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Merge tag 'ctsm5.2.028' into new_rawpftlai
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FATES history flushing update

This updates the way in which FATES history output is flushed during
model initialization
utilizing a new FATES-side subroutine, flush_all_hvars.  This update
also makes corrections
to a subset of FATES testmods as well as expands the FATES test list by
duplicating two
existing tests to run on different compilers for better coverage.  The
FATES submodule tag
has been updated to the latest scientific tag as well.
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@ekluzek
ekluzek committed Sep 5, 2024
2 parents 37d0e8f + b4199d8 commit ab90f43
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Showing 197 changed files with 999 additions and 643 deletions.
4 changes: 2 additions & 2 deletions .gitmodules
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@
[submodule "fates"]
path = src/fates
url = https://github.com/NGEET/fates
fxtag = sci.1.77.2_api.36.0.0
fxtag = sci.1.78.2_api.36.0.0
fxrequired = AlwaysRequired
# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
fxDONOTUSEurl = https://github.com/NCAR/fates-release
Expand Down 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
Expand Down
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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