Merge tag 'cam6_4_149' into frontogenesis-fv-fix

Include chemical heating in mid-top configurations

Author: cacraigucar

.gitmodules

@@ -9,7 +9,7 @@
 	path = src/physics/carma/base
 	url = https://github.com/ESCOMP/CARMA_base.git
         fxrequired = AlwaysRequired
-        fxtag = carma4_09
+        fxtag = carma4_10
         fxDONOTUSEurl = https://github.com/ESCOMP/CARMA_base.git
 
 [submodule "pumas-frozen"]
@@ -29,7 +29,7 @@
 [submodule "atmos_phys"]
 	path = src/atmos_phys
 	url = https://github.com/ESCOMP/atmospheric_physics
-	fxtag = atmos_phys0_20_000
+	fxtag = atmos_phys0_21_000
         fxrequired = AlwaysRequired
         fxDONOTUSEurl = https://github.com/ESCOMP/atmospheric_physics
 
@@ -107,6 +107,14 @@
         fxtag = clubb_4ncar_20240605_73d60f6_gpufixes_posinf
         fxDONOTUSEurl = https://github.com/larson-group/clubb_release
 
+[submodule "ext_co2_cooling"]
+	path = src/physics/ext_co2_cooling
+	url = https://github.com/fedef17/CO2_cool_fort.git
+	fxrequired = AlwaysRequired
+	fxsparse = ../.ext_co2_cooling_sparse_checkout
+	fxtag = v1.1
+	fxDONOTUSEurl = https://github.com/fedef17/CO2_cool_fort.git
+
 [submodule "rtm"]
 path = components/rtm
 url = https://github.com/ESCOMP/RTM
@@ -131,14 +139,14 @@ fxDONOTUSEurl = https://github.com/ESCOMP/mizuRoute
 [submodule "ccs_config"]
 path = ccs_config
 url = https://github.com/ESMCI/ccs_config_cesm.git
-fxtag = ccs_config_cesm1.0.65
+fxtag = ccs_config_cesm1.0.72
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git
 
 [submodule "cime"]
 path = cime
 url = https://github.com/ESMCI/cime
-fxtag = cime6.1.145
+fxtag = cime6.1.155
 fxrequired = ToplevelRequired
 fxDONOTUSEurl = https://github.com/ESMCI/cime
 

bld/build-namelist

@@ -1937,11 +1937,11 @@ if (($chem =~ /trop_mozart/ or $chem =~ /trop_strat/ or $chem =~ /waccm_tsmlt/)
                    'ISOP     -> ' => 'isop_emis_file',
                    'TOLUENE  -> ' => 'toluene_emis_file',
                    );
-    if (!($chem =~ /_vbs/) and !($chem =~ /_tsmlt/)) {
+    if (!($chem =~ /_vbs/) and !($chem =~ /_tsmlt/) and !($chem =~ /_t1s/)) {
         %species = (%species,
                     'NH3      -> ' => 'nh3_emis_file');
     }
-    if (!($chem =~ /_vbs/) and !($chem =~ /_tsmlt/)) {
+    if (!($chem =~ /_vbs/) and !($chem =~ /_tsmlt/) and !($chem =~ /_t1s/)) {
         %species = (%species,
                     'C10H16   -> ' => 'c10h16_emis_file', );
     }
@@ -2407,7 +2407,7 @@ if ($phys =~ /cam6/ or $phys =~ /cam7/) {
             %species = (%species,
                     'E90_srf_file' => 'E90' );
         }
-        if ($chem !~ /_ts4/ and $chem !~ /_t4ma/) {
+        if ($chem !~ /_t4s/ and $chem !~ /_t4ma/) {
 	    %species = (%species,
                     'BENZENE_an_srf_file' => 'BENZENE',
                     'BENZENE_bb_srf_file' => 'BENZENE',
@@ -2428,10 +2428,10 @@ if ($phys =~ /cam6/ or $phys =~ /cam7/) {
                     'XYLENES_an_srf_file' => 'XYLENES',
                     'XYLENES_bb_srf_file' => 'XYLENES' ) ;
         }
-        if ($chem =~ /trop_strat_mam4_ts2/ or $chem =~ /trop_strat_mam5_ts2/) {
+        if ($chem =~ /trop_strat_mam4_ts2/ or $chem =~ /trop_strat_mam5_t2s1/) {
             %species = (%species,
                     'MTERP_bb_srf_file' => 'APIN') ;
-        } elsif ($chem =~ /_ts4/ or $chem =~ /_t4ma/) {
+        } elsif ($chem =~ /_t4s/ or $chem =~ /_t4ma/) {
             %species = (%species,
                     'MTERP_bb_srf_file' => 'TERP') ;
 	} else {
@@ -2456,7 +2456,7 @@ if ($phys =~ /cam6/ or $phys =~ /cam7/) {
                     'IVOC_bb_srf_file' => 'IVOCbb',
                     'SVOC_an_srf_file' => 'SVOCff',
                     'SVOC_bb_srf_file' => 'SVOCbb' );
-        } elsif ($chem !~ /_ts4/ and $chem !~ /_t4ma/) {
+        } elsif ($chem !~ /_t4s/ and $chem !~ /_t4ma/) {
             %species = (%species,
                     'IVOC_an_srf_file' => 'IVOC',
                     'IVOC_bb_srf_file' => 'IVOC',
@@ -2481,7 +2481,7 @@ if ($phys =~ /cam6/ or $phys =~ /cam7/) {
             $first = 0;
         }
     }
-    if ($chem eq 'trop_mam4' or $chem eq 'waccm_sc_mam4' or $chem eq 'ghg_mam4' or $chem =~ /_ts4/ or $chem =~ /_t4ma/) {
+    if ($chem eq 'trop_mam4' or $chem eq 'waccm_sc_mam4' or $chem eq 'ghg_mam4' or $chem =~ /_t4s/ or $chem =~ /_t4ma/) {
 	# SOA yields (used for the interactive emissions) have been calculated based on the VBS yields in CAM-chem.
 	# Duseong S. Jo, et al. to be submitted to GMD, 2023 -- see https://github.com/ESCOMP/CAM/pull/727 discussion for additional detail.
         my %soae_fctrs = ('BENZENE_an_srf_file' => '2.5592D0',
@@ -2657,7 +2657,7 @@ if ($phys =~ /cam6/ or $phys =~ /cam7/) {
         add_default($nl, 'megan_factors_file');
         add_default($nl, 'megan_mapped_emisfctrs', 'val'=>'.false.');
     }
-    if ($chem =~ /trop_strat_mam4_vbs/ or $chem =~ /trop_strat_mam5_vbs/) {
+    if ($chem =~ /trop_strat_mam4_vbs/ or $chem =~ /trop_strat_mam5_vbsext/ or $chem =~ /trop_strat_mam5_t1s/) {
         my $val = "'ISOP = isoprene',"
                 . "'MTERP = carene_3 + pinene_a + thujene_a + bornene + terpineol_4 + terpineol_a + terpinyl_ACT_a "
                 . "+ myrtenal + sabinene + pinene_b + camphene + fenchene_a + limonene + phellandrene_a + terpinene_a "
@@ -2696,7 +2696,7 @@ if ($phys =~ /cam6/ or $phys =~ /cam7/) {
         add_default($nl, 'megan_factors_file');
         add_default($nl, 'megan_mapped_emisfctrs', 'val'=>'.false.');
     }
-    if ($chem =~ /trop_strat_mam5_ts4/ or $chem =~ /_t4ma/) {
+    if ($chem =~ /trop_strat_mam5_t4s2/ or $chem =~ /_t4ma/) {
         my $val = "'ISOP = isoprene',"
                 . "'TERP = carene_3 + pinene_a + thujene_a + bornene + terpineol_4 + terpineol_a + terpinyl_ACT_a +',"
                 . "' myrtenal + sabinene + pinene_b + camphene + fenchene_a + limonene + phellandrene_a + terpinene_a +',"
@@ -2728,7 +2728,7 @@ if ($phys =~ /cam6/ or $phys =~ /cam7/) {
         add_default($nl, 'megan_factors_file');
         add_default($nl, 'megan_mapped_emisfctrs', 'val'=>'.false.');
     }
-    if ($chem =~ /trop_strat_mam4_ts2/ or $chem =~ /trop_strat_mam5_ts2/) {
+    if ($chem =~ /trop_strat_mam4_ts2/ or $chem =~ /trop_strat_mam5_t2s1/) {
         my $val = "'ISOP = isoprene',"
                 . "'APIN = pinene_a + myrtenal',"
                 . "'BPIN = carene_3 + thujene_a + bornene + fenchene_a + pinene_b + sabinene + camphene + terpineol_4 + terpineol_a + terpinyl_ACT_a',"
@@ -3703,6 +3703,11 @@ if (!$simple_phys) {
     add_default($nl, 'do_iss');
 }
 
+# Sponge layer vertical diffusion
+if (!$simple_phys) {
+    add_default($nl, 'diff_sponge_fac');
+}
+
 # Convective water in radiation
 if (!$simple_phys) {
     add_default($nl, 'conv_water_in_rad');

bld/config_files/definition.xml

@@ -56,6 +56,9 @@ Model top specifier - set by compset definition
 <entry id="waccmx" valid_values="0,1" value="0">
 Option to turn on waccmx thermosphere/ionosphere extension: 0 => no, 1 => yes
 </entry>
+<entry id="ext_co2_cool" valid_values="0,1" value="0">
+Option to turn on extended non-LTE CO2 cooling: 0 => no, 1 => yes
+</entry>
 <entry id="ionosphere" valid_values="none,wxie" value="none">
 Ionosphere model used in WACCMX.
 </entry>
@@ -100,8 +103,8 @@ test_radiative (Radiatively Active Dust), test_swelling (Sea Salt), test_tracers
 trop_strat_soa1 (Trop Strat Aerosols SOA1),
 trop_strat_soa5 (Trop Strat Aerosols SOA5)
 </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_ts4,trop_strat_mam5_vbs,trop_strat_mam5_vbsext,trop_strat_noaero,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_t4ma_mam5,waccm_ma_noaero,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_ts4,trop_strat_mam5_vbs,trop_strat_mam5_vbsext,trop_strat_noaero,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_t4ma_mam5,waccm_ma_noaero,geoschem_mam4
+<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_t1s1,trop_strat_mam5_t1s2,trop_strat_mam5_t2s1,trop_strat_mam5_t4s2,trop_strat_mam5_vbsext,trop_strat_noaero,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_t4ma_mam5,waccm_ma_noaero,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_t1s1,trop_strat_mam5_t1s2,trop_strat_mam5_t2s1,trop_strat_mam5_t4s2,trop_strat_mam5_vbsext,trop_strat_noaero,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_t4ma_mam5,waccm_ma_noaero,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

@@ -64,10 +64,11 @@ OPTIONS
                         Default: none.
     -chem <name>        Build CAM with specified prognostic 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_ts4 | trop_strat_mam5_vbs | trop_strat_noaero |
-                         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_noaero | geoschem_mam4 ].
+			  trop_strat_mam4_vbs | trop_strat_mam4_vbsext | trop_strat_mam5_t1s1 | trop_strat_mam5_t2s2 |
+			  trop_strat_mam5_t2s1 | trop_strat_mam5_t4s2 | trop_strat_noaero | 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_t4ma_mam5 | waccm_ma_noaero | geoschem_mam4 ].
                         Default: trop_mam4 for cam6 and trop_mam3 for cam5.
      -[no]clubb_sgs     Switch on [off] CLUBB_SGS.  Default: on for cam6 and cam7, otherwise off.
      -clubb_opts <list> Comma separated list of CLUBB options to turn on/off.  By default they are all off.
@@ -80,6 +81,7 @@ OPTIONS
      -cpl               Coupling framework [mct | nuopc].  Default: mct.
      -dyn <name>        Dynamical core option: [fv | se | fv3 | mpas].  Default: fv.
      -edit_chem_mech    Invokes CAMCHEM_EDITOR to allow the user to edit the chemistry mechanism file
+     -ext_co2_cool      Switch on extended non-LTE CO2 cooling
      -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
@@ -300,6 +302,7 @@ GetOptions(
     "version"                   => \$opts{'version'},
     "waccm_phys"                => \$opts{'waccm_phys'},
     "waccmx"                    => \$opts{'waccmx'},
+    "ext_co2_cool"              => \$opts{'ext_co2_cool'},
 )  or usage();
 
 # Give usage message.
@@ -706,6 +709,12 @@ if (defined $opts{'waccmx'}) {
 my $waccmx = $cfg_ref->get('waccmx');
 my $ionos  = $cfg_ref->get('ionosphere');
 
+# Extended CO2 non-LTE option
+if (defined $opts{'ext_co2_cool'}) {
+    $cfg_ref->set('ext_co2_cool', $opts{'ext_co2_cool'});
+}
+my $ext_co2_cool = $cfg_ref->get('ext_co2_cool');
+
 #-----------------------------------------------------------------------------------------------
 
 # Prognostic species package(s)
@@ -1768,6 +1777,11 @@ if ($waccmx) {
     $cfg_cppdefs .= ' -DWACCMX_PHYS';
 }
 
+# Extended Non-LTE CO2 cooling
+if ($ext_co2_cool) {
+    $cfg_cppdefs .= ' -DEXT_CO2_COOL';
+}
+    
 # PIO
 my $pio2_build = (defined $opts{'pio2'}) ? 1 : 0;
 
@@ -1967,6 +1981,7 @@ sub write_filepath
     my $spmd          = $cfg_ref->get('spmd');
     my $offline_drv   = $cfg_ref->get('offline_drv');
     my $inic_val      = $cfg_ref->get('analytic_ic');
+    my $ext_co2_cool  = $cfg_ref->get('ext_co2_cool');
 
     # Root directory
     my $camsrcdir = $cfg_ref->get('cam_dir');
@@ -2058,6 +2073,10 @@ sub write_filepath
 	print $fh "$camsrcdir/src/physics/ali_arms/subs\n";
 	print $fh "$camsrcdir/src/physics/ali_arms/include\n";
     }
+    if ($ext_co2_cool) {
+        print $fh "$camsrcdir/src/physics/ext_co2_cooling/source/modules\n";
+    }	
+
     print $fh "$camsrcdir/src/ionosphere\n";
 
     print $fh "$camsrcdir/src/chemistry/mozart\n";