Merge remote-tracking branch 'upstream/cam_development' into CESM-GC_…

…rebased_on_cam6_0_034 This commit brings in cam6_3_111 # Conflicts: # bld/build-namelist # bld/config_files/definition.xml # bld/namelist_files/namelist_defaults_cam.xml # cime_config/config_component.xml Signed-off-by: Lizzie Lundgren <[email protected]>
ESCOMP · May 18, 2023 · 9ed40a2 · 9ed40a2
2 parents a16a4ff + 379603b
commit 9ed40a2
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diff --git a/Externals.cfg b/Externals.cfg
@@ -1,5 +1,5 @@
 [ccs_config]
-tag = ccs_config_cesm0.0.49
+tag = ccs_config_cesm0.0.59
 protocol = git
 repo_url = https://github.com/ESMCI/ccs_config_cesm
 local_path = ccs_config
@@ -13,22 +13,22 @@ local_path = components/cice5
 required = True
 
 [cice6]
-tag = cesm_cice6_2_0_35
+tag = cesm_cice6_4_1_3
 protocol = git
 repo_url = https://github.com/ESCOMP/CESM_CICE
 local_path = components/cice
 externals = Externals.cfg
 required = True
 
 [cmeps]
-tag = cmeps0.14.12
+tag = cmeps0.14.24
 protocol = git
 repo_url = https://github.com/ESCOMP/CMEPS.git
 local_path = components/cmeps
 required = True
 
 [cdeps]
-tag = cdeps0.12.67
+tag = cdeps1.0.8
 protocol = git
 repo_url = https://github.com/ESCOMP/CDEPS.git
 local_path = components/cdeps
@@ -57,14 +57,14 @@ local_path = libraries/mct
 required = True
 
 [parallelio]
-tag = pio2_5_9
+tag = pio2_5_10
 protocol = git
 repo_url = https://github.com/NCAR/ParallelIO
 local_path = libraries/parallelio
 required = True
 
 [cime]
-tag = cime6.0.82
+tag = cime6.0.94
 protocol = git
 repo_url = https://github.com/ESMCI/cime
 local_path = cime
@@ -79,7 +79,7 @@ externals = Externals_CISM.cfg
 required = True
 
 [clm]
-tag = ctsm5.1.dev114
+tag = ctsm5.1.dev120
 protocol = git
 repo_url = https://github.com/ESCOMP/CTSM
 local_path = components/clm
@@ -96,7 +96,7 @@ externals = Externals_FMS.cfg
 required = True
 
 [mosart]
-tag = mosart1_0_47
+tag = mosart1_0_48
 protocol = git
 repo_url = https://github.com/ESCOMP/MOSART
 local_path = components/mosart

diff --git a/Externals_CAM.cfg b/Externals_CAM.cfg
@@ -23,21 +23,21 @@ required = True
 local_path = src/physics/clubb
 protocol = svn
 repo_url = https://github.com/larson-group/clubb_release/tags/
-tag = clubb_4ncar_20221129_59cb19f/src/CLUBB_core
+tag = clubb_4ncar_20221129_59cb19f_20230330_branchtag/src/CLUBB_core
 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/src/SILHS
+tag = clubb_4ncar_20221129_59cb19f_20230330_branchtag/src/SILHS
 required = True
 
 [pumas]
 local_path = src/physics/pumas
 protocol = git
 repo_url = https://github.com/ESCOMP/PUMAS
-tag = pumas_cam-release_v1.28
+tag = pumas_cam-release_v1.29
 required = True
 
 [pumas-frozen]

diff --git a/bld/build-namelist b/bld/build-namelist
@@ -851,7 +851,7 @@ if (($chem =~ /waccm_ma/ or $chem =~ /waccm_tsmlt/) and !$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 !$co2_cycle_rad_passive) {
+elsif (($co2_cycle and !$co2_cycle_rad_passive) or ($chem =~ /ghg_mam4/)) {
     $radval .= ",'N:O2:O2','A:CO2:CO2'";
 }
 else {
@@ -877,7 +877,7 @@ if ($rad_prog_ozone) {
     die "ERROR: can not set ozone rad_climate specification\n";
 }
 
-if ((($chem =~ /waccm_ma/) or ($chem =~ /waccm_sc_mam/) or ($chem =~ /waccm_tsmlt/) or ($chem =~ /trop_strat/)) and !$chem_rad_passive ) {
+if ((($chem =~ /ghg_mam4/) or ($chem =~ /waccm_ma/) or ($chem =~ /waccm_sc_mam/) or ($chem =~ /waccm_tsmlt/) or ($chem =~ /trop_strat/)) and !$chem_rad_passive ) {
     $radval .= ",'A:N2O:N2O','A:CH4:CH4','N:CFC11STAR:CFC11','A:CFC12:CFC12'";
 } elsif ($prog_ghg1 and $prog_ghg2 and !$chem_rad_passive ) {
     $radval .= ",'A:N2O:N2O','A:CH4:CH4','A:CFC11:CFC11','A:CFC12:CFC12'";
@@ -1662,7 +1662,16 @@ if ($chem =~ /waccm_sc/) {
     add_default($nl, 'h2orates');
     add_default($nl, 'solar_parms_data_file');
 }
-
+if ($chem =~ /ghg_mam4/) {
+    add_default($nl, 'h2orates');
+    my $flbc_list = "'CH4','N2O','CO2','CFC11','CFC12'";
+    add_default($nl, 'flbc_list', 'val'=>$flbc_list);
+    unless (defined $nl->get_value('flbc_type')) {
+        add_default($nl, 'flbc_type',  'val'=>'CYCLICAL');
+        add_default($nl, 'flbc_cycle_yr',  'val'=>'2000');
+    }
+    add_default($nl, 'flbc_file');
+}
 if ( $prog_species ) {
     my $ddval;
     my $emisval;
@@ -2350,7 +2359,7 @@ if (($chem =~ /_mam4/ or $chem =~ /_mam5/) and ($phys =~ /cam6/ or $phys =~ /cam
             $first = 0;
         }
     }
-    if ($chem eq 'trop_mam4' or $chem eq 'waccm_sc_mam4') {
+    if ($chem eq 'trop_mam4' or $chem eq 'waccm_sc_mam4'or $chem eq 'ghg_mam4') {
 	# SOA yields (used for the interactive emissions) have been calculated based on the VBS yields in CAM-chem.
 	# Duseong S. Jo, et al. to be submitted to GMD, 2023 -- see https://github.com/ESCOMP/CAM/pull/727 discussion for additional detail.
         my %soae_fctrs = ('BENZENE_an_srf_file' => '3.4192D0',
@@ -2393,8 +2402,8 @@ if (($chem =~ /_mam4/ or $chem =~ /_mam5/) and ($phys =~ /cam6/ or $phys =~ /cam
                 'num_a2_cv_ext_file' => 'num_a2',
         );
 
-    # aircraft emissions
-    if ($chem !~ /trop_mam/ and $chem !~ /waccm_sc/) {
+    # air craft emissions
+    if ($chem !~ /trop_mam/ and $chem !~ /ghg_mam/ and $chem !~ /waccm_sc/) {
         %species = (%species,
                     'bc_a4_ar_ext_file'  => 'bc_a4',
                     'num_a4_ar_ext_file' => 'num_a4',
@@ -2450,7 +2459,7 @@ if (($chem =~ /_mam4/ or $chem =~ /_mam5/) and ($phys =~ /cam6/ or $phys =~ /cam
     }
 
     # MEGAN emissions
-    if (($chem eq 'trop_mam4' or $chem eq 'waccm_sc_mam4') and !$aqua_mode and !$scam){
+    if (($chem eq 'trop_mam4' or $chem eq 'waccm_sc_mam4' or $chem eq 'ghg_mam4') and !$aqua_mode and !$scam){
 	my $val = "'SOAE = 0.9058*isoprene + 5.8638*(carene_3 + pinene_a + thujene_a + bornene +',"
                 . "' terpineol_4 + terpineol_a + terpinyl_ACT_a + myrtenal + sabinene + pinene_b + camphene +',"
                 . "' fenchene_a + limonene + phellandrene_a + terpinene_a + terpinene_g + terpinolene +',"
@@ -2601,10 +2610,10 @@ if (($chem =~ /_mam4/ or $chem =~ /_mam5/) and ($phys =~ /cam6/ or $phys =~ /cam
     }
 }
 
-if ($chem eq 'trop_mam4' or $chem eq 'waccm_sc_mam4') {
+if (($chem eq 'trop_mam4') or ($chem eq 'waccm_sc_mam4') or ($chem eq 'ghg_mam4')) {
 
     # Prescribed species
-    if ($chem eq 'waccm_sc_mam4') {
+    if (($chem eq 'waccm_sc_mam4')or($chem eq 'ghg_mam4')) {
         add_default($nl, 'tracer_cnst_specifier', 'val'=>"'O3','OH','NO3','HO2','HALONS'");
         add_default($nl, 'tracer_cnst_file');
         add_default($nl, 'tracer_cnst_datapath');
@@ -2731,7 +2740,7 @@ if ($waccmx){
     $maxzen = 116.;
 } elsif ($chem =~ "trop_strat" or $chem =~ "waccm_") {
     $maxzen = 97.01;
-} elsif ($chem =~ "trop_mam" or $chem =~ "trop_mozart") {
+} elsif ($chem =~ "trop_mam" or $chem =~ "trop_mozart" or $chem =~ "ghg_mam") {
     $maxzen = 88.85;
 }
 if ($maxzen>0.0) {
@@ -3145,6 +3154,11 @@ if (!$simple_phys) {
     } else {
         add_default($nl, 'use_hetfrz_classnuc', 'val'=>'.false.');
     }
+    if ($nl->get_value('use_hetfrz_classnuc') =~ m/$TRUE/io) {
+	# set default scaling factors if het frz is turned on
+        add_default($nl, 'hetfrz_bc_scalfac');
+        add_default($nl, 'hetfrz_dust_scalfac');
+    }
     add_default($nl, 'use_preexisting_ice');
     if ($chem =~ /_mam7/) {
         if ($nl->get_value('use_preexisting_ice') =~ m/$TRUE/io) {
@@ -3541,14 +3555,16 @@ if ( length($nl->get_value('soil_erod_file'))>0 ) {
     else {
         if ($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($nl, 'lght_no_prd_factor' );
         }
         else {
             add_default($nl, 'dust_emis_fact');
         }
     }
 }
+if (chem_has_species($cfg, 'NO')) {
+    # set scaling of lightning NOx production
+    add_default($nl, 'lght_no_prd_factor' );
+}
 
 # Seasalt emissions tuning factor
 if ($chem =~ /_mam(\d)/) {
@@ -3924,7 +3940,6 @@ if ($dyn =~ /se/) {
     my @vars = qw(
                   se_ftype
                   se_horz_num_threads
-                  se_lcp_moist
 		  se_large_Courant_incr
                   se_hypervis_subcycle
                   se_hypervis_subcycle_sponge
@@ -3952,7 +3967,6 @@ if ($dyn =~ /se/) {
 		  se_fvm_supercycling_jet
 		  se_kmin_jet
 		  se_kmax_jet
-		  se_phys_dyn_cp
                   se_molecular_diff
         );
 
@@ -4177,6 +4191,21 @@ add_default($nl, 'cam_snapshot_before_num');
 add_default($nl, 'cam_snapshot_after_num');
 check_snapshot_settings();
 
+if ($opts{'cmeps'}) {
+  # advertise the nature of ozone data passed to surface models
+  if ($rad_prog_ozone) {
+    add_default($nl, 'atm_ozone_frequency', 'val'=>'subdaily');
+  } else {
+    add_default($nl, 'atm_ozone_frequency', 'val'=>'multiday_average');
+  }
+  # for lightning flash freq to CTSM
+  if ($simple_phys or $aqua_mode) {
+    add_default($nl, 'atm_provides_lightning', 'val'=>'.false.');
+  } else {
+    add_default($nl, 'atm_provides_lightning', 'val'=>'.true.');
+  }
+}
+
 #-----------------------------------------------------------------------------------------------
 # Write output files
 
@@ -4193,16 +4222,8 @@ my %nl_group = ();
 foreach my $name (@nl_groups) { $nl_group{$name} = ''; }
 
 # Dry deposition, MEGAN VOC emis and ozone namelists
-@comp_groups = qw(drydep_inparm megan_emis_nl fire_emis_nl carma_inparm ndep_inparm ozone_coupling_nl);
+@comp_groups = qw(drydep_inparm megan_emis_nl fire_emis_nl carma_inparm ndep_inparm ozone_coupling_nl lightning_coupling_nl);
 
-# nature of ozone data passed to surface models -- only if cmeps (nuopc) coupling is used
-if ($opts{'cmeps'}) {
-  if ($rad_prog_ozone) {
-    add_default($nl, 'atm_ozone_frequency', 'val'=>'subdaily');
-  } else {
-    add_default($nl, 'atm_ozone_frequency', 'val'=>'multiday_average');
-  }
-}
 $outfile = "$opts{'dir'}/drv_flds_in";
 $nl->write($outfile, 'groups'=>\@comp_groups);
 if ($print>=1) {

diff --git a/bld/config_files/definition.xml b/bld/config_files/definition.xml
@@ -98,8 +98,8 @@ 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,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,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 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

diff --git a/bld/configure b/bld/configure
@@ -63,7 +63,7 @@ OPTIONS
                           test_tracers, test_tracers2].
                         Default: none.
     -chem <name>       Build CAM with specified prognostic chemistry package
-                       [ none | terminator | trop_mam3 | trop_mam4 | trop_mam7 | trop_mozart | trop_strat_mam4_ts2 |
+                       [ 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 |
@@ -140,10 +140,6 @@ OPTIONS
      -verbose [or -v]   Turn on verbose echoing of settings made by configure.
      -version           Echo the CVS tag name used to check out this CAM distribution.
 
-  Options for surface components used in standalone CAM mode:
-
-     -ocn <name>        Build CAM with ocean model [docn | dom | som | socn | aquaplanet | pop]. Default: aquaplanet
-
   Options for building CAM via standalone scripts:
 
      -cam_bld <dir>     Directory where CAM will be built.  This is where configure will write the