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

.gitignore

@@ -9,6 +9,8 @@ src/physics/carma/base
 src/physics/clubb
 src/physics/cosp2/src
 src/physics/silhs
+src/chemistry/geoschem/geoschem_src
+src/hemco
 src/physics/pumas
 src/physics/pumas-frozen
 src/dynamics/fv3/atmos_cubed_sphere

Externals_CAM.cfg

@@ -76,11 +76,18 @@ sparse = ../.mpas_sparse_checkout
 hash = ff76a231
 required = True
 
+[geoschem]
+local_path = src/chemistry/geoschem/geoschem_src
+protocol = git
+repo_url = https://github.com/geoschem/geos-chem.git
+tag = 14.1.1
+required = True
+
 [hemco]
 local_path = src/hemco
-tag = hemco-cesm1_2_0_hemco3_6_2_cesm
 protocol = git
 repo_url = https://github.com/ESCOMP/HEMCO_CESM.git
+tag = hemco-cesm1_2_0_hemco3_6_2_cesm
 required = True
 externals = Externals_HCO.cfg
 

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
@@ -582,6 +582,11 @@ if ( ($chem ne 'none') or ( $prog_species ) ){
       add_default($nl, 'gas_wetdep_method' );
       add_default($nl, 'gas_wetdep_list', 'val'=>$gas_wetdep_list );
     }
+
+    if ($chem =~ /geoschem/) {
+      $prescribe_aerosols = $FALSE;
+    }
+
     if (length($aer_wetdep_list)>2){
         # determine if prescribed aerosols are not needed ...
         if ($aer_wetdep_list =~ /so4/i &&
@@ -612,6 +617,10 @@ if ( ($chem ne 'none') or ( $prog_species ) ){
     if (length($aer_drydep_list)>2){
         add_default($nl, 'aer_drydep_list', 'val'=>$aer_drydep_list );
     }
+    $nl->set_variable_value('aerosol_nl', 'aer_drydep_list', $aer_drydep_list);
+    $nl->set_variable_value('aerosol_nl', 'aer_wetdep_list', $aer_wetdep_list);
+    $nl->set_variable_value('drydep_inparm', 'drydep_list', $gas_drydep_list);
+    $nl->set_variable_value('wetdep_inparm', 'gas_wetdep_list', $gas_wetdep_list);
 }
 if ($chem) {
     # drydep_srf_file is only needed for prognostic MAM when the grid is unstructured.
@@ -862,7 +871,7 @@ 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 +906,8 @@ 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 {
     $radval .= ",'N:N2O:N2O','N:CH4:CH4','N:CFC11:CFC11','N:CFC12:CFC12'";
 }
@@ -2018,6 +2029,38 @@ if (($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',
+    #           'xs_coef_file','xs_short_file',
+    #           'xs_long_file', 'rsf_file',
+    #           'exo_coldens_file', 'sulf_file' );
+    @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 $val;
@@ -2364,10 +2407,12 @@ if (($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:
@@ -2428,10 +2473,12 @@ 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
@@ -2477,6 +2524,30 @@ 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 $val = "'ISOP = isoprene',"
                 . "'MTERP = carene_3 + pinene_a + thujene_a + bornene + terpineol_4 + terpineol_a + terpinyl_ACT_a "
@@ -2892,6 +2963,12 @@ if ($nl->get_value('use_hemco') =~ m/$TRUE/io) {
     # ignored at runtime when HEMCO is used.
     $nl->delete_variable('chem_inparm', 'ext_frc_specifier');
     $nl->delete_variable('chem_inparm', 'srf_emis_specifier');
+
+    # If using GEOS-Chem reset paths of HEMCO configuration files to local filename only
+    if ($chem =~ /geoschem/) {
+	$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
@@ -3020,7 +3097,7 @@ 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');
 }
 
@@ -3537,7 +3614,7 @@ 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.
@@ -80,6 +80,7 @@ OPTIONS
      -cpl               Coupling framework [mct | nuopc].  Default: mct.
      -dyn <name>        Dynamical core option: [eul | fv | se | fv3 | mpas].  Default: fv.
      -edit_chem_mech    Invokes CAMCHEM_EDITOR to allow the user to edit the chemistry mechanism file
+     -hemco             Switch enables the use of the Harmonized Emissions Component.
      -hgrid <name>      Specify horizontal grid.  Use nlatxnlon for spectral grids;
                         dlatxdlon for fv grids (dlat and dlon are the grid cell size
                         in degrees for latitude and longitude respectively); nexnp for
@@ -263,6 +264,7 @@ GetOptions(
     "fv3core_libdir=s"          => \$opts{'fv3core_libdir'},
     "gmake=s"                   => \$opts{'gmake'},
     "h|help"                    => \$opts{'help'},
+    "hemco"                     => \$opts{'hemco'},
     "hgrid=s"                   => \$opts{'hgrid'},
     "ionosphere=s"              => \$opts{'ionosphere'},
     "lapack_libdir=s"           => \$opts{'lapack_libdir'},
@@ -592,10 +594,10 @@ 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 ($chem_pkg ne 'terminator')) {
+        # the only valid chemistry options are 'none', 'terminator' and 'geoschem'
+        if (($chem_pkg ne 'none') and ($chem_pkg ne 'terminator') and !($chem_pkg =~ 'geoschem')) {
             die "configure ERROR: -phys=$phys_pkg  -chem=$chem_pkg\n".
-                "                 -chem can only be set to 'none' or 'terminator'.\n";
+                "                 -chem can only be set to 'none', 'terminator' or 'geoschem'.\n";
         }
     }
     elsif ($phys_pkg =~ m/^cam3$|^cam4$|^spcam_sam1mom$/) {
@@ -1356,7 +1358,11 @@ 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);
 }
 
@@ -1383,10 +1389,10 @@ 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);
 }
 
@@ -1400,6 +1406,13 @@ if ($chem_pkg =~ '_mam3') {
     $chem_cppdefs = ' -DMODAL_AERO -DMODAL_AERO_7MODE ';
 }
 
+# Set GEOS-Chem CPP definitions here
+if ($chem_pkg =~ 'geoschem') {
+    $chem_cppdefs .= ' -DEXTERNAL_GRID -DEXTERNAL_FORCING -DLINUX_IFORT -DUSE_REAL8 -DMODEL_ -DMODEL_CESM';
+    $chem_nadv = 267; # includes GC advected species (233), CO2 (1), and MAM aerosols (33)
+}
+
+
 # CARMA sectional microphysics
 #
 # New CARMA models need to define the number of advected constituents.
@@ -1563,6 +1576,12 @@ if ($print>=2) { print "Total advected constituents: $nadv$eol"; }
 
 #-----------------------------------------------------------------------------------------------
 
+# Harmonized Emissions Component (HEMCO)
+if (defined $opts{'hemco'}) {
+    $cfg_ref->set('hemco', $opts{'hemco'});
+}
+my $hemco  = $cfg_ref->get('hemco');
+
 #-----------------------------------------------------------------------------------------------
 # Makefile configuration #######################################################################
 #-----------------------------------------------------------------------------------------------
@@ -2093,6 +2112,7 @@ sub write_filepath
     my $waccm_phys    = $cfg_ref->get('waccm_phys');
     my $waccmx        = $cfg_ref->get('waccmx');
     my $ionos         = $cfg_ref->get('ionosphere');
+    my $hemco         = $cfg_ref->get('hemco');
     my $carma         = $cfg_ref->get('carma');
     my $rad           = $cfg_ref->get('rad');
     my $dyn           = $cfg_ref->get('dyn');
@@ -2157,10 +2177,21 @@ sub write_filepath
     if ($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";