3CHO = acetaldehyde', 'C2H5OH = ethanol',
+'CH2O = formaldehyde', 'CH3COOH = acetic_acid', 'CO = carbon_monoxide',
+'C2H6 = ethane', 'C2H4 = ethene', 'C3H8 = propane', 'C3H6 = propene',
+'SOAE = 0.5954*isoprene + 5.1004*(carene_3 + pinene_a + thujene_a + bornene +',
+        ' terpineol_4 + terpineol_a + terpinyl_ACT_a + myrtenal + sabinene + pinene_b + camphene +',
+        ' fenchene_a + limonene + phellandrene_a + terpinene_a + terpinene_g + terpinolene +',
+        ' phellandrene_b + linalool + ionone_b + geranyl_acetone + neryl_acetone + jasmone +',
+        ' verbenene + ipsenol + myrcene + ocimene_t_b + ocimene_al + ocimene_c_b + 2met_nonatriene) + ',
+        ' 12.3942*(farnescene_a + caryophyllene_b + acoradiene + aromadendrene + bergamotene_a +',
+        ' bergamotene_b + bisabolene_a + bisabolene_b + bourbonene_b + cadinene_d + cadinene_g +',
+        ' cedrene_a + copaene_a + cubebene_a + cubebene_b + elemene_b + farnescene_b +',
+        ' germacrene_B + germacrene_D + gurjunene_b + humulene_a + humulene_g + isolongifolene +',
+        ' longifolene + longipinene + muurolene_a + muurolene_g + selinene_b + selinene_d +',
+        ' nerolidol_c + nerolidol_t)'
+</megan_specifier>
 
 <megan_factors_file phys="clm6_0" >atm/cam/chem/trop_mozart/emis/megan21_emis_factors_78pft_c20161108.nc</megan_factors_file>
 <megan_factors_file phys="clm5_0" >atm/cam/chem/trop_mozart/emis/megan21_emis_factors_78pft_c20161108.nc</megan_factors_file>

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 = 3264;
+my $ntests = 3276;
 
 if ( defined($opts{'compare'}) ) {
-   $ntests += 1980;
+   $ntests += 1987;
 }
 plan( tests=>$ntests );
 

cime_config/testdefs/ExpectedTestFails.xml

@@ -36,6 +36,27 @@
     </phase>
   </test>
 
+  <test name="SMS_Ld5.f09_t232.ISSP245Clm60BgcCropCrujra.derecho_intel.clm-ciso_dec2050Start">
+    <phase name="SETUP">
+      <status>FAIL</status>
+      <issue>#2686</issue>
+    </phase>
+  </test>
+
+  <test name="SMS_Ld5.f09_t232.ISSP370Clm60BgcCropCrujra.derecho_intel.clm-ciso_dec2050Start">
+    <phase name="SETUP">
+      <status>FAIL</status>
+      <issue>#2686</issue>
+    </phase>
+  </test>
+
+  <test name="SMS_Ld5.f09_t232.ISSP585Clm60BgcCropCrujra.derecho_intel.clm-ciso_dec2050Start">
+    <phase name="SETUP">
+      <status>FAIL</status>
+      <issue>#2686</issue>
+    </phase>
+  </test>
+
   <test name="SMS_Ld5.f09_g17.IHistClm50Sp.derecho_intel.clm-nofire">
     <phase name="SHAREDLIB_BUILD">
       <status>FAIL</status>
@@ -114,9 +135,9 @@
   </test>
 
   <test name="SMS_D.f10_f10_mg37.I2000Clm60BgcCrop.derecho_nvhpc.clm-crop">
-    <phase name="RUN">
+    <phase name="SETUP">
       <status>FAIL</status>
-      <issue>#1733</issue>
+      <issue>#1733 and #3180</issue>
     </phase>
   </test>
 
@@ -138,6 +159,13 @@
     </phase>
   </test>
 
+  <test name="FUNITCTSM_P1x1.f10_f10_mg37.I2000Clm50Sp.izumi_intel"
+    <phase name="MODEL_BUILD">
+      <status>FAIL</status>
+      <issue>#3182</issue>
+    </phase>
+  </test>
+
   <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Bgc.izumi_nag.clm-default--clm-NEON-HARV--clm-matrixcnOn">
     <phase name="RUN">
       <status>FAIL</status>