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Merge pull request ESCOMP#2731 from ekluzek/merge-b4bdev-20240827
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Merge b4bdev 20240827
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@ekluzek
ekluzek authored Aug 29, 2024
2 parents 2b28850 + 4a62d0d commit 0999a32
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Showing 198 changed files with 936 additions and 620 deletions.
2 changes: 1 addition & 1 deletion .gitmodules
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Original file line number Diff line number Diff line change
Expand Up @@ -92,7 +92,7 @@ fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git
[submodule "cdeps"]
path = components/cdeps
url = https://github.com/ESCOMP/CDEPS.git
fxtag = cdeps1.0.34
fxtag = cdeps1.0.48
fxrequired = ToplevelRequired
# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
fxDONOTUSEurl = https://github.com/ESCOMP/CDEPS.git
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183 changes: 96 additions & 87 deletions bld/CLMBuildNamelist.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -159,16 +159,20 @@ OPTIONS
This turns on the namelist variable: use_crop
-csmdata "dir" Root directory of CESM input data.
Can also be set by using the CSMDATA environment variable.
-drydep Produce a drydep_inparm namelist that will go into the
-drydep Produce a drydep_inparm namelist for testing that will go into the
"drv_flds_in" file for the driver to pass dry-deposition to the atm.
This populates the namelist with valid drydep settings for testing.
Default: -no-drydep
Note: Can always add drydep fields to user_nl_clm even with --no-drydep
(Note: buildnml copies the file for use by the driver)
-dynamic_vegetation Toggle for dynamic vegetation model. (default is off)
(can ONLY be turned on when BGC type is 'bgc')
This turns on the namelist variable: use_cndv
(Deprecated, this will be removed)
-fire_emis Produce a fire_emis_nl namelist that will go into the
-fire_emis Produce a fire_emis_nl namelist for testing that will go into the
"drv_flds_in" file for the driver to pass fire emissions to the atm.
This populates the namelist with valid fire-emiss settings for testing.
Note: Can always add fire_emis fields to user_nl_clm even with --no-fire_emis
(Note: buildnml copies the file for use by the driver)
-glc_nec <name> Glacier number of elevation classes [0 | 3 | 5 | 10 | 36]
(default is 0) (standard option with land-ice model is 10)
Expand Down Expand Up @@ -204,9 +208,11 @@ OPTIONS
-namelist "namelist" Specify namelist settings directly on the commandline by supplying
a string containing FORTRAN namelist syntax, e.g.,
-namelist "&clm_inparm dt=1800 /"
-no-megan DO NOT PRODUCE a megan_emis_nl namelist that will go into the
-no-megan DO NOT PRODUCE a megan_emis_nl namelist for testing that will go into the
"drv_flds_in" file for the driver to pass VOCs to the atm.
MEGAN (Model of Emissions of Gases and Aerosols from Nature)
This removes setting default values for testing MEGAN fields
Note: Can always add megan fields to user_nl_clm even with --no-megan
(Note: buildnml copies the file for use by the driver)
-[no-]note Add note to output namelist [do NOT add note] about the
arguments to build-namelist.
Expand Down Expand Up @@ -1449,7 +1455,7 @@ sub setup_cmdl_vichydro {

sub process_namelist_commandline_namelist {
# Process the commandline '-namelist' arg.
my ($opts, $definition, $nl, $envxml_ref) = @_;
my ($opts, $definition, $nl, $envxml_ref, %settings) = @_;

if (defined $opts->{'namelist'}) {
# Parse commandline namelist
Expand All @@ -1470,6 +1476,32 @@ sub process_namelist_commandline_namelist {
}
}

sub process_namelist_infile {
my ($definition, $nl, $envxml_ref, $infile, %settings) = @_;

# Make sure a valid file was found
if ( -f "$infile" ) {
# Otherwise abort as a valid file doesn't exist
} else {
$log->fatal_error("input namelist file does NOT exist $infile.\n $@");
}
# Parse namelist input from the next file
my $nl_infile = Build::Namelist->new($infile);

# Validate input namelist -- trap exceptions
my $nl_infile_valid;
eval { $nl_infile_valid = $definition->validate($nl_infile); };
if ($@) {
$log->fatal_error("Invalid namelist variable in '-infile' $infile.\n $@");
}
# Go through all variables and expand any XML env settings in them
expand_xml_variables_in_namelist( $nl_infile_valid, $envxml_ref );

# Merge input values into namelist. Previously specified values have higher precedence
# and are not overwritten.
$nl->merge_nl($nl_infile_valid, %settings);
}

#-------------------------------------------------------------------------------

sub process_namelist_commandline_infile {
Expand All @@ -1479,27 +1511,7 @@ sub process_namelist_commandline_infile {
if (defined $opts->{'infile'}) {
my @infiles = split( /,/, $opts->{'infile'} );
foreach my $infile ( @infiles ) {
# Make sure a valid file was found
if ( -f "$infile" ) {
# Otherwise abort as a valid file doesn't exist
} else {
$log->fatal_error("input namelist file does NOT exist $infile.\n $@");
}
# Parse namelist input from the next file
my $nl_infile = Build::Namelist->new($infile);

# Validate input namelist -- trap exceptions
my $nl_infile_valid;
eval { $nl_infile_valid = $definition->validate($nl_infile); };
if ($@) {
$log->fatal_error("Invalid namelist variable in '-infile' $infile.\n $@");
}
# Go through all variables and expand any XML env settings in them
expand_xml_variables_in_namelist( $nl_infile_valid, $envxml_ref );

# Merge input values into namelist. Previously specified values have higher precedence
# and are not overwritten.
$nl->merge_nl($nl_infile_valid);
process_namelist_infile( $definition, $nl, $envxml_ref, $infile );
}
}
}
Expand Down Expand Up @@ -1750,25 +1762,29 @@ sub process_namelist_inline_logic {
##################################
setup_logic_lightning_streams($opts, $nl_flags, $definition, $defaults, $nl);

#################################
# namelist group: drydep_inparm #
#################################
setup_logic_dry_deposition($opts, $nl_flags, $definition, $defaults, $nl);

#################################
# namelist group: fire_emis_nl #
#################################
setup_logic_fire_emis($opts, $nl_flags, $definition, $defaults, $nl);

######################################
############################################################################################
# namelist options for dust emissions
######################################
# NOTE: This MUST be done before other drv_flds_in settings (megan, drydep, fire_emis etc.)
############################################################################################
setup_logic_dust_emis($opts, $nl_flags, $definition, $defaults, $nl, $envxml_ref);
setup_logic_prigent_roughness($opts, $nl_flags, $definition, $defaults, $nl);

#################################
# namelist group: megan_emis_nl #
#################################
#####################################
# namelist group: drydep_inparm #
# NOTE: After setup_logic_dust_emis #
#####################################
setup_logic_dry_deposition($opts, $nl_flags, $definition, $defaults, $nl);

#####################################
# namelist group: fire_emis_nl #
# NOTE: After setup_logic_dust_emis #
#####################################
setup_logic_fire_emis($opts, $nl_flags, $definition, $defaults, $nl);

#####################################
# namelist group: megan_emis_nl #
# NOTE: After setup_logic_dust_emis #
#####################################
setup_logic_megan($opts, $nl_flags, $definition, $defaults, $nl);

##################################
Expand Down Expand Up @@ -3994,17 +4010,18 @@ sub setup_logic_lightning_streams {
sub setup_logic_dry_deposition {
my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;

my @list = ( "drydep_list", "dep_data_file");
if ($opts->{'drydep'} ) {
if ( &value_is_true( $nl_flags->{'use_fates'}) && not &value_is_true( $nl_flags->{'use_fates_sp'}) ) {
$log->warning("DryDeposition can NOT be on when FATES is also on unless FATES-SP mode is on.\n" .
" Use the '--no-drydep' option when '-bgc fates' is activated");
}
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'drydep_list');
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'dep_data_file');
} else {
if ( defined($nl->get_value('drydep_list')) ) {
$log->fatal_error("drydep_list defined, but drydep option NOT set");
}
}
if ( &value_is_true( $nl_flags->{'use_fates'}) && not &value_is_true( $nl_flags->{'use_fates_sp'}) ) {
foreach my $var ( @list ) {
if ( defined($nl->get_value($var)) ) {
$log->warning("DryDeposition $var is being set and can NOT be on when FATES is also on unless FATES-SP mode is on.\n" .
" Use the '--no-drydep' option when '-bgc fates' is activated");
}
}
}
}

Expand All @@ -4013,20 +4030,20 @@ sub setup_logic_dry_deposition {
sub setup_logic_fire_emis {
my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;

my @list = ( "fire_emis_eleveated", "fire_emis_factors_file", "fire_emis_specifier");

if ($opts->{'fire_emis'} ) {
if ( &value_is_true( $nl_flags->{'use_fates'} ) ) {
$log->warning("Fire emission can NOT be on when FATES is also on.\n" .
" DON'T use the '-fire_emis' option when '-bgc fates' is activated");
}
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fire_emis_factors_file');
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fire_emis_specifier');
} else {
if ( defined($nl->get_value('fire_emis_elevated')) ||
defined($nl->get_value('fire_emis_factors_file')) ||
defined($nl->get_value('fire_emis_specifier')) ) {
$log->fatal_error("fire_emission setting defined: fire_emis_elevated, fire_emis_factors_file, or fire_emis_specifier, but fire_emis option NOT set");
}
}
foreach my $var ( @list ) {
if ( defined($nl->get_value($var)) ) {
if ( &value_is_true( $nl_flags->{'use_fates'} ) ) {
$log->warning("Fire emission option $var can NOT be on when FATES is also on.\n" .
" DON'T use the '--fire_emis' option when '--bgc fates' is activated");
}
}
}
}

#-------------------------------------------------------------------------------
Expand All @@ -4036,6 +4053,8 @@ sub setup_logic_dust_emis {
my ($opts, $nl_flags, $definition, $defaults, $nl, $envxml_ref) = @_;

# Only set dust emission settings -- if not connected to CAM
# Longer term plan is to remove this logic and have CTSM just set it and for CAM to use what CLM decides
# See: https://github.com/ESCOMP/CTSM/issues/2713
my $lnd_sets_dust = logical_to_fortran($envxml_ref->{'LND_SETS_DUST_EMIS_DRV_FLDS'});
if ( &value_is_true( $lnd_sets_dust)) {

Expand Down Expand Up @@ -4088,6 +4107,14 @@ sub setup_logic_dust_emis {
" connected to CAM as CAM should set them");
}
}
# Now process the CAM drv_flds_in to get the dust settings
# This requires that the CAM drv_flds_in namelist be created BEFORE CLM
# and that the path below NOT be changed. Hence, there's some fragility here
# to future changes.
my $infile = $opts->{'envxml_dir'} . "/Buildconf/camconf/drv_flds_in";
$log->verbose_message("Read in the drv_flds_in file generated by CAM's build-namelist");
# When merging the CAM namelist in -- die with an error if there's a conflict between CAM and CLM
process_namelist_infile( $definition, $nl, $envxml_ref, $infile, 'die_on_conflict'=>1 );
}
}

Expand All @@ -4108,17 +4135,15 @@ sub setup_logic_megan {
}

if ($nl_flags->{'megan'} ) {
if ( &value_is_true( $nl_flags->{'use_fates'} ) ) {
$log->warning("MEGAN can NOT be on when FATES is also on.\n" .
" Use the '-no-megan' option when '-bgc fates' is activated");
}
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'megan_specifier');
check_megan_spec( $opts, $nl, $definition );
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'megan_factors_file');
} else {
if ( defined($nl->get_value('megan_specifier')) ||
}
if ( defined($nl->get_value('megan_specifier')) ||
defined($nl->get_value('megan_factors_file')) ) {
$log->fatal_error("megan_specifier or megan_factors_file defined, but megan option NOT set");
check_megan_spec( $opts, $nl, $definition );
if ( &value_is_true( $nl_flags->{'use_fates'} ) ) {
$log->warning("MEGAN can NOT be on when FATES is also on.\n" .
" Use the '-no-megan' option when '-bgc fates' is activated");
}
}
}
Expand Down Expand Up @@ -5645,27 +5670,11 @@ sub check_megan_spec {

my $megan_spec = $nl->get_value('megan_specifier');
my @megan_spec_list = split( /\s*,\s*/, $megan_spec );
foreach $megan_spec ( @megan_spec_list ) {
if ( $megan_spec =~ /^['"]+[A-Za-z0-9]+\s*\=\s*([\sA-Za-z0-9+_-]+)["']+$/ ) {
my $megan_list = $1;
my @megan_cmpds = split( /\s*\+\s*/, $megan_list );
my $var = "megan_cmpds";
my $warn = 0;
foreach my $megan_cmpd ( @megan_cmpds ) {
if ( ! $definition->is_valid_value( $var, $megan_cmpd, 'noquotes'=>1 ) ) {
$log->warning("megan_compound $megan_cmpd NOT found in list" );
$warn++;
}
}
if ( $warn > 0 ) {
my @valid_values = $definition->get_valid_values( $var, 'noquotes'=>1 );
$log->warning("list of megan compounds includes:\n" .
"@valid_values\n" .
"Does your megan_factors_file include more compounds?\n" .
"If NOT your simulation will fail." );
}
} else {
$log->fatal_error("Bad format for megan_specifier = $megan_spec");
foreach my $spec ( @megan_spec_list ) {
$megan_spec = remove_leading_and_trailing_quotes($spec);
# Do simple validation of the expressions to just check for valid characters
if ( $megan_spec !~ /^([\s=A-Za-z0-9_\+\.\*\(\)-]+)$/ ) {
$log->warning("Bad format for megan_specifier = $megan_spec");
}
}
}
Expand Down
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