Merge pull request ESCOMP#1262 from fvitt/waccm7

cam6_4_077: WACCM7(x) compsets

Author: fvitt

bld/build-namelist

@@ -541,7 +541,7 @@ 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" or $chem =~ /geoschem/) and !($chem_rad_passive));
+my $rad_prog_ozone = (($chem =~ "mozart" or $chem =~ "waccm_ma" or $chem =~ "tsmlt" or $chem =~ "_t4ma" 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
@@ -881,7 +881,7 @@ my @aerosources = ();
 # and commas) that will be assigned to the namelist variable rad_climate.
 my $radval = "'A:Q:H2O'";
 
-if (($chem =~ /waccm_ma/ or $chem =~ /waccm_tsmlt/) and !$chem_rad_passive) {
+if (($chem =~ /waccm_ma/ or $chem =~ /waccm_tsmlt/ or $chem =~ /waccm_t4ma/) and !$chem_rad_passive) {
     $radval .= ",'A:O2:O2','A:CO2:CO2'";
 }
 elsif (($chem =~ /trop_strat/ or $chem =~ /geoschem/) and !$chem_rad_passive) {
@@ -911,7 +911,7 @@ if ($rad_prog_ozone) {
     die "ERROR: can not set ozone rad_climate specification\n";
 }
 
-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 ) {
+if ((($chem =~ /ghg_mam4/) or ($chem =~ /waccm_ma/) or ($chem =~ /waccm_t4ma/) or ($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 ) {
     $radval .= ",'A:N2O:N2O','A:CH4:CH4','A:CFC11:CFC11','A:CFC12:CFC12'";
@@ -2136,7 +2136,7 @@ if ($chem =~ /geoschem/) {
     }
 }
 
-if ($chem =~ /trop_mozart/ or $chem =~ /trop_strat/ or $chem =~ /waccm_tsmlt/) {
+if ($chem =~ /trop_mozart/ or $chem =~ /trop_strat/ or $chem =~ /waccm_tsmlt/ or $chem =~ /_t4ma/) {
 
     my $val;
 
@@ -2168,7 +2168,7 @@ if ($chem =~ /trop_mozart/ or $chem =~ /trop_strat/ or $chem =~ /waccm_tsmlt/) {
 
     my @files;
     # Datasets
-    if ($chem =~ /trop_strat/ or $chem =~ /waccm_tsmlt/) {
+    if ($chem =~ /trop_strat/ or $chem =~ /waccm_tsmlt/ or $chem =~ /waccm_t4ma/) {
        @files = ( 'flbc_file',
                   'xs_coef_file','xs_short_file','xs_long_file', 'rsf_file' );
     } else {
@@ -2351,7 +2351,7 @@ if ($phys =~ /cam6/ or $phys =~ /cam7/) {
     }
 
     # for mid-atmos gas-phase chemistry
-    if ($chem =~ /trop_strat/ or $chem =~ /_tsmlt/ or $chem =~ /waccm_ma/) {
+    if ($chem =~ /trop_strat/ or $chem =~ /_tsmlt/ or $chem =~ /waccm_ma/ or $chem =~ /waccm_t4ma/) {
         %species = (%species,
                     'NO_an_srf_file' => 'NO',
                     'NO_bb_srf_file' => 'NO',
@@ -2364,7 +2364,7 @@ if ($phys =~ /cam6/ or $phys =~ /cam7/) {
     }
 
      # for troposphere gas-phase chemistry
-    if ($chem =~ /trop_strat/ or $chem =~ /_tsmlt/) {
+    if ($chem =~ /trop_strat/ or $chem =~ /_tsmlt/ or $chem =~ /_t4ma/) {
         %species = (%species,
                     'BIGALK_an_srf_file' => 'BIGALK',
                     'BIGALK_bb_srf_file' => 'BIGALK',
@@ -2395,9 +2395,12 @@ if ($phys =~ /cam6/ or $phys =~ /cam7/) {
                     'ISOP_bb_srf_file' => 'ISOP',
                     'NH3_an_srf_file' => 'NH3',
                     'NH3_bb_srf_file' => 'NH3',
-                    'NH3_ot_srf_file' => 'NH3',
+                    'NH3_ot_srf_file' => 'NH3' ) ;
+        if (chem_has_species($cfg, 'E90')) {
+            %species = (%species,
                     'E90_srf_file' => 'E90' );
-        if ($chem !~ /_ts4/) {
+        }
+        if ($chem !~ /_ts4/ and $chem !~ /_t4ma/) {
 	    %species = (%species,
                     'BENZENE_an_srf_file' => 'BENZENE',
                     'BENZENE_bb_srf_file' => 'BENZENE',
@@ -2421,7 +2424,7 @@ if ($phys =~ /cam6/ or $phys =~ /cam7/) {
         if ($chem =~ /trop_strat_mam4_ts2/ or $chem =~ /trop_strat_mam5_ts2/) {
             %species = (%species,
                     'MTERP_bb_srf_file' => 'APIN') ;
-        } elsif ($chem =~ /_ts4/) {
+        } elsif ($chem =~ /_ts4/ or $chem =~ /_t4ma/) {
             %species = (%species,
                     'MTERP_bb_srf_file' => 'TERP') ;
 	} else {
@@ -2446,7 +2449,7 @@ if ($phys =~ /cam6/ or $phys =~ /cam7/) {
                     'IVOC_bb_srf_file' => 'IVOCbb',
                     'SVOC_an_srf_file' => 'SVOCff',
                     'SVOC_bb_srf_file' => 'SVOCbb' );
-        } elsif ($chem !~ /_ts4/) {
+        } elsif ($chem !~ /_ts4/ and $chem !~ /_t4ma/) {
             %species = (%species,
                     'IVOC_an_srf_file' => 'IVOC',
                     'IVOC_bb_srf_file' => 'IVOC',
@@ -2471,7 +2474,7 @@ if ($phys =~ /cam6/ or $phys =~ /cam7/) {
             $first = 0;
         }
     }
-    if ($chem eq 'trop_mam4' or $chem eq 'waccm_sc_mam4' or $chem eq 'ghg_mam4' or  $chem =~ /_ts4/) {
+    if ($chem eq 'trop_mam4' or $chem eq 'waccm_sc_mam4' or $chem eq 'ghg_mam4' or $chem =~ /_ts4/ or $chem =~ /_t4ma/) {
 	# SOA yields (used for the interactive emissions) have been calculated based on the VBS yields in CAM-chem.
 	# Duseong S. Jo, et al. to be submitted to GMD, 2023 -- see https://github.com/ESCOMP/CAM/pull/727 discussion for additional detail.
         my %soae_fctrs = ('BENZENE_an_srf_file' => '2.5592D0',
@@ -2686,7 +2689,7 @@ if ($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/) {
+    if ($chem =~ /trop_strat_mam5_ts4/ or $chem =~ /_t4ma/) {
         my $val = "'ISOP = isoprene',"
                 . "'TERP = carene_3 + pinene_a + thujene_a + bornene + terpineol_4 + terpineol_a + terpinyl_ACT_a +',"
                 . "' myrtenal + sabinene + pinene_b + camphene + fenchene_a + limonene + phellandrene_a + terpinene_a +',"
@@ -2757,7 +2760,7 @@ if ($phys =~ /cam6/ or $phys =~ /cam7/) {
         add_default($nl, 'megan_mapped_emisfctrs', 'val'=>'.false.');
     }
     if ($chem =~ /waccm_ma/) {
-        my $val = "'CH2O = formaldehyde', 'CO = carbon_monoxide'";
+        my $val = "'CH2O = formaldehyde','CO = carbon_monoxide'";
         add_default($nl, 'megan_specifier', 'val'=>$val);
         add_default($nl, 'megan_factors_file');
         add_default($nl, 'megan_mapped_emisfctrs', 'val'=>'.false.');
@@ -2891,12 +2894,13 @@ if ($chem eq 'trop_mam7') {
 }
 
 my $waccmx = $cfg->get('waccmx');
+my $model_top = $cfg->get('model_top');
 
 # set maximum solar zenith angle for photolysis
 my $maxzen = 0.0;
 if ($waccmx){
     $maxzen = 116.;
-} elsif ($chem =~ "trop_strat" or $chem =~ "waccm_") {
+} elsif ($chem =~ "trop_strat" or $chem =~ "waccm_" or $model_top eq "ht") {
     $maxzen = 97.01;
 } elsif ($chem =~ "trop_mam" or $chem =~ "trop_mozart" or $chem =~ "ghg_mam") {
     $maxzen = 88.85;
@@ -2907,17 +2911,17 @@ if ($maxzen>0.0) {
 
 # upper boundary specifier
 my $ubc_ver;
-if (($chem =~ /waccm_ma/ or $chem =~ /waccm_tsmlt/ ) and !$waccmx) {
+if (($chem =~ /waccm_ma/ or $chem =~ /waccm_tsmlt/ or $chem =~ /waccm_t4ma/) and !$waccmx) {
     $ubc_ver = 'waccmchem';
-} elsif ($chem =~ /waccm_sc/) {
+} elsif ($chem =~ /waccm_sc/ or ($model_top eq "ht" and $chem =~ /ghg_mam/)) {
     $ubc_ver = 'waccmsc';
 }
 if (defined $ubc_ver) {
     add_default($nl, 'ubc_specifier', 'ver'=>$ubc_ver);
 }
 
 # WACCM options.
-if ($chem =~ /waccm_ma/ or $chem =~ /waccm_tsmlt/) {
+if ($chem =~ /waccm_ma/ or $chem =~ /waccm_tsmlt/ or $chem =~ /waccm_t4ma/) {
 
     # Species with fixed lower boundary
     my $val = "'CCL4','CF2CLBR','CF3BR','CFC11','CFC113','CFC12','CH3BR','CH3CCL3','CH3CL','CH4','CO2'"

bld/config_files/definition.xml

@@ -46,10 +46,12 @@ 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">
+<entry id="model_top" valid_values="none,lt,mt,ht,xt" value="none">
 Model top specifier - set by compset definition
   lt: ~ 40 km top
   mt: ~ 80 km top
+  ht: ~ 140 km top
+  xt: ~ 500 km top
 </entry>
 <entry id="waccmx" valid_values="0,1" value="0">
 Option to turn on waccmx thermosphere/ionosphere extension: 0 => no, 1 => yes
@@ -101,8 +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_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_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_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>
 <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

@@ -89,7 +89,7 @@ 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 | pumas].
-     -model_top <name>  Specify the model_top option for cam7 [ lt | mt ].
+     -model_top <name>  Specify the model_top option for cam7 [ lt | mt | ht | xt ].
      -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>.
@@ -685,8 +685,8 @@ $waccm_phys = $cfg_ref->get('waccm_phys');
 
 if ($print>=2) { print "WACCM physics: $waccm_phys$eol"; }
 
-# WACCM includes 4 age of air tracers by default
-if ($chem_pkg =~ /waccm_ma/ or $chem_pkg =~ /waccm_tsmlt/) {
+# WACCM includes 3 age of air tracers by default
+if ($chem_pkg =~ /waccm_ma/ or $chem_pkg =~ /waccm_tsmlt/ or $chem_pkg =~ /waccm_t4ma/) {
     $cfg_ref->set('age_of_air_trcs', 1);
 }
 
@@ -1199,6 +1199,7 @@ $cfg_ref->set('model_top', $model_top);
 
 # user override
 if (defined $opts{'model_top'} and $opts{'model_top'} ne 'none') {
+    $model_top = lc($opts{'model_top'});
     if ($phys_pkg eq 'cam7') {
         $cfg_ref->set('model_top', $opts{'model_top'});
     } else {
@@ -1212,11 +1213,22 @@ if ($print>=2) { print "model_top: $model_top$eol"; }
 my $nlev = 0;
 
 # Defaults
-if ($waccmx) {
+if ($phys_pkg eq 'cam7') {
+    if ($model_top eq 'lt') {
+        $nlev = 58;
+    } elsif ($model_top eq 'mt') {
+        $nlev = 93;
+    } elsif ($model_top eq 'ht') {
+        $nlev = 135;
+    } elsif ($model_top eq 'xt') {
+        $nlev = 189;
+    } else {
+        $nlev = 32;  # this is for some old cam_dev tests
+    }
+}
+elsif ($waccmx) {
     if ($phys_pkg eq 'cam6') {
         $nlev = 130;
-    } elsif ($phys_pkg eq 'cam7') {
-        $nlev = 130;
     } else {
         $nlev = 126;
     }
@@ -1229,9 +1241,6 @@ elsif ($chem_pkg =~ /waccm_/) {
         $nlev = 70;
     }
 }
-elsif ($phys_pkg eq 'cam7') {
-    $nlev = 32;
-}
 elsif ($phys_pkg eq 'cam6') {
     $nlev = 32;
 }
@@ -1242,9 +1251,9 @@ elsif ($phys_pkg eq 'cam4') {
     $nlev = 26;
 }
 else {
-    # This will be used for Held-Suarez and other 'simple' physics
-    # We may change this to 32 once IC files are available.
-    $nlev = 30;
+    # Simple models use cam7-lt vertical grid.
+    # $nlev = 58; # - ERROR: No default value found for ncdata
+    $nlev = 30; # bit-for-bit baselines for now
 }
 
 # user override