cam6_3_147: GEOS-Chem chemistry and four new compsets that use it

.gitignore

@@ -9,6 +9,7 @@ src/physics/carma/base
 src/physics/clubb
 src/physics/cosp2/src
 src/physics/silhs
+src/chemistry/geoschem/geoschem_src
 src/physics/pumas
 src/physics/pumas-frozen
 src/dynamics/fv3/atmos_cubed_sphere

Externals_CAM.cfg

@@ -71,6 +71,13 @@ sparse = ../.mpas_sparse_checkout
 hash = b8c33daa
 required = True
 
+[geoschem]
+local_path = src/chemistry/geoschem/geoschem_src
+protocol = git
+repo_url = https://github.com/geoschem/geos-chem.git
+tag = 14.1.2
+required = True
+
 [hemco]
 local_path = src/hemco
 tag = hemco-cesm1_2_1_hemco3_6_3_cesm

bld/build-namelist

@@ -540,7 +540,7 @@ my $rad_prog_bcarb = (($prog_species =~ "BC"   or $aero_chem) and !($chem_rad_pa
 my $rad_prog_sulf  = (($prog_species =~ "SO4"  or $aero_chem) and !($chem_rad_passive));
 my $rad_prog_dust  = (($prog_species =~ "DST"  or $aero_chem) and !($chem_rad_passive));
 my $rad_prog_sslt  = (($prog_species =~ "SSLT" or $aero_chem) and !($chem_rad_passive));
-my $rad_prog_ozone = (($chem =~ "mozart" or $chem =~ "waccm_ma" or $chem =~ "tsmlt" or $chem =~ "trop_strat") and !($chem_rad_passive));
+my $rad_prog_ozone = (($chem =~ "mozart" or $chem =~ "waccm_ma" or $chem =~ "tsmlt" or $chem =~ "trop_strat" or $chem =~ /geoschem/) and !($chem_rad_passive));
 
 # Check for eruptive volcano emissions.  These will be radiatively active by default, but
 # only if using BAM and the camrt radiation package
@@ -576,12 +576,13 @@ if ( ($chem ne 'none') or ( $prog_species ) ){
 
     my ( $gas_wetdep_list, $aer_wetdep_list, $aer_sol_facti, $aer_sol_factb, $aer_scav_coef,
          $aer_drydep_list, $gas_drydep_list ) =
-           set_dep_lists( $cfgdir, $chem_proc_src, $chem_src_dir, $nl, $print );
+           set_dep_lists( $chem, $cfgdir, $chem_proc_src, $chem_src_dir, $nl, $print );
 
     if (length($gas_wetdep_list)>2){
       add_default($nl, 'gas_wetdep_method' );
       add_default($nl, 'gas_wetdep_list', 'val'=>$gas_wetdep_list );
     }
+
     if (length($aer_wetdep_list)>2){
         # determine if prescribed aerosols are not needed ...
         if ($aer_wetdep_list =~ /so4/i &&
@@ -862,7 +863,7 @@ my $radval = "'A:Q:H2O'";
 if (($chem =~ /waccm_ma/ or $chem =~ /waccm_tsmlt/) and !$chem_rad_passive) {
     $radval .= ",'A:O2:O2','A:CO2:CO2'";
 }
-elsif ($chem =~ /trop_strat/ and !$chem_rad_passive) {
+elsif (($chem =~ /trop_strat/ or $chem =~ /geoschem/) and !$chem_rad_passive) {
     $radval .= ",'N:O2:O2','A:CO2:CO2'";
 }
 elsif (($co2_cycle and !$co2_cycle_rad_passive) or ($chem =~ /ghg_mam4/)) {
@@ -897,6 +898,8 @@ if ((($chem =~ /ghg_mam4/) or ($chem =~ /waccm_ma/) or ($chem =~ /waccm_sc_mam/)
     $radval .= ",'A:N2O:N2O','A:CH4:CH4','A:CFC11:CFC11','A:CFC12:CFC12'";
 } elsif ($prog_ghg1 and !$prog_ghg2  and !$chem_rad_passive ) {
     $radval .= ",'A:N2O:N2O','A:CH4:CH4','N:CFC11:CFC11','N:CFC12:CFC12'";
+} elsif ($chem =~ /geoschem/) {
+    $radval .= ",'A:N2O:N2O','A:CH4:CH4','A:CFC11:CFC11','A:CFC12:CFC12'";
 } else {
     $radval .= ",'N:N2O:N2O','N:CH4:CH4','N:CFC11:CFC11','N:CFC12:CFC12'";
 }
@@ -2018,6 +2021,34 @@ if (($chem =~ /trop_mozart/ or $chem =~ /trop_strat/ or $chem =~ /waccm_tsmlt/)
     }
 }
 
+if ($chem =~ /geoschem/) {
+
+    my $val;
+
+    # Species with fixed lower boundary
+    $val = "'CCL4','CH4','N2O','CO2','CFC11','CFC12','CH3BR','CH3CCL3','CH3CL'"
+           .",'HCFC22','CFC114','CFC115','HCFC141B','HCFC142B','CH2BR2','CHBR3','H2402'";
+
+    if ($chem_has_ocs) {
+        $val .= ",'OCS'";
+    }
+    if (chem_has_species($cfg, 'SF6')) {
+        $val .= ",'SF6'";
+    }
+    add_default($nl, 'flbc_list', 'val'=>$val);
+    unless (defined $nl->get_value('flbc_type')) {
+        add_default($nl, 'flbc_type',  'val'=>'CYCLICAL');
+        add_default($nl, 'flbc_cycle_yr',  'val'=>'2000');
+    }
+
+    my @files;
+    # Datasets
+    @files = ( 'soil_erod_file', 'flbc_file' );
+    foreach my $file (@files) {
+        add_default($nl, $file);
+    }
+}
+
 if ($chem =~ /trop_mozart/ or $chem =~ /trop_strat/ or $chem =~ /waccm_tsmlt/) {
 
     my $val;
@@ -2364,10 +2395,12 @@ if (($chem =~ /_mam4/ or $chem =~ /_mam5/) and ($phys =~ /cam6/ or $phys =~ /cam
             }
         }
     }
-    add_default($nl, 'srf_emis_specifier', 'val'=>$val);
-    unless (defined $nl->get_value('srf_emis_type')) {
-        add_default($nl, 'srf_emis_type',      'val'=>'CYCLICAL');
-        add_default($nl, 'srf_emis_cycle_yr',  'val'=>2000);
+    if ($chem !~ /geoschem/) {
+        add_default($nl, 'srf_emis_specifier', 'val'=>$val);
+        unless (defined $nl->get_value('srf_emis_type')) {
+            add_default($nl, 'srf_emis_type',      'val'=>'CYCLICAL');
+            add_default($nl, 'srf_emis_cycle_yr',  'val'=>2000);
+        }
     }
 
     # Vertical emission datasets:
@@ -2433,10 +2466,12 @@ if (($chem =~ /_mam4/ or $chem =~ /_mam5/) and ($phys =~ /cam6/ or $phys =~ /cam
             $first = 0;
         }
     }
-    add_default($nl, 'ext_frc_specifier', 'val'=>$val);
-    unless (defined $nl->get_value('ext_frc_type')) {
-        add_default($nl, 'ext_frc_type',      'val'=>"'CYCLICAL'");
-        add_default($nl, 'ext_frc_cycle_yr',  'val'=>2000);
+    if ($chem !~ /geoschem/) {
+        add_default($nl, 'ext_frc_specifier', 'val'=>$val);
+        unless (defined $nl->get_value('ext_frc_type')) {
+            add_default($nl, 'ext_frc_type',      'val'=>"'CYCLICAL'");
+            add_default($nl, 'ext_frc_cycle_yr',  'val'=>2000);
+        }
     }
 
     # MEGAN emissions
@@ -2482,6 +2517,30 @@ if (($chem =~ /_mam4/ or $chem =~ /_mam5/) and ($phys =~ /cam6/ or $phys =~ /cam
         add_default($nl, 'megan_factors_file');
         add_default($nl, 'megan_mapped_emisfctrs', 'val'=>'.false.');
     }
+    if ($chem =~ /geoschem/) {
+        my $val = "'ISOP = isoprene',"
+                . "'MOH = methanol',"
+                . "'EOH = ethanol',"
+                . "'CH2O = formaldehyde',"
+                . "'ALD2 = acetaldehyde',"
+                . "'ACTA = acetic_acid',"
+                . "'ACET = acetone',"
+                . "'HCOOH = formic_acid',"
+                . "'HCN = hydrogen_cyanide',"
+                . "'CO = carbon_monoxide',"
+                . "'C2H6 = ethane',"
+                . "'C2H4 = ethene',"
+                . "'C3H8 = propane',"
+                . "'ALK4 = pentane + hexane + heptane + tricyclene',"
+                . "'PRPE = propene + butene',"
+                . "'TOLU = toluene',"
+                . "'LIMO = limonene',"
+                . "'MTPA = pinene_a + pinene_b + sabinene + carene_3',"
+                . "'MTPO = terpinene_g + terpinene_a + terpinolene + myrcene + ocimene_al + ocimene_t_b + ocimene_c_b + thujene_a + 2met_styrene + cymene_p + cymene_o + bornene + fenchene_a + camphene + phellandrene_a + phellandrene_b'";
+        add_default($nl, 'megan_specifier', 'val'=>$val);
+        add_default($nl, 'megan_factors_file');
+        add_default($nl, 'megan_mapped_emisfctrs', 'val'=>'.false.');
+    }
     if ($chem =~ /trop_strat_mam4_vbs/ or $chem =~ /trop_strat_mam5_vbs/) {
         my $val = "'ISOP = isoprene',"
                 . "'MTERP = carene_3 + pinene_a + thujene_a + bornene + terpineol_4 + terpineol_a + terpinyl_ACT_a "
@@ -2897,6 +2956,29 @@ if ($nl->get_value('use_hemco') =~ m/$TRUE/io) {
     # ignored at runtime when HEMCO is used.
     $nl->delete_variable('chem_inparm', 'ext_frc_specifier');
     $nl->delete_variable('chem_inparm', 'srf_emis_specifier');
+
+    if ($chem =~ /geoschem/) {
+
+        # For now, HEMCO config and diagnostic configuration files are always used from
+        # the case directory. Exit if user has specified other paths in the user namelist
+        # because it will not work.
+        if ($nl->get_value('hemco_config_file') ne "'" . $inputdata_rootdir . "/HEMCO_Config.rc'") {
+            die "CAM Namelist ERROR: When running with GEOS-Chem chemistry, hemco_config_file\n".
+                "must not be manually set in the namelist. Instead, modify (or symlink from) the HEMCO_Config.rc\n".
+                "in the case directory, which will be copied to the run directory when submitting.\n".
+                "Then remove the hemco_config_file option from the user namelist.\n";
+        }
+
+        if ($nl->get_value('hemco_diagn_file') ne "'" . $inputdata_rootdir . "/HEMCO_Diagn.rc'") {
+            die "CAM Namelist ERROR: When running with GEOS-Chem chemistry, hemco_diagn_file\n".
+                "must not be manually set in the namelist. Instead, modify (or symlink from) the HEMCO_Diagn.rc\n".
+                "in the case directory, which will be copied to the run directory when submitting.\n".
+                "Then remove the hemco_diagn_file option from the user namelist.\n";
+        }
+
+        $nl->set_variable_value('hemco_nl', 'hemco_config_file', "'HEMCO_Config.rc'");
+        $nl->set_variable_value('hemco_nl', 'hemco_diagn_file', "'HEMCO_Diagn.rc'");
+    }
 }
 
 # Physics options
@@ -3025,7 +3107,7 @@ if (!$simple_phys) {
 }
 
 # tropopause level used in gas-phase / aerosol processes
-if (($chem ne 'none') and ($chem ne 'terminator')) {
+if (($chem ne 'none') and ($chem ne 'terminator') and !($chem =~ /geoschem/)) {
     add_default($nl, 'chem_use_chemtrop');
 }
 
@@ -3562,7 +3644,7 @@ if ( length($nl->get_value('soil_erod_file'))>0 ) {
         add_default($nl, 'dust_emis_fact', 'tms'=>'1');
     }
     else {
-        if ($chem =~ /trop_strat/ or $chem =~ /waccm_ma/ or $chem =~ /waccm_tsmlt/ or $chem =~ /trop_mozart/) {
+        if ($chem =~ /trop_strat/ or $chem =~ /geoschem/ or $chem =~ /waccm_ma/ or $chem =~ /waccm_tsmlt/ or $chem =~ /trop_mozart/) {
             add_default($nl, 'dust_emis_fact', 'ver'=>'chem');
         }
         else {

bld/config_files/definition.xml

@@ -103,8 +103,8 @@ meteor_smoke (Meteor Smoke), mixed_sulfate (Meteor Smoke and Sulfate), pmc (Pola
 sulfate (Sulfate Aerosols), tholin (early earth haze), test_detrain (Detrainment), test_growth (Particle Growth), test_passive (Passive Dust),
 test_radiative (Radiatively Active Dust), test_swelling (Sea Salt), test_tracers (Asian Monsoon), test_tracers2 (Guam).
 </entry>
-<entry id="chem" valid_values="none,ghg_mam4,terminator,trop_mam3,trop_mam4,trop_mam7,trop_mozart,trop_strat_mam4_ts2,trop_strat_mam4_vbs,trop_strat_mam4_vbsext,trop_strat_mam5_ts2,trop_strat_mam5_vbs,trop_strat_mam5_vbsext,waccm_ma,waccm_mad,waccm_ma_sulfur,waccm_sc,waccm_sc_mam4,waccm_mad_mam4,waccm_ma_mam4,waccm_tsmlt_mam4,waccm_tsmlt_mam4_vbsext,waccm_mad_mam5,waccm_ma_mam5,waccm_tsmlt_mam5,waccm_tsmlt_mam5_vbsext" value="">
-  Chemistry package: none,ghg_mam4,terminator,trop_mam3,trop_mam4,trop_mam7,trop_mozart,trop_strat_mam4_ts2,trop_strat_mam4_vbs,trop_strat_mam4_vbsext,trop_strat_mam5_ts2,trop_strat_mam5_vbs,trop_strat_mam5_vbsext,waccm_ma,waccm_mad,waccm_ma_sulfur,waccm_sc,waccm_sc_mam4,waccm_mad_mam4,waccm_ma_mam4,waccm_tsmlt_mam4,waccm_tsmlt_mam4_vbsext,waccm_mad_mam5,waccm_ma_mam5,waccm_tsmlt_mam5,waccm_tsmlt_mam5_vbsext
+<entry id="chem" valid_values="none,ghg_mam4,terminator,trop_mam3,trop_mam4,trop_mam7,trop_mozart,trop_strat_mam4_ts2,trop_strat_mam4_vbs,trop_strat_mam4_vbsext,trop_strat_mam5_ts2,trop_strat_mam5_vbs,trop_strat_mam5_vbsext,waccm_ma,waccm_mad,waccm_ma_sulfur,waccm_sc,waccm_sc_mam4,waccm_mad_mam4,waccm_ma_mam4,waccm_tsmlt_mam4,waccm_tsmlt_mam4_vbsext,waccm_mad_mam5,waccm_ma_mam5,waccm_tsmlt_mam5,waccm_tsmlt_mam5_vbsext,geoschem_mam4" value="">
+  Chemistry package: none,ghg_mam4,terminator,trop_mam3,trop_mam4,trop_mam7,trop_mozart,trop_strat_mam4_ts2,trop_strat_mam4_vbs,trop_strat_mam4_vbsext,trop_strat_mam5_ts2,trop_strat_mam5_vbs,trop_strat_mam5_vbsext,waccm_ma,waccm_mad,waccm_ma_sulfur,waccm_sc,waccm_sc_mam4,waccm_mad_mam4,waccm_ma_mam4,waccm_tsmlt_mam4,waccm_tsmlt_mam4_vbsext,waccm_mad_mam5,waccm_ma_mam5,waccm_tsmlt_mam5,waccm_tsmlt_mam5_vbsext,geoschem_mam4
 </entry>
 <entry id="prog_species" valid_values="DST,SSLT,SO4,GHG,OC,BC,CARBON16" value="" list="1">
 Prognostic mozart species packages: list of any subset of the following: DST,SSLT,SO4,GHG,OC,BC,CARBON16

bld/configure

@@ -67,7 +67,7 @@ OPTIONS
                          trop_strat_mam4_vbs | trop_strat_mam4_vbsext | trop_strat_mam5_ts2 | trop_strat_mam5_vbs |
                          trop_strat_mam5_vbsext | waccm_ma | waccm_mad | waccm_ma_sulfur | waccm_sc | waccm_sc_mam4 |
                          waccm_mad_mam4 | waccm_ma_mam4 | waccm_tsmlt_mam4 | waccm_tsmlt_mam4_vbsext | waccm_mad_mam5 |
-                         waccm_ma_mam5 | waccm_tsmlt_mam5 | waccm_tsmlt_mam5_vbsext ].
+                         waccm_ma_mam5 | waccm_tsmlt_mam5 | waccm_tsmlt_mam5_vbsext | geoschem_mam4 ].
                         Default: trop_mam4 for cam6 and trop_mam3 for cam5.
      -[no]clubb_sgs     Switch on [off] CLUBB_SGS.  Default: on for cam6, otherwise off.
      -clubb_opts <list> Comma separated list of CLUBB options to turn on/off.  By default they are all off.
@@ -592,7 +592,6 @@ if (defined $opts{'chem'}) {
 
     # If the user has specified a simple physics package...
     if ($simple_phys) {
-        # the only valid chemistry options are 'none' and 'terminator'
         if (($chem_pkg ne 'none') and ($chem_pkg ne 'terminator')) {
             die "configure ERROR: -phys=$phys_pkg  -chem=$chem_pkg\n".
                 "                 -chem can only be set to 'none' or 'terminator'.\n";
@@ -1360,7 +1359,11 @@ my $chem_cppdefs = '';
 my $chem_src_dir = '';
 
 if (!$prog_species) {
-  $chem_src_dir = "$cam_dir/src/chemistry/pp_$chem_pkg";
+  if ($chem_pkg =~ 'geoschem') {
+    $chem_src_dir = "$cam_dir/src/chemistry/geoschem";
+  } else {
+    $chem_src_dir = "$cam_dir/src/chemistry/pp_$chem_pkg";
+  }
   $cfg_ref->set('chem_src_dir', $chem_src_dir);
 }
 
@@ -1387,10 +1390,10 @@ if ($customize) {
     }
     if ($print>=2) { print "Chem preprocessor compiler: $chemproc_fc $eol"; }
     ($chem_nadv) = chem_preprocess($cfg_ref,$print,$chemproc_fc);
-} elsif ($chem_pkg ne 'none') {
+} elsif ($chem_pkg ne 'none' and $chem_pkg !~ 'geoschem') {
    # copy over chem docs
-    copy("$chem_src_dir/chem_mech.doc",$cam_bld) or die "copy failed $! \n";
-    copy("$chem_src_dir/chem_mech.in" ,$cam_bld) or die "copy failed $! \n";
+    copy("$chem_src_dir/chem_mech.doc",$cam_bld) or die "copy of chem_mec.doc failed $! \n";
+    copy("$chem_src_dir/chem_mech.in" ,$cam_bld) or die "copy of chem_mech.in failed $! \n";
     ($chem_nadv) = chem_number_adv($chem_src_dir);
 }
 
@@ -1404,6 +1407,13 @@ if ($chem_pkg =~ '_mam3') {
     $chem_cppdefs = ' -DMODAL_AERO -DMODAL_AERO_7MODE ';
 }
 
+# Customize GEOS-Chem advected species and chemistry CPP definitions
+if ($chem_pkg =~ 'geoschem') {
+    $chem_cppdefs .= ' -DEXTERNAL_GRID -DEXTERNAL_FORCING ';
+    if ($chem_pkg =~ '_mam4') {
+        $chem_nadv = 267; # includes GC advected species (233), CO2 (1), and MAM aerosols (33)
+    }
+}
 # CARMA sectional microphysics
 #
 # New CARMA models need to define the number of advected constituents.
@@ -1565,8 +1575,6 @@ else {
 $nadv = $cfg_ref->get('nadv');
 if ($print>=2) { print "Total advected constituents: $nadv$eol"; }
 
-#-----------------------------------------------------------------------------------------------
-
 #-----------------------------------------------------------------------------------------------
 # Makefile configuration #######################################################################
 #-----------------------------------------------------------------------------------------------
@@ -1675,7 +1683,7 @@ elsif ($fc =~ /nvfor/)  { $fc_type = 'nvhpc'; }
 
 # User override for Fortran compiler type
 if (defined $opts{'fc_type'}) { $fc_type = $opts{'fc_type'}; }
-if ($fc_type == "oneapi") {$fc_type = 'intel'; }
+if ($fc_type eq "oneapi") {$fc_type = 'intel'; }
 if ($fc_type) {
     $cfg_ref->set('fc_type', $fc_type);
     if ($print>=2) { print "Fortran compiler type: $fc_type$eol"; }
@@ -1941,6 +1949,12 @@ if ($unicon) { $cfg_cppdefs .= ' -DUSE_UNICON'; }
 #   HEMCO_CESM - indicates CESM model environment. Deprecated, will be removed soon.
 $cfg_cppdefs .= ' -DMODEL_ -DMODEL_CESM -DHEMCO_CESM -DUSE_REAL8 ';
 
+# Compiler CPP definitions for GEOS-Chem
+if ($chem_pkg =~ 'geoschem') {
+    if    ($fc_type eq 'intel') { $cfg_cppdefs .= ' -DLINUX_IFORT'; }
+    elsif ($fc_type eq 'gnu')   { $cfg_cppdefs .= ' -DLINUX_GFORTRAN'; }
+}
+
 #-----------------------------------------------------------------------------------------------
 # CPP defines to put on Makefile
 
@@ -2161,10 +2175,21 @@ sub write_filepath
     if ($chem_src_dir) {
         print $fh "$chem_src_dir\n";
     }
+
+    # GEOS-Chem must be prior to Mozart
+    if ($chem_pkg =~ 'geoschem') {	
+	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";
+	print $fh "$chem_src_dir/geoschem_src/ISORROPIA\n";
+	print $fh "$chem_src_dir/geoschem_src/KPP/fullchem\n";
+	print $fh "$camsrcdir/src/chemistry/pp_none\n";
+    }
+
     if ($chem =~ /_mam/) {
-        print $fh "$camsrcdir/src/chemistry/modal_aero\n";
+	print $fh "$camsrcdir/src/chemistry/modal_aero\n";
     } else {
-        print $fh "$camsrcdir/src/chemistry/bulk_aero\n";
+	print $fh "$camsrcdir/src/chemistry/bulk_aero\n";
     }
     print $fh "$camsrcdir/src/chemistry/aerosol\n";