Merge pull request #99 from mvertens/feature/megan_cherrypick_ctsm_mv…

…ertens add MEGAN compatibility with FATES
NorESMhub · Nov 22, 2024 · ca5cddb · ca5cddb
2 parents 95a4d93 + c89f3cc
commit ca5cddb
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Showing 16 changed files with 981 additions and 703 deletions.
diff --git a/.gitmodules b/.gitmodules
@@ -27,8 +27,8 @@
 #
 [submodule "fates"]
 path = src/fates
-url = https://github.com/NGEET/fates
-fxtag = sci.1.78.3_api.36.1.0
+url = https://github.com/NorESMhub/fates
+fxtag = sci.1.78.3_api.36.1.0_noresm_v1
 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
@@ -978,7 +978,7 @@ sub setup_cmdl_bgc {
   # Set soil matrix (which is needed later for spinup)
   $var = "use_soil_matrixcn";
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var,
-              , 'use_fates'=>$nl_flags->{'use_fates'}, 
+              , 'use_fates'=>$nl_flags->{'use_fates'},
               , 'soil_decomp_method'=>$nl_flags->{'soil_decomp_method'},
               , 'phys'=>$nl_flags->{'phys'}, clm_accelerated_spinup=>$nl_flags->{'clm_accelerated_spinup'} );
   if ( &value_is_true($nl->get_value($var)) ) {
@@ -1214,7 +1214,7 @@ sub setup_cmdl_spinup {
   if ( &value_is_true($nl_flags->{'use_cn'}) ) {
     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition,
                 $defaults, $nl, "spinup_state", clm_accelerated_spinup=>$nl_flags->{'clm_accelerated_spinup'},
-                use_cn=>$nl_flags->{'use_cn'}, use_fates=>$nl_flags->{'use_fates'}, 
+                use_cn=>$nl_flags->{'use_cn'}, use_fates=>$nl_flags->{'use_fates'},
                 use_soil_matrixcn=>$nl_flags->{"use_soil_matrixcn"} );
     if ( $nl->get_value("spinup_state") ne 0 ) {
        $nl_flags->{'bgc_spinup'} = "on";
@@ -4148,12 +4148,8 @@ sub setup_logic_megan {
     add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'megan_factors_file');
   }
   if ( defined($nl->get_value('megan_specifier')) ||
-         defined($nl->get_value('megan_factors_file')) ) {
+       defined($nl->get_value('megan_factors_file')) ) {
     check_megan_spec( $opts, $nl, $definition );
-    if ( &value_is_true( $nl_flags->{'use_fates'} ) ) {
-      $log->warning("MEGAN can NOT be on when FATES is also on.\n" .
-                    "   Use the '-no-megan' option when '-bgc fates' is activated");
-    }
   }
 }
 
@@ -4966,7 +4962,7 @@ sub setup_logic_exice {
   # excess ice streams, must be set before initial conditions
   #
   my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_excess_ice', 'phys'=>$physv->as_string()); 
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_excess_ice', 'phys'=>$physv->as_string());
   my $use_exice = $nl->get_value( 'use_excess_ice' );
   # Put use_exice into nl_flags so can be referenced later
   if ( value_is_true($use_exice) ) {

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -553,8 +553,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- FATES default parameter file                                       -->
 <!-- ================================================================== -->
 
-<fates_paramfile>lnd/clm2/paramdata/fates_params_api.36.1.0_14pft_c241003.nc</fates_paramfile>
-
+<!-- <fates_paramfile>lnd/clm2/paramdata/fates_params_api.36.1.0_14pft_c241003.nc</fates_paramfile> -->
+<fates_paramfile>lnd/clm2/paramdata/fates_params_api.36.1.0_14pft_c241003_megan.nc</fates_paramfile>
 
 <!-- ================================================================== -->
 <!-- Default surface roughness parameterization                         -->
@@ -1908,10 +1908,10 @@ lnd/clm2/surfdata_esmf/NEON/ctsm5.3.0/surfdata_1x1_NEON_TOOL_hist_2000_78pfts_c2
 <!-- As of 2024/02/02 the Grids Support spreadsheet includes no 16-pft landuse files. -->
 <flanduse_timeseries hgrid="4x5"           sim_year_range="1850-2000"
  >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_4x5_SSP2-4.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
-<flanduse_timeseries hgrid="10x15"         sim_year_range="1850-2000" 
+<flanduse_timeseries hgrid="10x15"         sim_year_range="1850-2000"
  >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_10x15_SSP2-4.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
 
-<flanduse_timeseries hgrid="360x720cru"    sim_year_range="1850-2000" 
+<flanduse_timeseries hgrid="360x720cru"    sim_year_range="1850-2000"
 >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_360x720cru_SSP2-4.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
 
 <flanduse_timeseries hgrid="1x1_brazil"    sim_year_range="1850-2000"

diff --git a/cime_config/buildnml b/cime_config/buildnml
@@ -23,7 +23,7 @@ _config_cache_template = """
 <?xml version="1.0"?>
 <config_definition>
 <commandline></commandline>
-<entry id="phys" value="{clm_phys}" list="" valid_values="clm4_5,clm5_0,clm5_1,clm6_0">Specifies CTSM physics</entry>
+<entry id="phys" value="{clm_phys}" list="" valid_values="clm4_5,clm5_0,clm6_0">Specifies CTSM physics</entry>
 </config_definition>
 """
 
@@ -105,11 +105,6 @@ def buildnml(case, caseroot, compname):
         "clm5_0_QIAN": "clm5_0_GSWP3v1",
         "clm5_0_NLDAS2": "clm5_0_GSWP3v1",
         "clm5_0_ERA5": "clm5_0_GSWP3v1",
-        "clm5_1_1PT": "clm5_1_GSWP3v1",
-        "clm5_1_QIAN": "clm5_1_GSWP3v1",
-        "clm5_1_NLDAS2": "clm5_1_GSWP3v1",
-        "clm5_1_ERA5": "clm5_1_GSWP3v1",
-        "clm5_1_CRUv7": "clm5_1_GSWP3v1",
         "clm6_0_1PT": "clm6_0_GSWP3v1",
         "clm6_0_QIAN": "clm6_0_GSWP3v1",
         "clm6_0_NLDAS2": "clm6_0_GSWP3v1",
@@ -136,13 +131,9 @@ def buildnml(case, caseroot, compname):
     #  to the CAM version)
     tuning_based_on = {
         "clm6_0_GSWP3v1": "clm5_0_GSWP3v1",
-        "clm5_1_GSWP3v1": "clm5_0_GSWP3v1",
         "clm6_0_cam6.0": "clm5_0_cam6.0",
         "clm6_0_cam5.0": "clm5_0_cam6.0",
         "clm6_0_cam4.0": "clm5_0_cam6.0",
-        "clm5_1_cam6.0": "clm5_0_cam6.0",
-        "clm5_1_cam5.0": "clm5_0_cam6.0",
-        "clm5_1_cam4.0": "clm5_0_cam6.0",
         "clm5_0_cam5.0": "clm5_0_cam6.0",
         "clm5_0_cam4.0": "clm5_0_cam6.0",
         "clm4_5_cam6.0": "clm5_0_cam6.0",

diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml
@@ -15,7 +15,6 @@
   <description modifier_mode="1">
     <desc lnd="CLM45[%SP][%SP-VIC][%BGC][%BGC-CROP][%FATES][%BGCDV][%BGCDV-CROP]"                  >clm4.5:</desc>
     <desc lnd="CLM50[%SP][%SP-VIC][%SP-NOANTHRO][%BGC-NOANTHRO][%BGC][%BGC-CROP][%FATES][%BGCDV][%BGCDV-CROP][%BGC-CROP-CMIP6DECK][%BGC-CROP-CMIP6WACCMDECK][%NWP-SP][%NWP-BGC-CROP]">clm5.0:</desc>
-    <desc lnd="CLM51[%SP][%SP-NOANTHRO][%BGC-NOANTHRO][%BGC][%BGC-CROP][%FATES][%FATES-SP][%FATES-NOCOMP][%NWP-SP][%NWP-BGC-CROP]">clm5.1:</desc>
     <desc lnd="CLM60[%SP][%SP-NOANTHRO][%BGC-NOANTHRO][%BGC][%BGC-CROP][%FATES][%FATES-SP][%FATES-NOCOMP][%BGC-CROP-CMIP6DECK][%BGC-CROP-CMIP6WACCMDECK][%NWP-SP][%NWP-BGC-CROP]">clm6.0:</desc>
     <desc option="SP"              >Satellite phenology:</desc>
 
@@ -79,7 +78,7 @@
     </desc>
     <default_value>UNSET</default_value>
     <!-- 10 forcing options for each CLM physics option: CRUv7, GSWP3, cam7.0, cam6.0, cam5.0, cam4.0, QIAN, 1PT, NLDAS2, ERA5 -->
-    <valid_values>clm5_0_cam6.0,clm5_0_cam7.0,clm5_0_cam5.0,clm5_0_cam4.0,clm5_0_GSWP3v1,clm5_0_CRUv7,clm5_0_QIAN,clm5_0_1PT,clm5_0_NLDAS2,clm5_0_ERA5,clm4_5_CRUv7,clm4_5_GSWP3v1,clm4_5_QIAN,clm4_5_cam6.0,clm4_5_cam7.0,clm4_5_cam5.0,clm4_5_cam4.0,clm4_5_1PT,clm4_5_NLDAS2,clm4_5_ERA5,clm5_1_CRUv7,clm5_1_GSWP3v1,clm5_1_cam6.0,clm5_1_QIAN,clm5_1_1PT,clm5_1_NLDAS2,clm5_1_ERA5,clm6_0_CRUv7,clm6_0_GSWP3v1,clm6_0_cam6.0,clm6_0_cam7.0,clm6_0_cam5.0,clm6_0_cam4.0,clm6_0_QIAN,clm6_0_1PT,clm6_0_NLDAS2,clm6_0_ERA5</valid_values>
+    <valid_values>clm5_0_cam6.0,clm5_0_cam7.0,clm5_0_cam5.0,clm5_0_cam4.0,clm5_0_GSWP3v1,clm5_0_CRUv7,clm5_0_QIAN,clm5_0_1PT,clm5_0_NLDAS2,clm5_0_ERA5,clm4_5_CRUv7,clm4_5_GSWP3v1,clm4_5_QIAN,clm4_5_cam6.0,clm4_5_cam7.0,clm4_5_cam5.0,clm4_5_cam4.0,clm4_5_1PT,clm4_5_NLDAS2,clm4_5_ERA5,clm6_0_CRUv7,clm6_0_GSWP3v1,clm6_0_cam6.0,clm6_0_cam7.0,clm6_0_cam5.0,clm6_0_cam4.0,clm6_0_QIAN,clm6_0_1PT,clm6_0_NLDAS2,clm6_0_ERA5</valid_values>
     <values match="last">
       <!-- Options for atm forcing are: CRU, CRUv7, GSWP3, cam6.0 (also used for DATM%CPLHIST), cam5.0, cam4.0, QIAN, WISOQIA, 1PT, NLDAS2, and ERA5) -->
       <!-- All the clm4_5 physics options -->
@@ -114,14 +113,6 @@
       <value compset="DATM%1PT_CLM50"    >clm5_0_1PT</value>
       <value compset="DATM%NLDAS2_CLM50" >clm5_0_NLDAS2</value>
       <value compset="DATM%ERA5_CLM50"   >clm5_0_ERA5</value>
-      <!-- All the clm5_1 physics options -->
-      <value compset="DATM%GSWP3v1_CLM51">clm5_1_GSWP3v1</value>
-      <value compset="CAM[^_]*_CLM51"    >INVALID_USE_CLM60_NOT_CLM51</value>
-      <value compset="CAM40[^_]*_CLM51"  >clm5_1_cam4.0</value>
-      <value compset="CAM50[^_]*_CLM51"  >clm5_1_cam5.0</value>
-      <value compset="CAM60[^_]*_CLM51"  >clm5_1_cam6.0</value>
-      <value compset="CAM70[^_]*_CLM51"  >INVALID_USE_CLM60_NOT_CLM51_FOR_CAM70</value>
-      <value compset="DATM%CPLHIST_CLM51">INVALID_USE_CLM60_NOT_CLM51_FOR_CPLHIST</value>
       <!-- All the clm6_0 physics options -->
       <value compset="DATM%CRUv7_CLM60"  >clm6_0_CRUv7</value>
       <value compset="DATM%CRU_CLM60"    >clm6_0_CRUv7</value>
@@ -148,7 +139,7 @@
 
   <entry id="CLM_PHYSICS_VERSION" >
     <type>char</type>
-    <valid_values>clm4_5,clm5_0,clm5_1,clm6_0</valid_values>
+    <valid_values>clm4_5,clm5_0,clm6_0</valid_values>
     <!-- By setting the default_value to UNSET (or some other non-empty
          string that doesn't appear in the list of valid_values), the
          scripts will ensure that one of the below values is picked up
@@ -157,7 +148,6 @@
     <values>
       <value compset="_CLM45" >clm4_5</value>
       <value compset="_CLM50" >clm5_0</value>
-      <value compset="_CLM51" >clm5_1</value>
       <value compset="_CLM60" >clm6_0</value>
     </values>
     <group>run_component_ctsm</group>
@@ -172,11 +162,9 @@
     <type>logical</type>
     <valid_values>TRUE,FALSE</valid_values>
     <default_value>TRUE</default_value>
-    <!-- Until CAM sets dust settings in drv_flds_in this should only be TRUE
     <values>
-      <value compset="CAM"  >FALSE</value>
+      <value compset="CAM">FALSE</value>
     </values>
-    -->
     <group>run_component_cpl</group>
     <file>env_run.xml</file>
     <desc>If CTSM will set the dust settings in drv_flds_in (TRUE), or if ATM (i.e. CAM) will - DO NOT EDIT (set by compset name)</desc>
@@ -256,9 +244,9 @@
       <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>
-      <value compset="_CLM[^_]*FATES-NOCOMP">-bgc fates -no-megan</value>
+      <value compset="_CLM[^_]*FATES"       >-bgc fates -nomeg</value>
+      <value compset="_CLM[^_]*FATES-SP"    >-bgc fates</value>
+      <value compset="_CLM[^_]*FATES-NOCOMP">-bgc fates</value>
 
       <!-- Options specific for CLM4.5 -->
       <value compset="_CLM45%[^_]*BGCDV"	 >-bgc bgc -dynamic_vegetation</value>
@@ -367,12 +355,10 @@
     <valid_values></valid_values>
     <default_value></default_value>
     <values match="last">
-      <value                  compset="_CLM60%[^_]*FATES-SP[%_]"      >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/fates_sp</value>
-      <value                  compset="_CLM51%[^_]*FATES-SP[%_]"      >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/fates_sp</value>
-      <value                  compset="_CLM50%[^_]*CMIP6DECK[%_]"     >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_deck</value>
-      <value                  compset="_CLM51%[^_]*FATES-SP[%_]"      >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/fates_sp</value>
-      <value                  compset="_CLM51%[^_]*FATES-NOCOMP[%_]"  >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/fates_nocomp</value>
-      <value grid="l%1.9x2.5" compset="_CLM50%[^_]*CMIP6DECK[%_]"     >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_nociso_deck</value>
+      <value                  compset="_CLM60%[^_]*FATES-SP[%_]"    >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/fates_sp</value>
+      <value                  compset="_CLM60%[^_]*FATES-NOCOMP[%_]">$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/fates_nocomp</value>
+      <value                  compset="_CLM50%[^_]*CMIP6DECK[%_]"   >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_deck</value>
+      <value grid="l%1.9x2.5" compset="_CLM50%[^_]*CMIP6DECK[%_]"   >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_nociso_deck</value>
       <value                  compset="_CLM50%[^_]*CMIP6WACCMDECK[%_]">$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_waccm_deck</value>
       <value grid="l%1.9x2.5" compset="_CLM50%[^_]*CMIP6WACCMDECK[%_]">$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_waccm_nociso_deck</value>
       <value                  compset="_CLM60%[^_]*CMIP6DECK[%_]"     >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_deck</value>

diff --git a/cime_config/config_compsets.xml b/cime_config/config_compsets.xml
@@ -14,7 +14,7 @@
     Where for the CAM specific compsets below the following is supported
     TIME = Time period (e.g. 2000, HIST, SSP585...)
     ATM  = [CAM40, CAM50, CAM60]
-    LND  = [CLM45, CLM50, CLM51, CLM60, SLND]
+    LND  = [CLM45, CLM50, CLM60, SLND]
     ICE  = [CICE, DICE, SICE]
     OCN  = [DOCN, ,AQUAP, SOCN]
     ROF  = [RTM, SROF]
@@ -344,12 +344,6 @@
     <science_support grid="f19_g17"/>
   </compset>
 
-  <!-- Needed for testing until CAM removes used of CLM51 in compsets-->
-  <compset>
-    <alias>IHistClm51Sp</alias>
-    <lname>HIST_DATM%GSWP3v1_CLM51%SP_SICE_SOCN_MOSART_SGLC_SWAV</lname>
-  </compset>
-
   <compset>
     <alias>IHistClm60SpRs</alias>
     <lname>HIST_DATM%GSWP3v1_CLM60%SP_SICE_SOCN_SROF_SGLC_SWAV</lname>
@@ -407,7 +401,7 @@
     <lname>HIST_DATM%QIA_CLM60%BGC_SICE_SOCN_SROF_SGLC_SWAV</lname>
   </compset>
 
-<!-- 
+<!--
      future scenario compsets
 -->
   <compset>
@@ -610,7 +604,7 @@
     <lname>2000_DATM%CRUv7_CLM45%SP-VIC_SICE_SOCN_RTM_SGLC_SWAV</lname>
   </compset>
 
-<!-- 
+<!--
      IG compsets with active Glacier model
 -->
 
@@ -660,12 +654,6 @@
     <science_support grid="f19_g17"/>
     <science_support grid="ne30pg3_t232"/>
   </compset>
-  <!-- Needed for testing until removed by CESM -->
-  <compset>
-    <alias>I1850Clm51BgcCropG</alias>
-    <lname>1850_DATM%GSWP3v1_CLM51%BGC-CROP_SICE_SOCN_MOSART_CISM2%GRIS-EVOLVE_SWAV</lname>
-  </compset>
-
 
   <!-- Primarily for testing: same as I1850Clm50SpGag but with SROF -->
   <compset>