Resolving merge conflicts.

Author: mwaxmonsky

.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
 
@@ -80,7 +94,7 @@
 	url = https://github.com/MPAS-Dev/MPAS-Model.git
         fxrequired = AlwaysRequired
         fxsparse = ../.mpas_sparse_checkout
-        fxtag = b8c33daa
+        fxtag = v8.2.1
 	fxDONOTUSEurl = https://github.com/MPAS-Dev/MPAS-Model.git
 
 [submodule "cosp2"]
@@ -130,28 +144,28 @@ fxDONOTUSEurl = https://github.com/ESCOMP/mizuRoute
 [submodule "ccs_config"]
 path = ccs_config
 url = https://github.com/ESMCI/ccs_config_cesm.git
-fxtag = ccs_config_cesm1.0.0
+fxtag = ccs_config_cesm1.0.7
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git
 
 [submodule "cime"]
 path = cime
 url = https://github.com/ESMCI/cime
-fxtag = cime6.1.0
+fxtag = cime6.1.29
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESMCI/cime
 
 [submodule "cmeps"]
 path = components/cmeps
 url = https://github.com/ESCOMP/CMEPS.git
-fxtag = cmeps1.0.2
+fxtag = cmeps1.0.16
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git
 
 [submodule "cdeps"]
 path = components/cdeps
 url = https://github.com/ESCOMP/CDEPS.git
-fxtag = cdeps1.0.48
+fxtag = cdeps1.0.53
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/CDEPS.git
 
@@ -165,7 +179,7 @@ fxDONOTUSEurl = https://github.com/ESCOMP/CESM_share
 [submodule "parallelio"]
 path = libraries/parallelio
 url = https://github.com/NCAR/ParallelIO
-fxtag = pio2_6_2
+fxtag = pio2_6_3
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/NCAR/ParallelIO
 
@@ -179,13 +193,13 @@ fxDONOTUSEurl = https://github.com/ESCOMP/CESM_CICE
 [submodule "clm"]
 path = components/clm
 url = https://github.com/ESCOMP/CTSM
-fxtag = ctsm5.2.027
+fxtag = ctsm5.3.002
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/CTSM
 
 [submodule "fms"]
 path = libraries/FMS
 url = https://github.com/ESCOMP/FMS_interface
-fxtag = fi_240516
+fxtag = fi_240828
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESCOMP/FMS_interface

bld/build-namelist

@@ -608,8 +608,9 @@ if ( ($chem ne 'none') or ( $prog_species ) ){
            ($aer_wetdep_list =~ /ncl/i || $aer_wetdep_list =~ /sslt/i)) {
             $prescribe_aerosols = $FALSE;
         }
-
-        add_default($nl, 'aer_wetdep_list', 'val'=>$aer_wetdep_list );
+        if ($chem !~ /_mam/) {
+            add_default($nl, 'aer_wetdep_list', 'val'=>$aer_wetdep_list );
+        }
 
         if (!($chem =~ /_mam/)) {
             if (!defined $nl->get_value('aer_sol_facti')) {
@@ -2037,10 +2038,13 @@ if (($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) {

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
@@ -2191,9 +2191,9 @@ sub write_filepath
 
     if ($simple_phys) {
       print $fh "$camsrcdir/src/physics/simple\n";
-      print $fh "$camsrcdir/src/atmos_phys/kessler\n";
-      print $fh "$camsrcdir/src/atmos_phys/held_suarez\n";
-      print $fh "$camsrcdir/src/atmos_phys/tj2016\n";
+      print $fh "$camsrcdir/src/atmos_phys/schemes/kessler\n";
+      print $fh "$camsrcdir/src/atmos_phys/schemes/held_suarez\n";
+      print $fh "$camsrcdir/src/atmos_phys/schemes/tj2016\n";
     }
 
     # Weak scaling fix. This has to come before physics/cam and before dycores
@@ -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";
@@ -2334,8 +2336,10 @@ sub write_filepath
     print $fh "$camsrcdir/src/atmos_phys/to_be_ccppized/physics/cam\n";
 
     #Add the CCPP'ized subdirectories
-    print $fh "$camsrcdir/src/atmos_phys/zhang_mcfarlane\n";
-    print $fh "$camsrcdir/src/atmos_phys/dry_adiabatic_adjust\n";
+    print $fh "$camsrcdir/src/atmos_phys/schemes/tropopause_find\n";
+    print $fh "$camsrcdir/src/atmos_phys/schemes/zhang_mcfarlane\n";
+    print $fh "$camsrcdir/src/atmos_phys/schemes/dry_adiabatic_adjust\n";
+    print $fh "$camsrcdir/src/atmos_phys/schemes/utilities\n";
 
     # Dynamics package and test utilities
     print $fh "$camsrcdir/src/dynamics/$dyn\n";
@@ -2361,8 +2365,6 @@ sub write_filepath
     print $fh "$camsrcdir/src/control\n";
     print $fh "$camsrcdir/src/utils\n";
     print $fh "$camsrcdir/src/utils/cam_ccpp\n";
-    print $fh "$camsrcdir/src/atmos_phys/utilities\n";
-
 
     $fh->close;
 }

bld/namelist_files/geoschem_master_gas_drydep_list.xml

@@ -30,6 +30,7 @@
   ETHP
   ETNO3
   ETP
+  FURA
   GLYC
   GLYX
   H2O2

bld/namelist_files/geoschem_master_gas_wetdep_list.xml

@@ -20,6 +20,7 @@
   ETHN
   ETHP
   ETP
+  FURA
   GLYC
   GLYX
   H2O2

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>

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 -->
 
@@ -6238,19 +6249,19 @@ Default: set by build-namelist.
 </entry>
 
 <entry id="sol_factb_interstitial" type="real" category="cam_chem"
-       group="aerosol_nl" valid_values="" >
+       group="aero_wetdep_nl" valid_values="" >
 Tuning for below cloud scavenging of interstitial modal aerosols.
 Default: set by build-namelist.
 </entry>
 
 <entry id="sol_factic_interstitial" type="real" category="cam_chem"
-       group="aerosol_nl" valid_values="" >
+       group="aero_wetdep_nl" valid_values="" >
 Tuning for in-cloud scavenging of interstitial modal aerosols.
 Default: set by build-namelist.
 </entry>
 
 <entry id="sol_facti_cloud_borne" type="real" category="cam_chem"
-       group="aerosol_nl" valid_values="" >
+       group="aero_wetdep_nl" valid_values="" >
 Tuning for in-cloud scavenging of cloud-borne modal aerosols.
 Default: set by build-namelist.
 </entry>

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>

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>

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>