Added diffs from protected files

Externals_CAM.cfg

@@ -61,6 +61,14 @@ repo_url = https://github.com/NCAR/atmospheric_physics
 required = True
 local_path = src/atmos_phys
 
+[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
+required = True
+externals = Externals_HCO.cfg
+
 [camnor_phys]
 tag = camnor_noresm_v0.0.1
 protocol = git

bld/config_files/definition.xml

@@ -46,14 +46,17 @@ Switch to turn on analytic initial conditions for the dynamics state:
   0 => no
   1 => yes.
 </entry>
+<entry id="hemco" valid_values="0,1" value="0">
+Switch to turn on Harmonized Emissions Component (HEMCO) for chemistry: 0 => no, 1 => yes.
+ </entry>
 <entry id="waccmx" valid_values="0,1" value="0">
 Option to turn on waccmx thermosphere/ionosphere extension: 0 => no, 1 => yes
 </entry>
 <entry id="ionosphere" valid_values="none,wxie" value="none">
 Ionosphere model used in WACCMX.
 </entry>
-<entry id="phys" valid_values="cam3,cam4,cam5,cam6,cam_dev,held_suarez,adiabatic,kessler,tj2016,spcam_sam1mom,spcam_m2005" value="">
-Physics package: cam3, cam4, cam5, cam6, cam_dev, held_suarez, adiabatic, kessler, tj2016, spcam_sam1mom, spcam_m2005.
+<entry id="phys" valid_values="cam3,cam4,cam5,cam6,cam_dev,held_suarez,adiabatic,kessler,tj2016,grayrad,spcam_sam1mom,spcam_m2005" value="">
+Physics package: cam3, cam4, cam5, cam6, cam_dev, held_suarez, adiabatic, kessler, tj2016, grayrad, spcam_sam1mom, spcam_m2005.
 </entry>
 <entry id="camnor" valid_values="0,1" value="0">
 Option to turn on NorESM modifications to baseline CESM/CAM physics and dynamics

bld/configure

@@ -90,6 +90,7 @@ OPTIONS
      -max_n_rad_cnst <n> Maximum number of constituents that are either radiatively
                         active, or in any single diagnostic list for the radiation.
      -microphys <name>  Specify the microphysics option [mg1 | mg2 | mg3| rk].
+     -model_top <name>  Specify the model_top option [ lt | mt ].
      -nadv <n>          Set total number of advected species to <n>.
      -nadv_tt <n>       Set number of advected test tracers <n>.
      -nlev <n>          Set number of levels to <n>.
@@ -98,7 +99,7 @@ OPTIONS
      -pcols <n>         Set maximum number of columns in a chunk to <n>.
      -pergro            Switch enables building CAM for perturbation growth tests.
      -phys <name>       Physics option [cam3 | cam4 | cam5 | cam6 | cam_dev |
-                                        held_suarez | adiabatic | kessler | tj2016 |
+                                        held_suarez | adiabatic | kessler | tj2016 | grayrad
                                         spcam_sam1mom | spcam_m2005].  Default: cam6
      -prog_species <list>Comma-separate list of prognostic mozart species packages.
                         Currently available: DST,SSLT,SO4,GHG,OC,BC,CARBON16
@@ -270,6 +271,7 @@ GetOptions(
     "max_n_rad_cnst=s"          => \$opts{'max_n_rad_cnst'},
     "mct_libdir=s"              => \$opts{'mct_libdir'},
     "microphys=s"               => \$opts{'microphys'},
+    "model_top=s"               => \$opts{'model_top'},
     "mpi_inc=s"                 => \$opts{'mpi_inc'},
     "mpi_lib=s"                 => \$opts{'mpi_lib'},
     "nadv=s"                    => \$opts{'nadv'},
@@ -574,7 +576,7 @@ if ($print>=2) {
 
 # Set flag to indicate a simple physics option
 my $simple_phys = 0;
-if ($phys_pkg =~ m/^adiabatic$|^held_suarez$|^kessler$|^tj2016$/) {
+if ($phys_pkg =~ m/^adiabatic$|^held_suarez$|^kessler$|^tj2016$|^grayrad$/) {
     $simple_phys = 1;
 }
 
@@ -687,6 +689,17 @@ my $max_n_rad_cnst = $cfg_ref->get('max_n_rad_cnst');
 
 if ($print>=2) { print "Maximum radiatively active tracers: $max_n_rad_cnst$eol"; }
 
+#-----------------------------------------------------------------------------------------------
+# model_top - not set by default
+my $model_top = 'none';
+$cfg_ref->set('model_top', $model_top);
+
+# user override
+if (defined $opts{'model_top'}) {
+    $cfg_ref->set('model_top', $opts{'model_top'});
+}
+if ($print>=2) { print "model_top: $model_top$eol"; }
+
 #-----------------------------------------------------------------------------------------------
 # waccm physics
 my $waccm_phys = 0;
@@ -1913,9 +1926,20 @@ if ($silhs == 1) {
     $cfg_cppdefs .= ' -DSILHS';
 }
 
+# Simple Models
+if ($simple_phys) { $cfg_cppdefs .= ' -DSIMPLE'; }
+
 # UNICON
 if ($unicon) { $cfg_cppdefs .= ' -DUSE_UNICON'; }
 
+# Harmonized Emissions Component (HEMCO)
+# These CPP definitions are used by HEMCO to recognize -
+#   MODEL_     - HEMCO/GEOS-Chem components running in model environment
+#   MODEL_CESM - ...within CESM
+#   USE_REAL8  - HEMCO/GEOS-Chem should use real8 internal precision
+#   HEMCO_CESM - indicates CESM model environment. Deprecated, will be removed soon.
+$cfg_cppdefs .= ' -DMODEL_ -DMODEL_CESM -DHEMCO_CESM -DUSE_REAL8 ';
+
 #-----------------------------------------------------------------------------------------------
 # CPP defines to put on Makefile
 
@@ -2125,6 +2149,20 @@ sub write_filepath
     print $fh "$camsrcdir/src/ionosphere\n";
 
     print $fh "$camsrcdir/src/chemistry/mozart\n";
+
+    print $fh "$camsrcdir/src/hemco\n";
+
+    # shared dependencies for HEMCO (Harmonized Emissions Component)
+    print $fh "$camsrcdir/src/hemco/HEMCO/src/Shared\n";
+    print $fh "$camsrcdir/src/hemco/HEMCO/src/Shared/Headers\n";
+    print $fh "$camsrcdir/src/hemco/HEMCO/src/Shared/GeosUtil\n";
+    print $fh "$camsrcdir/src/hemco/HEMCO/src/Shared/NcdfUtil\n";
+
+    # HEMCO source code directory paths from HEMCO external
+    print $fh "$camsrcdir/src/hemco/HEMCO/src/Core\n";
+    print $fh "$camsrcdir/src/hemco/HEMCO/src/Extensions\n";
+    print $fh "$camsrcdir/src/hemco/HEMCO/src/Interfaces/Shared\n";
+
     print $fh "$camsrcdir/src/chemistry/utils\n";
 
     if ($rad eq 'rrtmg') {
@@ -2284,6 +2322,7 @@ EOF
     $fh_in->close;
 }
 
+
 #-------------------------------------------------------------------------------
 
 sub write_config_h