Merge pull request ESCOMP#1093 from geoschem/feature/geoschem_14.4

cam6_4_038: GEOS-Chem 14.4 and dependencies
nusbaume · Oct 1, 2024 · 1abe4a8 · 1abe4a8
2 parents cf436f7 + b68495c
commit 1abe4a8
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diff --git a/.gitmodules b/.gitmodules
@@ -51,13 +51,27 @@
 	path = src/chemistry/geoschem/geoschem_src
 	url = https://github.com/geoschem/geos-chem.git
         fxrequired = AlwaysRequired
-        fxtag = 14.1.2
+        fxtag = 14.4.3
         fxDONOTUSEurl = https://github.com/geoschem/geos-chem.git
 
+[submodule "cloud_j"]
+	path = src/chemistry/cloud_j
+	url = https://github.com/geoschem/cloud-j.git
+        fxrequired = AlwaysRequired
+        fxtag = 7.7.3
+        fxDONOTUSEurl = https://github.com/geoschem/cloud-j.git
+
+[submodule "hetp"]
+	path = src/chemistry/hetp
+	url = https://github.com/geoschem/heterogeneous-vectorized-or-parallel.git
+        fxrequired = AlwaysRequired
+        fxtag = geoschem_hetp_1.0
+        fxDONOTUSEurl = https://github.com/geoschem/heterogeneous-vectorized-or-parallel.git
+
 [submodule "hemco"]
 	path = src/hemco
 	url = https://github.com/ESCOMP/HEMCO_CESM.git
-        fxtag = hemco-cesm1_2_1_hemco3_6_3_cesm_rme01
+        fxtag = hemco-cesm2_0_hemco3_9_0
         fxrequired = AlwaysRequired
 	fxDONOTUSEurl = https://github.com/ESCOMP/HEMCO_CESM.git
 

diff --git a/bld/build-namelist b/bld/build-namelist
@@ -2038,10 +2038,13 @@ if (($chem =~ /trop_mozart/ or $chem =~ /trop_strat/ or $chem =~ /waccm_tsmlt/)
 
 if ($chem =~ /geoschem/) {
 
-    my $val;
+    # Input directories
+    add_default($nl, 'geoschem_chem_inputs');
+    add_default($nl, 'geoschem_aeropt_inputs');
+    add_default($nl, 'geoschem_photol_inputs');
 
     # Species with fixed lower boundary
-    $val = "'CCL4','CH4','N2O','CO2','CFC11','CFC12','CH3BR','CH3CCL3','CH3CL'"
+    my $val = "'CCL4','CH4','N2O','CO2','CFC11','CFC12','CH3BR','CH3CCL3','CH3CL'"
            .",'HCFC22','CFC114','CFC115','HCFC141B','HCFC142B','CH2BR2','CHBR3','H2402'";
 
     if ($chem_has_ocs) {

diff --git a/bld/configure b/bld/configure
@@ -1450,9 +1450,9 @@ if ($chem_pkg =~ '_mam3') {
 
 # Customize GEOS-Chem advected species and chemistry CPP definitions
 if ($chem_pkg =~ 'geoschem') {
-    $chem_cppdefs .= ' -DEXTERNAL_GRID -DEXTERNAL_FORCING ';
+    $chem_cppdefs .= ' -DEXTERNAL_GRID -DEXTERNAL_FORCING -DMODEL_CESM -DMODEL_GEOSCHEM';
     if ($chem_pkg =~ '_mam4') {
-        $chem_nadv = 267; # includes GC advected species (233), CO2 (1), and MAM aerosols (33)
+        $chem_nadv = 269; # includes all GEOS-Chem advected species, CO2, and MAM aerosols
     }
 }
 # CARMA sectional microphysics
@@ -2219,8 +2219,10 @@ sub write_filepath
         print $fh "$chem_src_dir\n";
     }
 
-    # GEOS-Chem must be prior to Mozart
+    # GEOS-Chem and dependencies; GEOS-Chem must be prior to Mozart
     if ($chem_pkg =~ 'geoschem') {
+	print $fh "$camsrcdir/src/chemistry/cloud_j/src/Core\n";
+	print $fh "$camsrcdir/src/chemistry/hetp/src/Core\n";
 	print $fh "$chem_src_dir/geoschem_src/GeosCore\n";
 	print $fh "$chem_src_dir/geoschem_src/GeosUtil\n";
 	print $fh "$chem_src_dir/geoschem_src/Headers\n";

diff --git a/bld/namelist_files/geoschem_master_gas_drydep_list.xml b/bld/namelist_files/geoschem_master_gas_drydep_list.xml
@@ -30,6 +30,7 @@
   ETHP
   ETNO3
   ETP
+  FURA
   GLYC
   GLYX
   H2O2

diff --git a/bld/namelist_files/geoschem_master_gas_wetdep_list.xml b/bld/namelist_files/geoschem_master_gas_wetdep_list.xml
@@ -20,6 +20,7 @@
   ETHN
   ETHP
   ETP
+  FURA
   GLYC
   GLYX
   H2O2

diff --git a/bld/namelist_files/namelist_defaults_cam.xml b/bld/namelist_files/namelist_defaults_cam.xml
@@ -2026,7 +2026,7 @@
 
 <!-- effective Henry's coef data for wet and dry deposition -->
 <dep_data_file>atm/cam/chem/trop_mozart/dvel/dep_data_c20221208.nc</dep_data_file>
-<dep_data_file chem="geoschem_mam4">atm/cam/chem/geoschem/dvel/dep_data_file_geoschem_c230417.nc</dep_data_file>
+<dep_data_file chem="geoschem_mam4">atm/cam/chem/geoschem/dvel/dep_data_file_geoschem_v14.3_2023Jan08.nc</dep_data_file>
 
 <!-- photolysis inputs -->
 <xs_coef_file>atm/waccm/phot/effxstex.txt</xs_coef_file>
@@ -3700,4 +3700,9 @@
 <hemco_grid_xdim hgrid="1.9x2.5">144</hemco_grid_xdim>
 <hemco_grid_ydim hgrid="1.9x2.5">91</hemco_grid_ydim>
 
+<!-- GEOS-Chem chemistry -->
+<geoschem_chem_inputs chem="geoschem_mam4">atm/cam/geoschem/emis/ExtData/CHEM_INPUTS</geoschem_chem_inputs>
+<geoschem_aeropt_inputs chem="geoschem_mam4">atm/cam/geoschem/emis/ExtData/CHEM_INPUTS/FAST_JX/v2024-05/</geoschem_aeropt_inputs>
+<geoschem_photol_inputs chem="geoschem_mam4">atm/cam/geoschem/emis/ExtData/CHEM_INPUTS/CLOUD_J/v2023-05/</geoschem_photol_inputs>
+
 </namelist_defaults>
diff --git a/bld/namelist_files/namelist_definition.xml b/bld/namelist_files/namelist_definition.xml
@@ -5241,12 +5241,23 @@ Default: set by build-namelist for climo cases, otherwise -1 to use model clock.
 
 <!-- GEOS-Chem model -->
 
-<entry id="geoschem_cheminputs" type="char*256" input_pathname="abs" category="geoschem"
+<entry id="geoschem_chem_inputs" type="char*256" input_pathname="abs" category="geoschem"
        group="geoschem_nl" valid_values="" >
-Full pathname to GEOS-Chem chemistry inputs directory
+Full pathname of the GEOS-Chem chemistry inputs directory.
 Default: set by build-namelist.
 </entry>
 
+<entry id="geoschem_aeropt_inputs" type="char*256" input_pathname="abs" category="geoschem"
+       group="geoschem_nl" valid_values="" >
+Full pathname of the aerosols optical property inputs directory used in GEOS-Chem outside of Cloud-J.
+Default: set by build-namelist.
+</entry>
+
+<entry id="geoschem_photol_inputs" type="char*256" input_pathname="abs" category="geoschem"
+       group="geoschem_nl" valid_values="" >
+Full pathname of the Cloud-J photolysis inputs directory used in GEOS-Chem.
+Default: set by build-namelist.
+</entry>
 
 <!-- Reference Pressures -->
 

diff --git a/bld/namelist_files/use_cases/2000_geoschem.xml b/bld/namelist_files/use_cases/2000_geoschem.xml
@@ -6,8 +6,6 @@
 
 <!-- Settings for using GEOS-Chem specifically -->
 
-<geoschem_cheminputs>atm/cam/geoschem/ExtData/CHEM_INPUTS/</geoschem_cheminputs>
-
 <ncdata dyn="fv"  hgrid="0.9x1.25">atm/cam/geoschem/initial_conditions/f.e20.FC2010.f09_f09.144.GC_vbsext.001.cam.i.0007-01-01-00000.nc</ncdata>
 
 <ncdata dyn="fv"  hgrid="1.9x2.5">atm/cam/geoschem/initial_conditions/f.e20.FC2010.f19_f19.144.GC_vbsext.001.cam.i.0007-01-01-00000.nc</ncdata>

diff --git a/bld/namelist_files/use_cases/2010_geoschem.xml b/bld/namelist_files/use_cases/2010_geoschem.xml
@@ -4,8 +4,6 @@
 
 <!-- Settings in this file were adapted from 2010_trop_strat_vbs_cam6.xml -->
 
-<geoschem_cheminputs>atm/cam/geoschem/ExtData/CHEM_INPUTS/</geoschem_cheminputs>
-
 <ncdata dyn="fv"  hgrid="0.9x1.25">atm/cam/geoschem/initial_conditions/f.e20.FC2010.f09_f09.144.GC_vbsext.001.cam.i.0007-01-01-00000.nc</ncdata>
 
 <ncdata dyn="fv"  hgrid="1.9x2.5">atm/cam/geoschem/initial_conditions/f.e20.FC2010.f19_f19.144.GC_vbsext.001.cam.i.0007-01-01-00000.nc</ncdata>

diff --git a/bld/namelist_files/use_cases/hist_geoschem.xml b/bld/namelist_files/use_cases/hist_geoschem.xml
@@ -6,8 +6,6 @@
 
 <!-- Settings for using GEOS-Chem -->
 
-<geoschem_cheminputs>atm/cam/geoschem/ExtData/CHEM_INPUTS/</geoschem_cheminputs>
-
 <ncdata dyn="fv"  hgrid="0.9x1.25">atm/cam/geoschem/initial_conditions/f.e20.FC2010.f09_f09.144.GC_vbsext.001.cam.i.0007-01-01-00000.nc</ncdata>
 
 <ncdata dyn="fv"  hgrid="1.9x2.5">atm/cam/geoschem/initial_conditions/f.e20.FC2010.f19_f19.144.GC_vbsext.001.cam.i.0007-01-01-00000.nc</ncdata>
@@ -29,7 +27,7 @@
 <gw_qbo_hdepth_scaling>0.25D0</gw_qbo_hdepth_scaling>
 
 <flbc_type>SERIAL</flbc_type>
-<flbc_file>atm/waccm/lb/LBC_1750-2014_CMIP6_0p5degLat_c170126.nc</flbc_file>
+<flbc_file>atm/waccm/lb/LBC_17500116-25001216_CMIP6_SSP585_0p5degLat_c20200824.nc</flbc_file>
 
 <prescribed_strataero_type>SERIAL</prescribed_strataero_type>
 

diff --git a/bld/namelist_files/use_cases/hist_geoschem_nudged.xml b/bld/namelist_files/use_cases/hist_geoschem_nudged.xml
@@ -6,8 +6,6 @@
 
 <!-- Settings for using GEOS-Chem -->
 
-<geoschem_cheminputs>atm/cam/geoschem/ExtData/CHEM_INPUTS/</geoschem_cheminputs>
-
 <ncdata dyn="fv"  hgrid="0.9x1.25">atm/cam/geoschem/initial_conditions/f.e20.FC2010.f09_f09.144.GC_vbsext.001.cam.i.0007-01-01-00000.nc</ncdata>
 
 <ncdata dyn="fv"  hgrid="1.9x2.5">atm/cam/geoschem/initial_conditions//f.e20.FC2010.f19_f19.144.GC_vbsext.001.cam.i.0007-01-01-00000.nc</ncdata>
@@ -29,7 +27,7 @@
 <gw_qbo_hdepth_scaling>0.25D0</gw_qbo_hdepth_scaling>
 
 <flbc_type>SERIAL</flbc_type>
-<flbc_file>atm/waccm/lb/LBC_1750-2014_CMIP6_0p5degLat_c170126.nc</flbc_file>
+<flbc_file>atm/waccm/lb/LBC_17500116-25001216_CMIP6_SSP585_0p5degLat_c20200824.nc</flbc_file>
 
 <prescribed_strataero_type>SERIAL</prescribed_strataero_type>
 

diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml
@@ -10,8 +10,8 @@
    -->
     <desc atm="CAM70[%LT][%MT][%CCTS1][%CCTS4]"                                                                                                 >CAM cam7 physics:</desc>
     <desc atm="CAM60[%1PCT][%4xCO2][%CCTS1][%CCTS2][%CFIRE][%CVBSX][%NUDG][%PORT][%RCO2][%SCAM][%SDYN][%WCCM][%WCMD][%WCSC][%WCTS][%WXIE][%WXIED][%HEMCO][%GEOSCHEM][%SCAMARM95][%SCAMARM97][%SCAMATEX][%SCAMBOMEX][%SCAMCGILSS11][%SCAMCGILSS12][%SCAMCGILSS6][%SCAMDYCOMSRF01][%SCAMDYCOMSRF02][%SCAMGATE3][%SCAMMPACE][%SCAMRICO][%SCAMSPARTICUS][%SCAMTOGA2][%SCAMTWP06][%SCAMCAMFRC]"               >CAM cam6 physics:</desc>
-    <desc atm="CAM50[%CCTS1][%CLB][%PORT][%RCO2][%MAM7][%SCAM][%SDYN][%WCSC][%WCTS][%GEOSCHEM][%SCAMARM95][%SCAMARM97][%SCAMATEX][%SCAMBOMEX][%SCAMCGILSS11][%SCAMCGILSS12][%SCAMCGILSS6][%SCAMDYCOMSRF01][%SCAMDYCOMSRF02][%SCAMGATE3][%SCAMMPACE][%SCAMRICO][%SCAMSPARTICUS][%SCAMTOGA2][%SCAMTWP06][%SCAMCAMFRC]"                                                                                     >CAM cam5 physics:</desc>
-    <desc atm="CAM40[%PORT][%RCO2][%SCAM][%SDYN][%TMOZ][%WX][%WXIE][%WXIED][%WCCM][%WCMD][%GEOSCHEM][%SCAMARM95][%SCAMARM97][%SCAMATEX][%SCAMBOMEX][%SCAMCGILSS11][%SCAMCGILSS12][%SCAMCGILSS6][%SCAMDYCOMSRF01][%SCAMDYCOMSRF02][%SCAMGATE3][%SCAMMPACE][%SCAMRICO][%SCAMSPARTICUS][%SCAMTOGA2][%SCAMTWP06][%SCAMCAMFRC]"                                                                               >CAM cam4 physics:</desc>
+    <desc atm="CAM50[%CCTS1][%CLB][%PORT][%RCO2][%MAM7][%SCAM][%SDYN][%WCSC][%WCTS][%SCAMARM95][%SCAMARM97][%SCAMATEX][%SCAMBOMEX][%SCAMCGILSS11][%SCAMCGILSS12][%SCAMCGILSS6][%SCAMDYCOMSRF01][%SCAMDYCOMSRF02][%SCAMGATE3][%SCAMMPACE][%SCAMRICO][%SCAMSPARTICUS][%SCAMTOGA2][%SCAMTWP06][%SCAMCAMFRC]"                                                                                     >CAM cam5 physics:</desc>
+    <desc atm="CAM40[%PORT][%RCO2][%SCAM][%SDYN][%TMOZ][%WX][%WXIE][%WXIED][%WCCM][%WCMD][%SCAMARM95][%SCAMARM97][%SCAMATEX][%SCAMBOMEX][%SCAMCGILSS11][%SCAMCGILSS12][%SCAMCGILSS6][%SCAMDYCOMSRF01][%SCAMDYCOMSRF02][%SCAMGATE3][%SCAMMPACE][%SCAMRICO][%SCAMSPARTICUS][%SCAMTOGA2][%SCAMTWP06][%SCAMCAMFRC]"                                                                               >CAM cam4 physics:</desc>
     <desc atm="CAM[%ADIAB][%DABIP04][%TJ16][%GRAYRAD][%HS94][%KESSLER][%RCO2][%SPCAMS][%SPCAMCLBS][%SPCAMM][%SPCAMCLBM]"                                     >CAM simplified and non-versioned physics :</desc>
 
   <!--

diff --git a/cime_config/config_compsets.xml b/cime_config/config_compsets.xml
@@ -413,6 +413,10 @@
     <alias>FC2000climo_HCO</alias>
     <lname>2000_CAM60%CCTS1%HEMCO_CLM50%SP_CICE%PRES_DOCN%DOM_MOSART_SGLC_SWAV</lname>
   </compset>
+  <compset>
+    <alias>FC2000climo_GC</alias>
+    <lname>2000_CAM60%GEOSCHEM%HEMCO_CLM50%SP_CICE%PRES_DOCN%DOM_MOSART_SGLC_SWAV</lname>
+  </compset>
 
   <compset>
     <alias>FC2010climo</alias>
@@ -422,11 +426,20 @@
     <alias>FC2010climo_HCO</alias>
     <lname>2010_CAM60%CCTS1%HEMCO_CLM50%SP_CICE%PRES_DOCN%DOM_MOSART_SGLC_SWAV</lname>
   </compset>
+  <compset>
+    <alias>FC2010climo_GC</alias>
+    <lname>2010_CAM60%GEOSCHEM%HEMCO_CLM50%SP_CICE%PRES_DOCN%DOM_MOSART_SGLC_SWAV</lname>
+  </compset>
 
   <compset>
     <alias>FCHIST</alias>
     <lname>HIST_CAM60%CCTS1_CLM50%SP_CICE%PRES_DOCN%DOM_MOSART_SGLC_SWAV</lname>
   </compset>
+    <compset>
+    <alias>FCHIST_GC</alias>
+    <lname>HIST_CAM60%GEOSCHEM%HEMCO_CLM50%SP_CICE%PRES_DOCN%DOM_MOSART_CISM2%NOEVOLVE_SWAV</lname>
+  </compset>
+
   <compset>
     <alias>FCLTHIST</alias>
     <lname>HIST_CAM70%LT%CCTS1_CLM60%SP_CICE%PRES_DOCN%DOM_MOSART_SGLC_SWAV</lname>
@@ -456,6 +469,11 @@
     <alias>FCnudged</alias>
     <lname>HIST_CAM60%CCTS1%NUDG_CLM50%SP_CICE%PRES_DOCN%DOM_MOSART_SGLC_SWAV</lname>
   </compset>
+    <compset>
+    <alias>FCnudged_GC</alias>
+    <lname>HIST_CAM60%GEOSCHEM%NUDG%HEMCO_CLM50%SP_CICE%PRES_DOCN%DOM_MOSART_SGLC_SWAV</lname>
+  </compset>
+
   <compset>
     <alias>FCts2nudged</alias>
     <lname>HIST_CAM60%CCTS2%NUDG_CLM50%SP_CICE%PRES_DOCN%DOM_MOSART_SGLC_SWAV</lname>
@@ -644,26 +662,6 @@
     <lname>HIST_CAM60%WXIED%SDYN_CLM50%SP_CICE%PRES_DOCN%DOM_MOSART_SGLC_SWAV</lname>
   </compset>
 
-  <compset>
-    <alias>FC2000climo_GC</alias>
-    <lname>2000_CAM60%GEOSCHEM%HEMCO_CLM50%SP_CICE%PRES_DOCN%DOM_MOSART_CISM2%NOEVOLVE_SWAV</lname>
-  </compset>
-
-  <compset>
-    <alias>FC2010climo_GC</alias>
-    <lname>2010_CAM60%GEOSCHEM%HEMCO_CLM50%SP_CICE%PRES_DOCN%DOM_MOSART_CISM2%NOEVOLVE_SWAV</lname>
-  </compset>
-
-  <compset>
-    <alias>FCHIST_GC</alias>
-    <lname>HIST_CAM60%GEOSCHEM%HEMCO_CLM50%SP_CICE%PRES_DOCN%DOM_MOSART_CISM2%NOEVOLVE_SWAV</lname>
-  </compset>
-
-  <compset>
-    <alias>FCnudged_GC</alias>
-    <lname>HIST_CAM60%GEOSCHEM%HEMCO%NUDG_CLM50%SP_CICE%PRES_DOCN%DOM_MOSART_SGLC_SWAV</lname>
-  </compset>
-
   <!-- ENTRIES -->
 
   <entries>

diff --git a/cime_config/testdefs/testlist_cam.xml b/cime_config/testdefs/testlist_cam.xml
@@ -17,14 +17,6 @@
       <option name="wallclock">00:10:00</option>
     </options>
   </test>
-  <test compset="FC2000climo_GC" grid="f09_f09_mg17" name="ERP_Ln9" testmods="cam/outfrq9s">
-    <machines>
-      <machine name="derecho" compiler="intel" category="geoschem"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:10:00</option>
-    </options>
-  </test>
   <test compset="F2000climo" grid="f09_f09_mg17" name="ERP_D_Ln9" testmods="cam/outfrq9s">
     <machines>
       <machine name="izumi"    compiler="nag" category="aux_cam_one"/>
@@ -42,14 +34,6 @@
       <option name="wallclock">00:10:00</option>
     </options>
   </test>
-  <test compset="FC2010climo_GC" grid="f09_f09_mg17" name="ERP_Ln9" testmods="cam/outfrq9s">
-    <machines>
-      <machine name="derecho" compiler="intel" category="geoschem"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:10:00</option>
-    </options>
-  </test>
   <test compset="F2000climo" grid="f10_f10_mg37" name="SMS_Lm13" testmods="cam/outfrq1m" supported="false">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_cam"/>
@@ -1890,6 +1874,14 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
+  <test compset="FC2010climo_GC" grid="f09_f09_mg17" name="ERP_Ln9" testmods="cam/outfrq9s">
+    <machines>
+      <machine name="derecho" compiler="intel" category="geoschem"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+    </options>
+  </test>
   <test compset="FC2000climo" grid="f09_f09_mg17" name="ERP_Ln9" testmods="cam/outfrq9s_wetdep">
     <machines>
       <machine name="derecho" compiler="intel" category="camchem"/>
@@ -1900,6 +1892,11 @@
       <machine name="derecho" compiler="intel" category="camchem"/>
     </machines>
   </test>
+  <test compset="FC2000climo_GC" grid="f09_f09_mg17" name="ERP_Ln9" testmods="cam/outfrq9s">
+    <machines>
+      <machine name="derecho" compiler="intel" category="geoschem"/>
+    </machines>
+  </test>
   <test compset="FCHIST" grid="ne30_ne30_mg17" name="SMS_Ld1" testmods="cam/outfrq1d">
     <machines>
       <machine name="derecho" compiler="intel" category="prebeta"/>