ESCOMP · fritzt · Jan 16, 2019 · Jan 16, 2019 · Jan 17, 2019 · Jan 18, 2019
diff --git a/.gitignore b/.gitignore
@@ -7,7 +7,8 @@ src/physics/carma/base
 src/physics/clubb
 src/physics/cosp2/src
 src/physics/silhs
-
+src/chemistry/geoschem/geoschem_src
+src/hemco
 
 # Ignore compiled python
 buildnmlc

diff --git a/Externals.cfg b/Externals.cfg
@@ -2,44 +2,44 @@
 schema_version = 1.0.0
 
 [cice]
-tag = cice5_cesm2_0_rel_01
+tag = cice5_20190318
 protocol = git
 repo_url = https://github.com/ESCOMP/CESM_CICE5
 required = True
 local_path = components/cice
 
 [cime]
-tag = cime_cesm2_0_rel_06
+tag = cime5.6.13
 protocol = git
 repo_url = https://github.com/ESMCI/cime
 required = True
 local_path = cime
 
 [cism]
-tag = release-cesm2.0.01
+tag = release-cesm2.0.04
 protocol = git
 repo_url = https://github.com/ESCOMP/cism-wrapper
 externals = Externals_CISM.cfg
 required = True
 local_path = components/cism
 
 [clm]
-tag = release-clm5.0.01
+tag = release-clm5.0.20
 protocol = git
 repo_url = https://github.com/ESCOMP/ctsm
 externals = Externals_CLM.cfg
 required = True
 local_path = components/clm
 
 [mosart]
-tag = release-cesm2.0.00
+tag = release-cesm2.0.03
 protocol = git
 repo_url = https://github.com/ESCOMP/mosart
 required = True
 local_path = components/mosart 
 
 [rtm]
-tag = release-cesm2.0.00
+tag = release-cesm2.0.02
 protocol = git
 repo_url = https://github.com/ESCOMP/rtm
 required = True

diff --git a/Externals_CAM.cfg b/Externals_CAM.cfg
@@ -1,22 +1,22 @@
 [chem_proc]
 local_path = chem_proc
 protocol = svn
-repo_url = https://svn-ccsm-models.cgd.ucar.edu/tools/proc_atm/chem_proc/trunk_tags/
-tag = chem_proc5_0_03
+repo_url = https://svn-ccsm-models.cgd.ucar.edu/tools/proc_atm/chem_proc/release_tags/
+tag = chem_proc5_0_03_rel
 required = True
 
 [carma]
 local_path = src/physics/carma/base
 protocol = svn
-repo_url = https://svn-ccsm-models.cgd.ucar.edu/carma/trunk_tags/
-tag = carma3_49
+repo_url = https://svn-ccsm-models.cgd.ucar.edu/carma/release_tags/
+tag = carma3_49_rel
 required = True
 
 [clubb]
 local_path = src/physics/clubb
 protocol = svn
-repo_url = https://svn-ccsm-models.cgd.ucar.edu/clubb_core/branch_tags/
-tag = vendor_clubb_r8099_tags/vendor_clubb_r8099_n02
+repo_url = https://svn-ccsm-models.cgd.ucar.edu/clubb_core/release_tags/
+tag = clubb_r8099_n02_rel
 required = True
 
 [cosp2]
@@ -26,6 +26,21 @@ repo_url = https://github.com/CFMIP/COSPv2.0/tags/
 tag = v2.0.3cesm/src
 required = True
 
+[geoschem]
+local_path = src/chemistry/geoschem/geoschem_src
+protocol = git
+branch = CESM
+repo_url = https://github.com/CESM-GC/geos-chem
+required = True
+
+[hemco]
+local_path = src/hemco
+protocol = git
+branch = development
+repo_url = https://github.com/jimmielin/HEMCO_CESM.git
+required = True
+externals = Externals_HCO.cfg
+
 [externals_description]
 schema_version = 1.0.0
 
diff --git a/README.md b/README.md
@@ -1,7 +1,5 @@
 # CAM: The Community Atmosphere Model
 
-## NOTE: This is unsupported development code and is subject to the [CESM developer's agreement](http://www.cgd.ucar.edu/cseg/development-code.html).
-
 CAM Documentation - https://ncar.github.io/CAM/doc/build/html/index.html
 
 CAM6 namelist settings - http://www.cesm.ucar.edu/models/cesm2/settings/current/cam_nml.html

diff --git a/bld/build-namelist b/bld/build-namelist
@@ -665,7 +665,7 @@ 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
@@ -707,6 +707,11 @@ 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 ($aer_wetdep_list =~ /so4/i &&
@@ -740,6 +745,10 @@ if ( ($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) {
     # Dry Deposition -- The responsibility for dry deposition is shared between CAM and CLM.
@@ -895,9 +904,17 @@ if ($co2_cycle) {
         # Check whether user has explicitly turned off reading the aircraft CO2 dataset.
         # (user specification has higher precedence than the true value set above)
         if ($nl->get_value('co2_readflux_aircraft') =~ /$TRUE/io) {
-            add_default($nl, 'aircraft_specifier');
+
+            my $rel_filepath = get_default_value('ac_CO2_emis');
+            my $emisval = quote_string('ac_CO2 -> ' . $rel_filepath);
+            add_default($nl, 'aircraft_specifier', 'val'=>$emisval);
+
             add_default($nl, 'aircraft_datapath');
             add_default($nl, 'aircraft_type');
+            # This should be the same file as the one in the aircraft_specifier file.
+            # This is a workaround to get this filepath into the cam.input_data_list file
+            # to allow the CESM scripts to obtain all required data for a run.
+            add_default($nl, 'aircraft_co2_file');
         }
     }
 }
@@ -981,7 +998,7 @@ 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 !$co2_cycle_rad_passive) {
@@ -1016,6 +1033,8 @@ if ((($chem =~ /waccm_ma/) or ($chem =~ /waccm_sc_mam/) or ($chem =~ /waccm_tsml
     $radval .= ",'A:N2O:N2O','A:CH4:CH4','A:CFC11:CFC11','A:CFC12:CFC12'";
 } elsif ($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 {
     $radval .= ",'N:N2O:N2O','N:CH4:CH4','N:CFC11:CFC11','N:CFC12:CFC12'";
 }
@@ -2068,6 +2087,38 @@ if (($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 $val;
@@ -2363,7 +2414,7 @@ if ($chem =~ /_mam4/ and $phys =~ /cam6/) {
                 'num_a2_cv_ext_file' => 'num_a2',
         );
 
-    # air craft emissions
+    # aircraft emissions
     if ($chem !~ /trop_mam/ and $chem !~ /waccm_sc/) {
         %species = (%species,
                     'bc_a4_ar_ext_file'  => 'bc_a4',
@@ -2418,7 +2469,7 @@ if ($chem =~ /_mam4/ and $phys =~ /cam6/) {
     }
 
     # MEGAN emissions
-    if ($chem =~ /trop_strat/ or $chem =~ /_tsmlt/) {
+    if ($chem =~ /trop_strat/ or $chem =~ /_tsmlt/ or $chem =~ /geoschem/) {
         my $val = "'ISOP = isoprene',"
                 . "'MTERP = pinene_a + carene_3 + thujene_a + 2met_styrene + cymene_p + cymene_o + terpinolene + bornene "
                 . "+ fenchene_a + ocimene_al + pinene_b + sabinene + camphene + limonene + phellandrene_a + terpinene_g "
@@ -2744,6 +2795,9 @@ else {
     }
 }
 
+# HEMCO
+$nl->set_variable_value('hemco_nl', 'hemco_config_File', "'HEMCO_Config.rc'");
+
 # Physics options
 
 # Add the name of the physics package based on the info in configure.  If the user tries
@@ -2859,7 +2913,7 @@ 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');
 }
 
@@ -2967,7 +3021,7 @@ if ($clubb_sgs  =~ /$TRUE/io) {
    add_default($nl, 'clubb_history');
    add_default($nl, 'clubb_rad_history');
 
-   if ($nl->get_value('clubb_history') =~ "true" &&  $nl->get_value('atm_nthreads') != 1) {
+   if ($nl->get_value('clubb_history') =~ "true" &&  $nl->get_value('atm_nthreads') > 1) {
      die "$ProgName - ERROR: clubb_history = .true. with multiple threads is not supported. \n";
    }
 
@@ -3143,7 +3197,7 @@ 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');
             # set scaling of lightning NOx production
 	    add_default($nl, 'lght_no_prd_factor' );
@@ -3416,6 +3470,11 @@ if ($cfg->get('camiop')) {
 
 if ($dyn =~ /se/) {
 
+    ## topography not supported for CESM2.0
+    if (!defined $use_topo_file or ($use_topo_file =~ m/$TRUE/io)) {
+      die "$ProgName - ERROR: Use of topography not currently supported with SE dycore\n";
+    }
+
     ####################################################
     # namelist group: dyn_se_inparm (for CAM_SE) #
     ####################################################

diff --git a/bld/config_files/definition.xml b/bld/config_files/definition.xml
@@ -52,6 +52,10 @@ Option to turn on waccmx thermosphere/ionosphere extension: 0 => no, 1 => yes
 <entry id="ionosphere" valid_values="none,wxi,wxie" value="none">
 Ionosphere model used in WACCMX.
 </entry>
+<entry id="hemco" valid_values="0,1" value="1">
+Switch to turn on Harmonized Emissions Component (HEMCO): 0 => no, 1 => yes.
+WARNING THIS IS ON BY DEFAULT FOR DEVELOPMENT - DO NOT SUBMIT THIS TO PRODUCTION CODE
+</entry>
 <entry id="phys" valid_values="cam3,cam4,cam5,cam6,held_suarez,adiabatic,kessler,tj2016,spcam_sam1mom,spcam_m2005" value="">
 Physics package: cam3, cam4, cam5, cam6, held_suarez, adiabatic, kessler, tj2016, spcam_sam1mom, spcam_m2005.
 </entry>
@@ -93,6 +97,8 @@ test_radiative (Radiatively Active Dust), test_swelling (Sea Salt), test_tracers
 </entry>
 <entry id="chem" valid_values="trop_mam3,trop_mam4,trop_mam7,trop_mozart,trop_strat_mam4_vbs,trop_strat_mam4_vbsext,waccm_ma,waccm_mad,waccm_mad_mam4,waccm_ma_mam4,waccm_ma_sulfur,waccm_sc,waccm_sc_mam4,waccm_tsmlt_mam4,terminator,none" value="">
 Chemistry package: trop_mam3 trop_mam4 trop_mam7 trop_mozart trop_strat_mam4_vbs trop_strat_mam4_vbsext waccm_ma waccm_mad waccm_mad_mam4 waccm_ma_mam4 waccm_ma_sulfur waccm_sc waccm_sc_mam4 waccm_tsmlt_mam4 terminator none
+<entry id="chem" valid_values="trop_mam3,trop_mam4,trop_mam7,trop_mozart,trop_strat_mam4_vbs,trop_strat_mam4_vbsext,waccm_ma,waccm_mad,waccm_mad_mam4,waccm_ma_mam4,waccm_ma_sulfur,waccm_sc,waccm_sc_mam4,waccm_tsmlt_mam4,terminator,geoschem,geoschem_mam4,none" value="">
+Chemistry package: trop_mam3 trop_mam4 trop_mam7 trop_mozart trop_strat_mam4_vbs trop_strat_mam4_vbsext waccm_ma waccm_mad waccm_mad_mam4 waccm_ma_mam4 waccm_ma_sulfur waccm_sc waccm_sc_mam4 waccm_tsmlt_mam4 terminator GEOS-Chem none
 </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