Modifications to 'noresm_v4_cam6_3_112-13-g7c4d42ad' for merging with…

… CAM-Nor

- Configuration and code changes from ESCOMP between cam6_3_112 and cam6_3_123
- Adjust compsets, tests, and externals to be compatible with cam6_3_123 settings.

.gitignore

@@ -13,6 +13,7 @@ src/physics/silhs
 src/physics/pumas
 src/physics/pumas-frozen
 src/dynamics/fv3/atmos_cubed_sphere
+src/hemco
 libraries/FMS
 libraries/mct
 libraries/parallelio

Externals.cfg

@@ -3,15 +3,15 @@
 #-----------------------------
 
 [parallelio]
-tag = pio2_5_10
 protocol = git
+tag = pio2_5_10
 repo_url = https://github.com/NCAR/ParallelIO
 local_path = libraries/parallelio
 required = True
 
 [mct]
-tag = MCT_2.11.0
 protocol = git
+tag = MCT_2.11.0
 repo_url = https://github.com/MCSclimate/MCT
 local_path = libraries/mct
 required = True
@@ -21,15 +21,15 @@ required = True
 #-----------------------------
 
 [ccs_config]
-tag = ccs_config_noresm0.0.13
 protocol = git
+tag = ccs_config_noresm0.0.14
 repo_url = https://github.com/NorESMhub/ccs_config_noresm.git
 local_path = ccs_config
 required = True
 
 [cime]
-tag = cime6.0.105_noresm_v2
 protocol = git
+tag = cime6.0.105_noresm_v4
 repo_url = https://github.com/NorESMhub/cime.git
 local_path = cime
 required = True
@@ -39,8 +39,8 @@ required = True
 #-----------------------------
 
 [share]
-tag = share1.0.17_noresm_v1
 protocol = git
+tag = share1.0.17_noresm_v1
 repo_url = https://github.com/NorESMHub/NorESM_share
 local_path = share
 required = True
@@ -50,24 +50,24 @@ required = True
 #-----------------------------
 
 [cice6]
-tag = cesm_cice6_4_1_7_noresm_v1
 protocol = git
+tag = cesm_cice6_4_1_7_noresm_v1
 repo_url = https://github.com/NorESMhub/NorESM_CICE
 local_path = components/cice
 externals = Externals.cfg
 required = True
 
 [cdeps]
-tag = cdeps1.0.10
 protocol = git
+tag = cdeps1.0.10
 repo_url = https://github.com/NorESMhub/CDEPS.git
 local_path = components/cdeps
 externals =  Externals_CDEPS.cfg
 required = True
 
 [cmeps]
-tag = cmeps0.14.32_noresm_v0
 protocol = git
+tag = cmeps0.14.32_noresm_v2
 repo_url = https://github.com/NorESMhub/CMEPS.git
 local_path = components/cmeps
 required = True
@@ -81,30 +81,30 @@ externals = Externals_CISM.cfg
 required = True
 
 [clm]
-tag = ctsm5.1.dev124-noresm_v1
 protocol = git
+tag = ctsm5.1dev130-noresm_v1
 repo_url = https://github.com/NorESMhub/CTSM
 local_path = components/clm
 externals = Externals_CLM.cfg
 required = True
 
 [mosart]
-tag = mosart1_0_48_noresm_v1
 protocol = git
+tag = mosart1_0_48_noresm_v1
 repo_url = https://github.com/NorESMhub/MOSART
 local_path = components/mosart
 required = True
 
 [rtm]
-tag = rtm1_0_78
 protocol = git
+tag = rtm1_0_78
 repo_url = https://github.com/ESCOMP/RTM
 local_path = components/rtm
 required = True
 
 [cam]
-local_path = .
 protocol = externals_only
+local_path = .
 externals = Externals_CAM.cfg
 required = True
 

Externals_CAM.cfg

@@ -1,72 +1,80 @@
 [chem_proc]
-local_path = chem_proc
 protocol = git
-repo_url = https://github.com/ESCOMP/CHEM_PREPROCESSOR.git
 tag = chem_proc5_0_05
+repo_url = https://github.com/ESCOMP/CHEM_PREPROCESSOR.git
+local_path = chem_proc
 required = True
 
 [carma]
-local_path = src/physics/carma/base
 protocol = git
-repo_url = https://github.com/ESCOMP/CARMA_base.git
 tag = carma4_00
+repo_url = https://github.com/ESCOMP/CARMA_base.git
+local_path = src/physics/carma/base
 required = True
 
 [cosp2]
-local_path = src/physics/cosp2/src
 protocol = svn
-repo_url = https://github.com/CFMIP/COSPv2.0/tags/
 tag = v2.1.4cesm/src
+repo_url = https://github.com/CFMIP/COSPv2.0/tags/
+local_path = src/physics/cosp2/src
 required = True
 
 [clubb]
-local_path = src/physics/clubb
 protocol = svn
-repo_url = https://github.com/larson-group/clubb_release/tags/
 tag = clubb_4ncar_20221129_59cb19f_20230330_branchtag/src/CLUBB_core
+repo_url = https://github.com/larson-group/clubb_release/tags/
+local_path = src/physics/clubb
 required = True
 
 [silhs]
-local_path = src/physics/silhs
 protocol = svn
-repo_url = https://github.com/larson-group/clubb_release/tags/
 tag = clubb_4ncar_20221129_59cb19f_20230330_branchtag/src/SILHS
+repo_url = https://github.com/larson-group/clubb_release/tags/
+local_path = src/physics/silhs
 required = True
 
 [pumas]
-local_path = src/physics/pumas
 protocol = git
-repo_url = https://github.com/ESCOMP/PUMAS
 tag = pumas_cam-release_v1.29
+repo_url = https://github.com/ESCOMP/PUMAS
+local_path = src/physics/pumas
 required = True
 
 [pumas-frozen]
-local_path = src/physics/pumas-frozen
 protocol = git
-repo_url = https://github.com/ESCOMP/PUMAS
 tag = pumas_cam-release_v1.17_rename
+repo_url = https://github.com/ESCOMP/PUMAS
+local_path = src/physics/pumas-frozen
 required = True
 
 [ali_arms]
-local_path = src/physics/ali_arms
 protocol = git
+tag = ALI_ARMS_v1.0.1
 repo_url = https://github.com/ESCOMP/ALI-ARMS
-tag = ALI_ARMS_v1.0.0
+local_path = src/physics/ali_arms
 required = True
 
 [atmos_phys]
-tag = atmos_phys0_00_011
 protocol = git
+tag = atmos_phys0_00_011
 repo_url = https://github.com/NCAR/atmospheric_physics
-required = True
 local_path = src/atmos_phys
+required = True
 
 [camnor_phys]
-tag = camnor_noresm_v0.0.1
 protocol = git
+tag = camnor_noresm_v0.0.3
 repo_url = https://github.com/NorESMhub/CAM-Nor-physics
-required = True
 local_path = src/physics/camnor_phys
+required = True
+
+[hemco]
+protocol = git
+tag = hemco-cesm1_2_0_hemco3_6_2_cesm
+repo_url = https://github.com/ESCOMP/HEMCO_CESM.git
+local_path = src/hemco
+required = True
+externals = Externals_HCO.cfg
 
 [externals_description]
-schema_version = 1.0.0
+schema_version = 1.0.01

bld/config_files/definition.xml

@@ -46,14 +46,22 @@ Switch to turn on analytic initial conditions for the dynamics state:
   0 => no
   1 => yes.
 </entry>
+<entry id="model_top" valid_values="none,lt,mt" value="none">
+Model top specifier - set by compset definition
+  lt: ~ 40 km top
+  mt: ~ 80 km top
+</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="hemco" valid_values="0,1" value="0">
+Switch to turn on Harmonized Emissions Component (HEMCO) for chemistry: 0 => no, 1 => yes.
 </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 +689,18 @@ 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;
@@ -1559,6 +1573,8 @@ $nadv = $cfg_ref->get('nadv');
 if ($print>=2) { print "Total advected constituents: $nadv$eol"; }
 
 #-----------------------------------------------------------------------------------------------
+
+##-----------------------------------------------------------------------------------------------
 # Makefile configuration #######################################################################
 #-----------------------------------------------------------------------------------------------
 
@@ -1913,9 +1929,20 @@ 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 +2152,21 @@ 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') {