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Merge tag 'cam6_3_150' into cam_zm_clean_up
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Merge pull request ESCOMP#943 from megandevlan/gustMods
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@cacraigucar
cacraigucar committed Mar 6, 2024
2 parents bd1f004 + f9b91b9 commit 5bcf7aa
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Showing 83 changed files with 15,997 additions and 1,753 deletions.
3 changes: 3 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,11 @@ src/physics/carma/base
src/physics/clubb
src/physics/cosp2/src
src/physics/silhs
src/chemistry/geoschem/geoschem_src
src/physics/pumas
src/physics/pumas-frozen
src/physics/rrtmgp/data
src/physics/rrtmgp/ext
src/dynamics/fv3/atmos_cubed_sphere
libraries/FMS
libraries/mct
Expand Down
12 changes: 6 additions & 6 deletions Externals.cfg
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
[ccs_config]
tag = ccs_config_cesm0.0.82
tag = ccs_config_cesm0.0.85
protocol = git
repo_url = https://github.com/ESMCI/ccs_config_cesm
local_path = ccs_config
Expand All @@ -21,14 +21,14 @@ externals = Externals.cfg
required = True

[cmeps]
tag = cmeps0.14.43
tag = cmeps0.14.49
protocol = git
repo_url = https://github.com/ESCOMP/CMEPS.git
local_path = components/cmeps
required = True

[cdeps]
tag = cdeps1.0.24
tag = cdeps1.0.26
protocol = git
repo_url = https://github.com/ESCOMP/CDEPS.git
local_path = components/cdeps
Expand All @@ -43,7 +43,7 @@ local_path = components/cpl7
required = True

[share]
tag = share1.0.17
tag = share1.0.18
protocol = git
repo_url = https://github.com/ESCOMP/CESM_share
local_path = share
Expand All @@ -64,7 +64,7 @@ local_path = libraries/parallelio
required = True

[cime]
tag = cime6.0.175
tag = cime6.0.217_httpsbranch02
protocol = git
repo_url = https://github.com/ESMCI/cime
local_path = cime
Expand All @@ -79,7 +79,7 @@ externals = Externals_CISM.cfg
required = True

[clm]
tag = ctsm5.1.dev142
tag = ctsm5.1.dev145
protocol = git
repo_url = https://github.com/ESCOMP/CTSM
local_path = components/clm
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21 changes: 21 additions & 0 deletions Externals_CAM.cfg
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Original file line number Diff line number Diff line change
Expand Up @@ -71,6 +71,13 @@ sparse = ../.mpas_sparse_checkout
hash = b8c33daa
required = True

[geoschem]
local_path = src/chemistry/geoschem/geoschem_src
protocol = git
repo_url = https://github.com/geoschem/geos-chem.git
tag = 14.1.2
required = True

[hemco]
local_path = src/hemco
tag = hemco-cesm1_2_1_hemco3_6_3_cesm
Expand All @@ -79,5 +86,19 @@ repo_url = https://github.com/ESCOMP/HEMCO_CESM.git
required = True
externals = Externals_HCO.cfg

[rte-rrtmgp]
local_path = src/physics/rrtmgp/ext
protocol = git
repo_url = https://github.com/earth-system-radiation/rte-rrtmgp.git
tag = v1.7
required = True

[rrtmgp-data]
local_path = src/physics/rrtmgp/data
protocol = git
repo_url = https://github.com/earth-system-radiation/rrtmgp-data.git
tag = v1.8
required = True

[externals_description]
schema_version = 1.0.0
159 changes: 138 additions & 21 deletions bld/build-namelist
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Original file line number Diff line number Diff line change
Expand Up @@ -540,7 +540,7 @@ 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 $chem =~ "trop_strat") and !($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));

# Check for eruptive volcano emissions. These will be radiatively active by default, but
# only if using BAM and the camrt radiation package
Expand Down Expand Up @@ -576,12 +576,13 @@ if ( ($chem ne 'none') or ( $prog_species ) ){

my ( $gas_wetdep_list, $aer_wetdep_list, $aer_sol_facti, $aer_sol_factb, $aer_scav_coef,
$aer_drydep_list, $gas_drydep_list ) =
set_dep_lists( $cfgdir, $chem_proc_src, $chem_src_dir, $nl, $print );
set_dep_lists( $chem, $cfgdir, $chem_proc_src, $chem_src_dir, $nl, $print );

if (length($gas_wetdep_list)>2){
add_default($nl, 'gas_wetdep_method' );
add_default($nl, 'gas_wetdep_list', 'val'=>$gas_wetdep_list );
}

if (length($aer_wetdep_list)>2){
# determine if prescribed aerosols are not needed ...
if ($aer_wetdep_list =~ /so4/i &&
Expand Down Expand Up @@ -693,6 +694,23 @@ my $rad_pkg = $cfg->get('rad');
if ($rad_pkg eq 'camrt') {
add_default($nl, 'absems_data');
}
elsif ($rad_pkg =~ m/rrtmgp/) {
# Dataset for gas optics are checked out of an external repo into
# the source code directory. The paths to this data are relative
# to the root directory of the cam component.
my $cam_dir = $cfg->get('cam_dir');

add_default($nl, 'rrtmgp_coefs_lw_file');
my $rel_path = $nl->get_value('rrtmgp_coefs_lw_file');
my $abs_path = quote_string(set_abs_filepath($rel_path, $cam_dir));
# Overwrite the relative pathname with the absolute pathname in the namelist object
$nl->set_variable_value('radiation_nl', 'rrtmgp_coefs_lw_file', $abs_path);

add_default($nl, 'rrtmgp_coefs_sw_file');
$rel_path = $nl->get_value('rrtmgp_coefs_sw_file');
my $abs_path = quote_string(set_abs_filepath($rel_path, $cam_dir));
$nl->set_variable_value('radiation_nl', 'rrtmgp_coefs_sw_file', $abs_path);
}

# Solar irradiance

Expand All @@ -704,15 +722,20 @@ if (defined $nl->get_value('solar_const') and

}

if ($rad_pkg eq 'rrtmg' or $chem =~ /waccm/) {
if ($rad_pkg =~ /rrtmg/ or $chem =~ /waccm/) {

if (defined $nl->get_value('solar_const')) {
die "$ProgName - ERROR: Specifying solar_const with RRTMG or WACCM is not allowed.\n"
die "$ProgName - ERROR: Specifying solar_const with RRTMG/RRTMGP or WACCM is not allowed.\n"
}

# use solar data file as the default for rrtmg and waccm_ma
add_default($nl, 'solar_irrad_data_file');
add_default($nl, 'solar_htng_spctrl_scl', 'val'=>'.true.');

# This option only used by camrt and rrtmg radiation schemes.
# The solar spectral scaling is done internal to RRTMGP code.
if ($rad_pkg ne 'rrtmgp') {
add_default($nl, 'solar_htng_spctrl_scl', 'val'=>'.true.');
}

}
elsif (!$simple_phys) {
Expand Down Expand Up @@ -842,7 +865,6 @@ if ($chem_rad_passive or $aqua_mode) {

# The aerosol optics depend on which radiative transfer model is used due to differing
# wavelength bands used.
my $rrtmg = $rad_pkg eq 'rrtmg' ? 1 : 0;

# @aero_names contains the names of the entities (bulk aerosols and modes)
# that are externally mixed in aerosol optics calculation. These entities are all
Expand All @@ -862,7 +884,7 @@ my $radval = "'A:Q:H2O'";
if (($chem =~ /waccm_ma/ or $chem =~ /waccm_tsmlt/) and !$chem_rad_passive) {
$radval .= ",'A:O2:O2','A:CO2:CO2'";
}
elsif ($chem =~ /trop_strat/ 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 !$co2_cycle_rad_passive) or ($chem =~ /ghg_mam4/)) {
Expand Down Expand Up @@ -897,6 +919,8 @@ if ((($chem =~ /ghg_mam4/) or ($chem =~ /waccm_ma/) or ($chem =~ /waccm_sc_mam/)
$radval .= ",'A:N2O:N2O','A:CH4:CH4','A:CFC11:CFC11','A:CFC12:CFC12'";
} elsif ($prog_ghg1 and !$prog_ghg2 and !$chem_rad_passive ) {
$radval .= ",'A:N2O:N2O','A:CH4:CH4','N:CFC11:CFC11','N:CFC12:CFC12'";
} elsif ($chem =~ /geoschem/) {
$radval .= ",'A:N2O:N2O','A:CH4:CH4','A:CFC11:CFC11','A:CFC12:CFC12'";
} else {
$radval .= ",'N:N2O:N2O','N:CH4:CH4','N:CFC11:CFC11','N:CFC12:CFC12'";
}
Expand Down Expand Up @@ -1118,15 +1142,15 @@ if ($aer_model eq 'mam' ) {
}

if ($rad_prog_sslt) {
if ($rrtmg) {
if ($rad_pkg =~ /rrtmg/) {
push(@aero_names, "SSLT01", "SSLT02", "SSLT03", "SSLT04");
push(@aerosources, "A:", "A:", "A:", "A:" );
} else {
push(@aero_names, "SSLTA", "SSLTC");
push(@aerosources, "N:", "N:");
}
} elsif ($moz_aero_data =~ /$TRUE/io ) {
if ($rrtmg) {
if ($rad_pkg =~ /rrtmg/) {
push(@aero_names, "sslt1", "sslt2", "sslt3", "sslt4");
push(@aerosources, "N:", "N:", "N:", "N:" );
} else {
Expand Down Expand Up @@ -1221,7 +1245,7 @@ if ($carma eq 'bc_strat') {
}
}

if ($rrtmg) {
if ($rad_pkg eq 'rrtmg') {

# CARMA Microphysics - RRTMG Only
#
Expand Down Expand Up @@ -1641,11 +1665,25 @@ if ($rad_pkg ne 'none') {
}

# Cloud optics
if ($rrtmg) {
if ($rad_pkg =~ m/rrtmg/) { # matches both rrtmg and rrtmgp
add_default($nl, 'liqcldoptics');
add_default($nl, 'icecldoptics');
add_default($nl, 'liqopticsfile');
add_default($nl, 'iceopticsfile');

# rrtmgp only implemented with mitchell and gammadist cloud optics
if ($rad_pkg =~ m/rrtmgp/) {
my $liqcldoptics = $nl->get_value('liqcldoptics');
if ($liqcldoptics !~ m/gammadist/) {
die "$ProgName - ERROR: RRTMGP only implemented with gammadist liquid cloud optics\n" .
"liqcldoptics = $liqcldoptics\n";
}
my $icecldoptics = $nl->get_value('icecldoptics');
if ($icecldoptics !~ m/mitchell/) {
die "$ProgName - ERROR: RRTMGP only implemented with mitchell ice cloud optics\n" .
"icecldoptics = $icecldoptics\n";
}
}
}

# Volcanic Aerosol Mass climatology dataset
Expand Down Expand Up @@ -2018,6 +2056,34 @@ if (($chem =~ /trop_mozart/ or $chem =~ /trop_strat/ or $chem =~ /waccm_tsmlt/)
}
}

if ($chem =~ /geoschem/) {

my $val;

# Species with fixed lower boundary
$val = "'CCL4','CH4','N2O','CO2','CFC11','CFC12','CH3BR','CH3CCL3','CH3CL'"
.",'HCFC22','CFC114','CFC115','HCFC141B','HCFC142B','CH2BR2','CHBR3','H2402'";

if ($chem_has_ocs) {
$val .= ",'OCS'";
}
if (chem_has_species($cfg, 'SF6')) {
$val .= ",'SF6'";
}
add_default($nl, 'flbc_list', 'val'=>$val);
unless (defined $nl->get_value('flbc_type')) {
add_default($nl, 'flbc_type', 'val'=>'CYCLICAL');
add_default($nl, 'flbc_cycle_yr', 'val'=>'2000');
}

my @files;
# Datasets
@files = ( 'soil_erod_file', 'flbc_file' );
foreach my $file (@files) {
add_default($nl, $file);
}
}

if ($chem =~ /trop_mozart/ or $chem =~ /trop_strat/ or $chem =~ /waccm_tsmlt/) {

my $val;
Expand Down Expand Up @@ -2364,10 +2430,12 @@ if (($chem =~ /_mam4/ or $chem =~ /_mam5/) and ($phys =~ /cam6/ or $phys =~ /cam
}
}
}
add_default($nl, 'srf_emis_specifier', 'val'=>$val);
unless (defined $nl->get_value('srf_emis_type')) {
add_default($nl, 'srf_emis_type', 'val'=>'CYCLICAL');
add_default($nl, 'srf_emis_cycle_yr', 'val'=>2000);
if ($chem !~ /geoschem/) {
add_default($nl, 'srf_emis_specifier', 'val'=>$val);
unless (defined $nl->get_value('srf_emis_type')) {
add_default($nl, 'srf_emis_type', 'val'=>'CYCLICAL');
add_default($nl, 'srf_emis_cycle_yr', 'val'=>2000);
}
}

# Vertical emission datasets:
Expand Down Expand Up @@ -2433,10 +2501,12 @@ if (($chem =~ /_mam4/ or $chem =~ /_mam5/) and ($phys =~ /cam6/ or $phys =~ /cam
$first = 0;
}
}
add_default($nl, 'ext_frc_specifier', 'val'=>$val);
unless (defined $nl->get_value('ext_frc_type')) {
add_default($nl, 'ext_frc_type', 'val'=>"'CYCLICAL'");
add_default($nl, 'ext_frc_cycle_yr', 'val'=>2000);
if ($chem !~ /geoschem/) {
add_default($nl, 'ext_frc_specifier', 'val'=>$val);
unless (defined $nl->get_value('ext_frc_type')) {
add_default($nl, 'ext_frc_type', 'val'=>"'CYCLICAL'");
add_default($nl, 'ext_frc_cycle_yr', 'val'=>2000);
}
}

# MEGAN emissions
Expand Down Expand Up @@ -2482,6 +2552,30 @@ if (($chem =~ /_mam4/ or $chem =~ /_mam5/) and ($phys =~ /cam6/ or $phys =~ /cam
add_default($nl, 'megan_factors_file');
add_default($nl, 'megan_mapped_emisfctrs', 'val'=>'.false.');
}
if ($chem =~ /geoschem/) {
my $val = "'ISOP = isoprene',"
. "'MOH = methanol',"
. "'EOH = ethanol',"
. "'CH2O = formaldehyde',"
. "'ALD2 = acetaldehyde',"
. "'ACTA = acetic_acid',"
. "'ACET = acetone',"
. "'HCOOH = formic_acid',"
. "'HCN = hydrogen_cyanide',"
. "'CO = carbon_monoxide',"
. "'C2H6 = ethane',"
. "'C2H4 = ethene',"
. "'C3H8 = propane',"
. "'ALK4 = pentane + hexane + heptane + tricyclene',"
. "'PRPE = propene + butene',"
. "'TOLU = toluene',"
. "'LIMO = limonene',"
. "'MTPA = pinene_a + pinene_b + sabinene + carene_3',"
. "'MTPO = terpinene_g + terpinene_a + terpinolene + myrcene + ocimene_al + ocimene_t_b + ocimene_c_b + thujene_a + 2met_styrene + cymene_p + cymene_o + bornene + fenchene_a + camphene + phellandrene_a + phellandrene_b'";
add_default($nl, 'megan_specifier', 'val'=>$val);
add_default($nl, 'megan_factors_file');
add_default($nl, 'megan_mapped_emisfctrs', 'val'=>'.false.');
}
if ($chem =~ /trop_strat_mam4_vbs/ or $chem =~ /trop_strat_mam5_vbs/) {
my $val = "'ISOP = isoprene',"
. "'MTERP = carene_3 + pinene_a + thujene_a + bornene + terpineol_4 + terpineol_a + terpinyl_ACT_a "
Expand Down Expand Up @@ -2897,6 +2991,29 @@ if ($nl->get_value('use_hemco') =~ m/$TRUE/io) {
# ignored at runtime when HEMCO is used.
$nl->delete_variable('chem_inparm', 'ext_frc_specifier');
$nl->delete_variable('chem_inparm', 'srf_emis_specifier');

if ($chem =~ /geoschem/) {

# For now, HEMCO config and diagnostic configuration files are always used from
# the case directory. Exit if user has specified other paths in the user namelist
# because it will not work.
if ($nl->get_value('hemco_config_file') ne "'" . $inputdata_rootdir . "/HEMCO_Config.rc'") {
die "CAM Namelist ERROR: When running with GEOS-Chem chemistry, hemco_config_file\n".
"must not be manually set in the namelist. Instead, modify (or symlink from) the HEMCO_Config.rc\n".
"in the case directory, which will be copied to the run directory when submitting.\n".
"Then remove the hemco_config_file option from the user namelist.\n";
}

if ($nl->get_value('hemco_diagn_file') ne "'" . $inputdata_rootdir . "/HEMCO_Diagn.rc'") {
die "CAM Namelist ERROR: When running with GEOS-Chem chemistry, hemco_diagn_file\n".
"must not be manually set in the namelist. Instead, modify (or symlink from) the HEMCO_Diagn.rc\n".
"in the case directory, which will be copied to the run directory when submitting.\n".
"Then remove the hemco_diagn_file option from the user namelist.\n";
}

$nl->set_variable_value('hemco_nl', 'hemco_config_file', "'HEMCO_Config.rc'");
$nl->set_variable_value('hemco_nl', 'hemco_diagn_file', "'HEMCO_Diagn.rc'");
}
}

# Physics options
Expand Down Expand Up @@ -3025,7 +3142,7 @@ if (!$simple_phys) {
}

# tropopause level used in gas-phase / aerosol processes
if (($chem ne 'none') and ($chem ne 'terminator')) {
if (($chem ne 'none') and ($chem ne 'terminator') and !($chem =~ /geoschem/)) {
add_default($nl, 'chem_use_chemtrop');
}

Expand Down Expand Up @@ -3562,7 +3679,7 @@ if ( length($nl->get_value('soil_erod_file'))>0 ) {
add_default($nl, 'dust_emis_fact', 'tms'=>'1');
}
else {
if ($chem =~ /trop_strat/ or $chem =~ /waccm_ma/ or $chem =~ /waccm_tsmlt/ or $chem =~ /trop_mozart/) {
if ($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');
}
else {
Expand Down
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