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build-namelist
executable file
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build-namelist
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#!/usr/bin/env perl
#-----------------------------------------------------------------------------------------------
#
# build-namelist
#
# This script builds the namelists for the MPASO configuration of E3SM
#
# build-namelist uses a config_cache.xml file that current contains the ocean grid information.
# build-namelist reads this file to obtain information it needs to provide
# default values that are consistent with the MPASO XML file. For example, the grid resolution
# is obtained from the cache file and used to determine appropriate defaults for namelist input
# that is resolution dependent.
#
# The simplest use of build-namelist is to execute it from the build directory where configure
# was run. By default it will use the config_cache.xml file that was written by configure to
# determine the build time properties of the executable, and will write the files that contain
# the output namelists in that same directory.
#
#
# Date Contributor Modification
# -------------------------------------------------------------------------------------------
# 2015-01-28 djacobsen Original version
#--------------------------------------------------------------------------------------------
use strict;
use Cwd qw(getcwd abs_path);
use English;
use Getopt::Long;
use IO::File;
#-----------------------------------------------------------------------------------------------
sub usage {
die <<EOF;
SYNOPSIS
build-namelist [options]
OPTIONS
-infile "filepath" Specify a file containing namelists to read values from.
-namelist "namelist" Specify namelist settings directly on the commandline by supplying
a string containing FORTRAN namelist syntax, e.g.,
-namelist "&mpaso_nml dt=1800 /"
-help [or -h] Print usage to STDOUT.
-test Enable checking that input datasets exist on local filesystem.
-verbose Turn on verbose echoing of informational messages.
-caseroot CASEROOT directory variable
-casebuild CASEBUILD directory variable
-cimeroot CIMEROOT directory variable
-ocn_grid OCN_GRID variable
-ocn_forcing variable for defining if the ocn model is forced with an active atm
or using CORE forcing.
Options are: active_atm, datm_forced, datm_forced_restoring
-ocn_iceberg variable for defining if the ocn model is expecting coupling fields
for icebergs from the seaice model
Options are: false, true
-ocn_ismf variable for defining how the ocn model will handle ice shelf melt
fluxes
Options are: none, data, internal, coupled
-decomp_prefix decomp_prefix variable
-date_stamp date_stamp variable
-cfg_grid Directory containing MPASO configuration scripts.
If not defined, location is set as \$ProgDir or \$cwd
(Needed to run build-namelist from SourceMods dir)
-inst_string inst_string variable
-ocn_bgc ocean BGC configuration
-ocn_wave ocean wave coupling flag
-ocn_co2_type how atm co2 is set within MPASO
-atm_co2_const_val value of atm co2 if ocn_co2_type = constant
-ice_bgc check for coupling with sea ice BGC
-ntasks_ocn NTASKS_OCN for this case
-ninst_ocn NINST_OCN for this case
NOTE: The precedence for setting the values of namelist variables is (highest to lowest):
1. namelist values set by specific command-line options, i.e. (none right now)
2. values set on the command-line using the -namelist option,
3. values read from the file specified by -infile,
4. values from the namelist defaults file - or values specifically set in build-namelist
EOF
}
#-----------------------------------------------------------------------------------------------
# Set the directory that contains the MPASO configuration scripts. If the command was
# issued using a relative or absolute path, that path is in $ProgDir. Otherwise assume the
# command was issued from the current working directory.
(my $ProgName = $0) =~ s!(.*)/!!; # name of this script
my $ProgDir = $1; # name of directory containing this script -- may be a
# relative or absolute path, or null if the script is in
# the user's PATH
my $cwd = getcwd(); # current working directory
my $cfgdir; # absolute pathname of directory that contains this script
if ($ProgDir) {
$cfgdir = abs_path($ProgDir);
} else {
$cfgdir = $cwd;
}
#-----------------------------------------------------------------------------------------------
# Process command-line options.
my %opts = ( help => 0,
test => 0,
verbose => 0,
preview => 0,
caseroot => undef,
casebuild => undef,
cimeroot => undef,
inst_string => undef,
ocn_grid => undef,
ocn_forcing => undef,
ocn_iceberg => undef,
ocn_ismf => undef,
decomp_prefix => undef,
date_stamp => undef,
ocn_bgc => undef,
ocn_wave => undef,
ocn_co2_type => undef,
atm_co2_const_val => undef,
ice_bgc => undef,
cfg_dir => $cfgdir,
ntasks_ocn => 0,
ninst_ocn => 0,
);
GetOptions(
"h|help" => \$opts{'help'},
"infile=s" => \$opts{'infile'},
"namelist=s" => \$opts{'namelist'},
"v|verbose" => \$opts{'verbose'},
"caseroot=s" => \$opts{'caseroot'},
"casebuild=s" => \$opts{'casebuild'},
"cimeroot=s" => \$opts{'cimeroot'},
"inst_string=s" => \$opts{'inst_string'},
"ocn_grid=s" => \$opts{'ocn_grid'},
"ocn_forcing=s" => \$opts{'ocn_forcing'},
"ocn_iceberg=s" => \$opts{'ocn_iceberg'},
"ocn_ismf=s" => \$opts{'ocn_ismf'},
"decomp_prefix=s" => \$opts{'decomp_prefix'},
"date_stamp=s" => \$opts{'date_stamp'},
"ocn_bgc=s" => \$opts{'ocn_bgc'},
"ocn_wave=s" => \$opts{'ocn_wave'},
"ocn_co2_type=s" => \$opts{'ocn_co2_type'},
"atm_co2_const_val=s" => \$opts{'atm_co2_const_val'},
"ice_bgc=s" => \$opts{'ice_bgc'},
"cfg_dir=s" => \$opts{'cfg_dir'},
"ntasks_ocn=i" => \$opts{'ntasks_ocn'},
"ninst_ocn=i" => \$opts{'ninst_ocn'},
"preview" => \$opts{'preview'},
) or usage();
# Give usage message.
usage() if $opts{'help'};
# Check for unparsed arguments
if (@ARGV) {
print "ERROR: unrecognized arguments: @ARGV\n";
usage();
}
# Define print levels:
# 0 - only issue fatal error messages
# 1 - only informs what files are created (currently not used)
# 2 - verbose
my $print = 0;
my $preview = 0;
if ($opts{'verbose'}) { $print = 2; }
if ($opts{'preview'}) { $preview = 1; }
my $eol = "\n";
if ($print>=2) { print "Setting MPASO configuration script directory to $cfgdir$eol"; }
my $CASEROOT = $opts{'caseroot'};
my $CASEBUILD = $opts{'casebuild'};
my $CIMEROOT = $opts{'cimeroot'};
my $inst_string = $opts{'inst_string'};
my $OCN_GRID = $opts{'ocn_grid'};
my $OCN_FORCING = $opts{'ocn_forcing'};
my $OCN_ICEBERG = $opts{'ocn_iceberg'};
my $OCN_ISMF = $opts{'ocn_ismf'};
my $decomp_prefix = $opts{'decomp_prefix'};
my $date_stamp = $opts{'date_stamp'};
my $ocn_bgc = $opts{'ocn_bgc'};
my $ocn_wave = $opts{'ocn_wave'};
my $ocn_co2_type = $opts{'ocn_co2_type'};
my $atm_co2_const_val = $opts{'atm_co2_const_val'};
my $ice_bgc = $opts{'ice_bgc'};
my $NINST_OCN = $opts{'ninst_ocn'};
my $NTASKS_OCN = $opts{'ntasks_ocn'};
$cfgdir = $opts{'cfg_dir'};
my $CIMEROOT;
if ( defined $opts{'cimeroot'} ) {
$CIMEROOT = $opts{'cimeroot'};
}
# Validate some of the commandline option values.
validate_options("commandline", \%opts);
# build config_cache.xml file (needed below)
my $config_cache = "${CASEBUILD}/mpasoconf/config_cache.xml";
my $fh = new IO::File;
$fh->open(">$config_cache") or die "** can't open file: $config_cache\n";
print $fh <<"EOF";
<?xml version="1.0"?>
<config_definition>
<entry id="ocn_grid" value="$OCN_GRID">
<entry id="ocn_forcing" value="$OCN_FORCING">
<entry id="decomp_prefix" value="$decomp_prefix">
<entry id="date_stamp" value="$date_stamp">
</config_definition>
EOF
$fh->close;
if ($print>=2) { print "Wrote file $config_cache $eol"; }
(-f "config_cache.xml") or die <<"EOF";
** $ProgName - Cannot find configuration cache file: config_cache.xml\" **
EOF
#-----------------------------------------------------------------------------------------------
# Make sure we can find required perl modules, definition, and defaults files.
# Look for them under the directory that contains the configure script.
# The root directory for the input data files must be specified.
my $srcroot = abs_path("$CIMEROOT/../");
if (! -d "$srcroot") {
die "** Invalid srcroot directory: $srcroot ** ";
}
print "SRCROOT IS: $srcroot\n";
my $perl5lib = "$CIMEROOT/utils/perl5lib";
if (! -d "$perl5lib") {
die "** Invalid perl5lib root directory: $perl5lib ** ";
}
# The Build::Config module provides utilities to access the configuration information
# in the config_cache.xml file
(-f "$perl5lib/Build/Config.pm") or die <<"EOF";
** $ProgName - Cannot find perl module \"Build/Config.pm\" in directory \"$perl5lib\" **
EOF
# The Build::NamelistDefinition module provides utilities to validate that the output
# namelists are consistent with the namelist definition file
(-f "$perl5lib/Build/NamelistDefinition.pm") or die <<"EOF";
** $ProgName - Cannot find perl module \"Build/NamelistDefinition.pm\" in directory \"$perl5lib\" **
EOF
# The Build::NamelistDefaults module provides a utility to obtain default values of namelist
# variables based on finding a best fit with the attributes specified in the defaults file.
(-f "$perl5lib/Build/NamelistDefaults.pm") or die <<"EOF";
** $ProgName - Cannot find perl module \"Build/NamelistDefaults.pm\" in directory \"$perl5lib\" **
EOF
# The Build::Namelist module provides utilities to parse input namelists, to query and modify
# namelists, and to write output namelists.
(-f "$perl5lib/Build/Namelist.pm") or die <<"EOF";
** $ProgName - Cannot find perl module \"Build/Namelist.pm\" in directory \"$perl5lib\" **
EOF
# The namelist definition file contains entries for all namelist variables that
# can be output by build-namelist. The version of the file that is associate with a
# fixed MPASO tag is $cfgdir/namelist_files/namelist_definition.xml. To aid developers
# who make use of the SourceMods/src.mpaso directory - we allow the definition file
# to come from that directory
my $nl_definition_file;
if (-f "${CASEROOT}/SourceMods/src.mpaso/namelist_definition_mpaso.xml") {
$nl_definition_file = "${CASEROOT}/SourceMods/src.mpaso/namelist_definition_mpaso.xml";
}
if (! defined $nl_definition_file) {
# default location of namelist definition file
$nl_definition_file = "$cfgdir/namelist_files/namelist_definition_mpaso.xml";
(-f "$nl_definition_file") or die <<"EOF";
** $ProgName - ERROR: Cannot find namelist definition file \"$nl_definition_file\" **
EOF
}
if ($print>=2) { print "Using namelist definition file $nl_definition_file$eol"; }
# The namelist defaults file contains default values for all required namelist variables.
my $nl_defaults_file;
if (-f "${CASEROOT}/SourceMods/src.mpaso/namelist_defaults_mpaso.xml") {
$nl_defaults_file = "${CASEROOT}/SourceMods/src.mpaso/namelist_defaults_mpaso.xml";
}
if (! defined $nl_defaults_file) {
$nl_defaults_file = "$cfgdir/namelist_files/namelist_defaults_mpaso.xml";
(-f "$nl_defaults_file") or die <<"EOF";
** $ProgName - Cannot find namelist defaults file \"$nl_defaults_file\" **
EOF
}
if ($print>=2) { print "Using namelist defaults file $nl_defaults_file$eol"; }
#-----------------------------------------------------------------------------------------------
# Add $perl5lib_dir to the list of paths that Perl searches for modules
unshift @INC, "$perl5lib";
#require XML::Lite;
require Build::Config;
require Build::NamelistDefinition;
require Build::NamelistDefaults;
require Build::Namelist;
require Config::SetupTools;
#-----------------------------------------------------------------------------------------------
# Create a configuration object from the MPASO config_cache.xml file- created by
# mpaso.cpl7.template in $CASEBUILD/mpasoconf
my $cfg = Build::Config->new('config_cache.xml');
# Create a namelist definition object. This object provides a method for verifying that the
# output namelist variables are in the definition file, and are output in the correct
# namelist groups.
my $definition = Build::NamelistDefinition->new($nl_definition_file);
# Create a namelist defaults object. This object provides default values for variables
# contained in the input defaults file. The configuration object provides attribute
# values that are relevent for the MPASO library for which the namelist is being produced.
my $defaults = Build::NamelistDefaults->new($nl_defaults_file, $cfg);
# Create an empty namelist object. Add values to it in order of precedence.
my $nl = Build::Namelist->new();
#-----------------------------------------------------------------------------------------------
# Process the user input in order of precedence. At each point we'll only add new
# values to the namelist and not overwrite previously specified specified values which
# have higher precedence.
# Process the commandline args that provide specific namelist values.
# Process the -namelist arg.
if (defined $opts{'namelist'}) {
# Parse commandline namelist
my $nl_arg = Build::Namelist->new($opts{'namelist'});
# Validate input namelist -- trap exceptions
my $nl_arg_valid;
eval { $nl_arg_valid = $definition->validate($nl_arg); };
if ($@) {
die "$ProgName - ERROR: Invalid namelist variable in commandline arg '-namelist'.\n $@";
}
# Merge input values into namelist. Previously specified values have higher precedence
# and are not overwritten.
$nl->merge_nl($nl_arg_valid);
}
# Process the -infile arg.
if (defined $opts{'infile'}) {
# Parse namelist input from a file
my $nl_infile = Build::Namelist->new($opts{'infile'});
my $nl_infile_valid = Build::Namelist->new();
# Validate namelist variables (going to do this one variable at a time)
for my $group ($nl_infile->get_group_names()) {
for my $var ($nl_infile->get_variable_names($group)) {
my $var_local; # Name of variable to write to infile
my $nl_check_var = Build::Namelist->new();
my $nl_check_valid;
my $val = $nl_infile->get_variable_value($group, $var);
my @broken = split(/&/,$var);
my $check_grp = 0; # If 1, make sure group found in definitions file
# matches that specified in user_nl_mpaso
# if variable has ampersand, truncate it unless it is type derived
if ($broken[1]) {
my $nl_check_amp = Build::Namelist->new();
$nl_check_amp->set_variable_value($group, $var, $val);
eval { $definition->validate($nl_check_amp) };
if (not $@) {
# & is required in variable name
$var_local = $var;
} else {
# & should not be in variable name
$var_local = $broken[0];
$check_grp = 1;
}
} else {
$var_local = $var;
}
# Make sure variable is defined in namelist_definition_mpaso.xml
$nl_check_var->set_variable_value($group, $var_local,$val);
eval { $nl_check_valid = $definition->validate($nl_check_var); };
(not $@) or die <<"EOF";
** ERROR: either $var_local is not a valid MPASO namelist variable or $var_local = $val is not a valid value; please fix user_nl_mpaso. Note that $var_local may appear in multiple namelists, in which case you need to specify the correct namelist in user_nl_mpaso using the format $var_local\&namelist_nml = $val, where \&namelist_nml is the mpaso_in namelist containing $var_local.**
EOF
# If group was specified in user_nl_mpaso, make sure it matches
# the group in the definitions file.
my @group_valid = $nl_check_valid->get_group_names();
((not $check_grp) or ($broken[1] eq $group_valid[0])) or die <<"EOF";
** ERROR: $broken[0] is in $group_valid[0], not $broken[1]! Please fix this in user_nl_mpaso. **
EOF
# Add variable to validated namelist
$nl_infile_valid->set_variable_value($group_valid[0], $var_local, $val);
}
}
# If preview is desired and something has been changed in $nl_infile_valid,
# output everything in $nl_infile_valid
if (($preview == 1) && ($nl_infile_valid->get_group_names)) {
print " - The following values have been set in user_nl_mpaso:\n";
print_nl_to_screen($nl_infile_valid);
}
# Merge input values into namelist. Previously specified values have higher
# precedence and are not overwritten.
$nl->merge_nl($nl_infile_valid);
}
#-----------------------------------------------------------------------------------------------
# Determine xml variables
#unshift @INC, "$CASEROOT/Tools";
#require XML::Lite;
#require SetupTools;
my %xmlvars = ();
SetupTools::getxmlvars($CASEROOT, \%xmlvars);
foreach my $attr (keys %xmlvars) {
$xmlvars{$attr} = SetupTools::expand_xml_var($xmlvars{$attr}, \%xmlvars);
}
my $RUNDIR = "$xmlvars{'RUNDIR'}";
my $CODEROOT = "$xmlvars{'CODEROOT'}";
my $DIN_LOC_ROOT = "$xmlvars{'DIN_LOC_ROOT'}";
my $CASE = "$xmlvars{'CASE'}";
my $CALENDAR = "$xmlvars{'CALENDAR'}";
my $NCPL_BASE_PERIOD = "$xmlvars{'NCPL_BASE_PERIOD'}";
my $OCN_NCPL = "$xmlvars{'OCN_NCPL'}";
my $OCN_COUPLING = "$xmlvars{'OCN_COUPLING'}";
my $OCN_ICE_FORCING = "$xmlvars{'OCN_ICE_FORCING'}";
my $INFO_DBUG = "$xmlvars{'INFO_DBUG'}";
my $RUN_TYPE = "$xmlvars{'RUN_TYPE'}";
my $RUN_STARTDATE = "$xmlvars{'RUN_STARTDATE'}";
my $START_TOD = "$xmlvars{'START_TOD'}";
my $RUN_REFDATE = "$xmlvars{'RUN_REFDATE'}";
my $CONTINUE_RUN = "$xmlvars{'CONTINUE_RUN'}";
my $output_r = "./${CASE}.mpaso.r";
my $output_h = "./${CASE}.mpaso.h";
my $output_d = "./${CASE}.mpaso.d";
if ($inst_string) {
$output_r = "./${CASE}.mpaso${inst_string}.r";
$output_h = "./${CASE}.mpaso${inst_string}.h";
$output_d = "./${CASE}.mpaso${inst_string}.d";
}
# Environment variables set in mpaso.buildnml.csh that are not xml variables
my $RESTART_INPUT_TS_FMT = "$ENV{'RESTART_INPUT_TS_FMT'}";
my $LID = $ENV{'LID'};
my $ntasks = $NTASKS_OCN / $NINST_OCN;
print "MPASO build-namelist: ocn_grid is $OCN_GRID \n";
print "MPASO build-namelist: ocn_forcing is $OCN_FORCING \n";
(-d $DIN_LOC_ROOT) or mkdir $DIN_LOC_ROOT;
if ($print>=2) { print "CIME inputdata root directory: $DIN_LOC_ROOT$eol"; }
#-----------------------------------------------------------------------------------------------
# Determine namelist
#-----------------------------------------------------------------------------------------------
#############################
# Namelist group: run_modes #
#############################
add_default($nl, 'config_ocean_run_mode');
###################################
# Namelist group: time_management #
###################################
if ($CONTINUE_RUN eq 'TRUE') {
add_default($nl, 'config_do_restart', 'val'=>".true.");
} else {
add_default($nl, 'config_do_restart', 'val'=>".false.");
}
add_default($nl, 'config_restart_timestamp_name');
add_default($nl, 'config_calendar_type', 'calendar'=>"$CALENDAR");
if ($CONTINUE_RUN eq 'TRUE') {
add_default($nl, 'config_start_time', 'val'=>"'file'");
} else {
add_default($nl, 'config_start_time', 'val'=>"'${RUN_STARTDATE}_${START_TOD}'");
}
add_default($nl, 'config_output_reference_time');
######################
# Namelist group: io #
######################
add_default($nl, 'config_write_output_on_startup');
add_default($nl, 'config_pio_num_iotasks');
add_default($nl, 'config_pio_stride');
#################################
# Namelist group: decomposition #
#################################
add_default($nl, 'config_num_halos');
add_default($nl, 'config_block_decomp_file_prefix', 'val'=>"'${DIN_LOC_ROOT}/ocn/mpas-o/${OCN_GRID}/${decomp_prefix}${date_stamp}.part.'");
add_default($nl, 'config_number_of_blocks');
add_default($nl, 'config_explicit_proc_decomp');
add_default($nl, 'config_proc_decomp_file_prefix');
####################################
# Namelist group: time_integration #
####################################
add_default($nl, 'config_dt');
add_default($nl, 'config_time_integrator');
add_default($nl, 'config_number_of_time_levels');
########################
# Namelist group: hmix #
########################
add_default($nl, 'config_hmix_scaleWithMesh');
add_default($nl, 'config_maxMeshDensity');
add_default($nl, 'config_hmix_use_ref_cell_width');
add_default($nl, 'config_hmix_ref_cell_width');
add_default($nl, 'config_apvm_scale_factor');
#############################
# Namelist group: hmix_del2 #
#############################
add_default($nl, 'config_use_mom_del2');
add_default($nl, 'config_mom_del2');
add_default($nl, 'config_use_tracer_del2');
add_default($nl, 'config_tracer_del2');
#############################
# Namelist group: hmix_del4 #
#############################
add_default($nl, 'config_use_mom_del4');
add_default($nl, 'config_mom_del4');
add_default($nl, 'config_mom_del4_div_factor');
add_default($nl, 'config_use_tracer_del4');
add_default($nl, 'config_tracer_del4');
##############################
# Namelist group: hmix_Leith #
##############################
add_default($nl, 'config_use_Leith_del2');
add_default($nl, 'config_Leith_parameter');
add_default($nl, 'config_Leith_dx');
add_default($nl, 'config_Leith_visc2_max');
#########################################
# Namelist group: Redi_isopycnal_mixing #
#########################################
add_default($nl, 'config_use_Redi');
add_default($nl, 'config_Redi_closure');
add_default($nl, 'config_Redi_constant_kappa');
add_default($nl, 'config_Redi_maximum_slope');
add_default($nl, 'config_Redi_use_slope_taper');
add_default($nl, 'config_Redi_use_surface_taper');
add_default($nl, 'config_Redi_limit_term1');
add_default($nl, 'config_Redi_use_quasi_monotone_limiter');
add_default($nl, 'config_Redi_quasi_monotone_safety_factor');
add_default($nl, 'config_Redi_min_layers_diag_terms');
add_default($nl, 'config_Redi_horizontal_taper');
add_default($nl, 'config_Redi_horizontal_ramp_min');
add_default($nl, 'config_Redi_horizontal_ramp_max');
######################################################
# Namelist group: submesoscale_eddy_parameterization #
######################################################
add_default($nl, 'config_submesoscale_enable');
add_default($nl, 'config_submesoscale_tau');
add_default($nl, 'config_submesoscale_Ce');
add_default($nl, 'config_submesoscale_Lfmin');
add_default($nl, 'config_submesoscale_ds_max');
############################################
# Namelist group: GM_eddy_parameterization #
############################################
add_default($nl, 'config_use_GM');
add_default($nl, 'config_GM_closure');
add_default($nl, 'config_GM_constant_kappa');
add_default($nl, 'config_GM_constant_bclModeSpeed');
add_default($nl, 'config_GM_minBclModeSpeed_method');
add_default($nl, 'config_GM_spatially_variable_min_kappa');
add_default($nl, 'config_GM_spatially_variable_max_kappa');
add_default($nl, 'config_GM_spatially_variable_baroclinic_mode');
add_default($nl, 'config_GM_Visbeck_alpha');
add_default($nl, 'config_GM_Visbeck_max_depth');
add_default($nl, 'config_GM_EG_riMin');
add_default($nl, 'config_GM_EG_kappa_factor');
add_default($nl, 'config_GM_EG_Rossby_factor');
add_default($nl, 'config_GM_EG_Rhines_factor');
add_default($nl, 'config_GM_horizontal_taper');
add_default($nl, 'config_GM_horizontal_ramp_min');
add_default($nl, 'config_GM_horizontal_ramp_max');
add_default($nl, 'config_GMRedi_Rossby_ramp_min');
add_default($nl, 'config_GMRedi_Rossby_ramp_max');
#########################################
# Namelist group: eddy_parameterization #
#########################################
add_default($nl, 'config_eddyMLD_dens_threshold');
add_default($nl, 'config_eddyMLD_reference_depth');
add_default($nl, 'config_eddyMLD_reference_pressure');
add_default($nl, 'config_eddyMLD_use_old');
#########################
# Namelist group: cvmix #
#########################
add_default($nl, 'config_use_cvmix');
add_default($nl, 'config_cvmix_prandtl_number');
add_default($nl, 'config_cvmix_background_scheme');
add_default($nl, 'config_cvmix_background_diffusion');
add_default($nl, 'config_cvmix_background_viscosity');
add_default($nl, 'config_cvmix_BryanLewis_bl1');
add_default($nl, 'config_cvmix_BryanLewis_bl2');
add_default($nl, 'config_cvmix_BryanLewis_transitionDepth');
add_default($nl, 'config_cvmix_BryanLewis_transitionWidth');
add_default($nl, 'config_use_cvmix_convection');
add_default($nl, 'config_cvmix_convective_diffusion');
add_default($nl, 'config_cvmix_convective_viscosity');
add_default($nl, 'config_cvmix_convective_basedOnBVF');
add_default($nl, 'config_cvmix_convective_triggerBVF');
add_default($nl, 'config_use_cvmix_shear');
add_default($nl, 'config_cvmix_num_ri_smooth_loops');
add_default($nl, 'config_cvmix_use_BLD_smoothing');
add_default($nl, 'config_cvmix_shear_mixing_scheme');
add_default($nl, 'config_cvmix_shear_PP_nu_zero');
add_default($nl, 'config_cvmix_shear_PP_alpha');
add_default($nl, 'config_cvmix_shear_PP_exp');
add_default($nl, 'config_cvmix_shear_KPP_nu_zero');
add_default($nl, 'config_cvmix_shear_KPP_Ri_zero');
add_default($nl, 'config_cvmix_shear_KPP_exp');
add_default($nl, 'config_use_cvmix_tidal_mixing');
add_default($nl, 'config_use_cvmix_double_diffusion');
add_default($nl, 'config_use_cvmix_kpp');
add_default($nl, 'config_use_cvmix_fixed_boundary_layer');
add_default($nl, 'config_cvmix_kpp_boundary_layer_depth');
add_default($nl, 'config_cvmix_kpp_criticalBulkRichardsonNumber');
add_default($nl, 'config_cvmix_kpp_matching');
add_default($nl, 'config_cvmix_kpp_EkmanOBL');
add_default($nl, 'config_cvmix_kpp_MonObOBL');
add_default($nl, 'config_cvmix_kpp_interpolationOMLType');
add_default($nl, 'config_cvmix_kpp_surface_layer_extent');
add_default($nl, 'config_cvmix_kpp_surface_layer_averaging');
add_default($nl, 'configure_cvmix_kpp_minimum_OBL_under_sea_ice');
add_default($nl, 'config_cvmix_kpp_stop_OBL_search');
add_default($nl, 'config_cvmix_kpp_use_enhanced_diff');
add_default($nl, 'config_cvmix_kpp_nonlocal_with_implicit_mix');
if ($ocn_wave eq 'true' ) {
add_default($nl, 'config_cvmix_kpp_use_theory_wave', 'val'=>'.false.');
add_default($nl, 'config_cvmix_kpp_use_active_wave', 'val'=>'.true.');
add_default($nl, 'config_cvmix_kpp_langmuir_mixing_opt', 'val'=>'LWF16');
add_default($nl, 'config_cvmix_kpp_langmuir_entrainment_opt', 'val'=>'LWF16');
} else {
add_default($nl, 'config_cvmix_kpp_use_theory_wave');
add_default($nl, 'config_cvmix_kpp_langmuir_mixing_opt');
add_default($nl, 'config_cvmix_kpp_langmuir_entrainment_opt');
}
#################################
# Namelist group: wave_coupling #
#################################
if ($ocn_wave eq 'true' ) {
add_default($nl, 'config_use_active_wave', 'val'=>'.true.');
} else {
add_default($nl, 'config_use_active_wave', 'val'=>'.false.');
}
add_default($nl, 'config_n_stokes_drift_wavenumber_partitions');
########################
# Namelist group: gotm #
########################
add_default($nl, 'config_use_gotm');
add_default($nl, 'config_gotm_namelist_file');
add_default($nl, 'config_gotm_constant_surface_roughness_length');
add_default($nl, 'config_gotm_constant_bottom_roughness_length');
add_default($nl, 'config_gotm_constant_bottom_drag_coeff');
###########################
# Namelist group: forcing #
###########################
add_default($nl, 'config_use_variable_drag');
add_default($nl, 'config_use_bulk_wind_stress');
add_default($nl, 'config_use_bulk_thickness_flux');
add_default($nl, 'config_flux_attenuation_coefficient');
add_default($nl, 'config_flux_attenuation_coefficient_runoff');
############################
# Namelist group: coupling #
############################
if (($OCN_ICEBERG eq 'true') && ($OCN_FORCING eq 'active_atm')) {
add_default($nl, 'config_remove_AIS_coupler_runoff', 'val'=>".true.");
} else {
add_default($nl, 'config_remove_AIS_coupler_runoff', 'val'=>".false.");
}
######################################
# Namelist group: shortwaveRadiation #
######################################
add_default($nl, 'config_sw_absorption_type');
add_default($nl, 'config_jerlov_water_type');
add_default($nl, 'config_surface_buoyancy_depth');
add_default($nl, 'config_enable_shortwave_energy_fixer');
###########################################
# Namelist group: self_attraction_loading #
###########################################
add_default($nl, 'config_use_self_attraction_loading');
add_default($nl, 'config_self_attraction_loading_smoothing_width');
add_default($nl, 'config_mpas_to_grid_weights_file');
add_default($nl, 'config_grid_to_mpas_weights_file');
add_default($nl, 'config_self_attraction_loading_compute_interval');
add_default($nl, 'config_nLatitude');
add_default($nl, 'config_nLongitude');
add_default($nl, 'config_use_parallel_self_attraction_loading');
add_default($nl, 'config_parallel_self_attraction_loading_order');
add_default($nl, 'config_parallel_self_attraction_loading_n_cells_per_block');
add_default($nl, 'config_parallel_self_attraction_loading_bfb');
###########################################
# Namelist group: tidal_potential_forcing #
###########################################
add_default($nl, 'config_use_tidal_potential_forcing');
add_default($nl, 'config_tidal_potential_reference_time');
add_default($nl, 'config_use_tidal_potential_forcing_M2');
add_default($nl, 'config_use_tidal_potential_forcing_S2');
add_default($nl, 'config_use_tidal_potential_forcing_N2');
add_default($nl, 'config_use_tidal_potential_forcing_K2');
add_default($nl, 'config_use_tidal_potential_forcing_K1');
add_default($nl, 'config_use_tidal_potential_forcing_O1');
add_default($nl, 'config_use_tidal_potential_forcing_Q1');
add_default($nl, 'config_use_tidal_potential_forcing_P1');
add_default($nl, 'config_tidal_potential_ramp');
add_default($nl, 'config_self_attraction_and_loading_beta');
##############################
# Namelist group: frazil_ice #
##############################
add_default($nl, 'config_use_frazil_ice_formation');
add_default($nl, 'config_frazil_in_open_ocean');
add_default($nl, 'config_frazil_under_land_ice');
add_default($nl, 'config_frazil_heat_of_fusion');
add_default($nl, 'config_frazil_ice_density');
add_default($nl, 'config_frazil_fractional_thickness_limit');
add_default($nl, 'config_specific_heat_sea_water');
add_default($nl, 'config_frazil_maximum_depth');
add_default($nl, 'config_frazil_sea_ice_reference_salinity');
add_default($nl, 'config_frazil_land_ice_reference_salinity');
add_default($nl, 'config_frazil_maximum_freezing_temperature');
add_default($nl, 'config_frazil_use_surface_pressure');
###################################
# Namelist group: land_ice_fluxes #
###################################
if ($OCN_ISMF eq 'coupled') {
add_default($nl, 'config_land_ice_flux_mode', 'val'=>"coupled");
} elsif ($OCN_ISMF eq 'internal') {
add_default($nl, 'config_land_ice_flux_mode', 'val'=>"standalone");
} elsif ($OCN_ISMF eq 'data') {
add_default($nl, 'config_land_ice_flux_mode', 'val'=>"data");
} else {
add_default($nl, 'config_land_ice_flux_mode');
}
add_default($nl, 'config_land_ice_flux_formulation');
add_default($nl, 'config_land_ice_flux_useHollandJenkinsAdvDiff');
add_default($nl, 'config_land_ice_flux_attenuation_coefficient');
add_default($nl, 'config_land_ice_flux_boundaryLayerThickness');
add_default($nl, 'config_land_ice_flux_boundaryLayerNeighborWeight');
add_default($nl, 'config_land_ice_flux_cp_ice');
add_default($nl, 'config_land_ice_flux_rho_ice');
add_default($nl, 'config_land_ice_flux_explicit_topDragCoeff');
add_default($nl, 'config_land_ice_flux_ISOMIP_gammaT');
add_default($nl, 'config_land_ice_flux_rms_tidal_velocity');
add_default($nl, 'config_land_ice_flux_jenkins_heat_transfer_coefficient');
add_default($nl, 'config_land_ice_flux_jenkins_salt_transfer_coefficient');
#############################
# Namelist group: advection #
#############################
add_default($nl, 'config_vert_advection_method');
add_default($nl, 'config_vert_remap_order');
add_default($nl, 'config_vert_remap_interval');
add_default($nl, 'config_vert_tracer_adv_flux_order');
add_default($nl, 'config_horiz_tracer_adv_order');
add_default($nl, 'config_coef_3rd_order');
add_default($nl, 'config_flux_limiter');
add_default($nl, 'config_remap_limiter');
add_default($nl, 'config_thickness_flux_type');
###############################
# Namelist group: bottom_drag #
###############################
add_default($nl, 'config_bottom_drag_mode');
add_default($nl, 'config_implicit_bottom_drag_type');
add_default($nl, 'config_implicit_constant_bottom_drag_coeff');
add_default($nl, 'config_use_implicit_top_drag');
add_default($nl, 'config_implicit_top_drag_coeff');
add_default($nl, 'config_loglaw_bottom_roughness');
add_default($nl, 'config_loglaw_layer_depth_max');
add_default($nl, 'config_loglaw_bottom_drag_min');
add_default($nl, 'config_loglaw_bottom_drag_max');
add_default($nl, 'config_explicit_bottom_drag_coeff');
add_default($nl, 'config_use_topographic_wave_drag');
add_default($nl, 'config_topographic_wave_drag_coeff');
add_default($nl, 'config_thickness_drag_type');
####################################
# Namelist group: Rayleigh_damping #
####################################
add_default($nl, 'config_Rayleigh_damping_coeff');
add_default($nl, 'config_Rayleigh_damping_depth_variable');
add_default($nl, 'config_Rayleigh_bottom_friction');
add_default($nl, 'config_Rayleigh_bottom_damping_coeff');
###################################
# Namelist group: vegetation_drag #
###################################
add_default($nl, 'config_use_vegetation_drag');
add_default($nl, 'config_vegetation_drag_coefficient');
###################################
# Namelist group: ocean_constants #
###################################
add_default($nl, 'config_density0');
#####################################
# Namelist group: pressure_gradient #
#####################################
add_default($nl, 'config_pressure_gradient_type');
add_default($nl, 'config_common_level_weight');
add_default($nl, 'config_zonal_ssh_grad');
add_default($nl, 'config_meridional_ssh_grad');
#######################
# Namelist group: eos #
#######################
add_default($nl, 'config_eos_type');
add_default($nl, 'config_open_ocean_freezing_temperature_coeff_0');
add_default($nl, 'config_open_ocean_freezing_temperature_coeff_S');
add_default($nl, 'config_open_ocean_freezing_temperature_coeff_p');
add_default($nl, 'config_open_ocean_freezing_temperature_coeff_pS');
add_default($nl, 'config_open_ocean_freezing_temperature_coeff_mushy_az1_liq');
add_default($nl, 'config_land_ice_cavity_freezing_temperature_coeff_0');
add_default($nl, 'config_land_ice_cavity_freezing_temperature_coeff_S');
add_default($nl, 'config_land_ice_cavity_freezing_temperature_coeff_p');
add_default($nl, 'config_land_ice_cavity_freezing_temperature_coeff_pS');
##############################
# Namelist group: eos_linear #
##############################
add_default($nl, 'config_eos_linear_alpha');
add_default($nl, 'config_eos_linear_beta');
add_default($nl, 'config_eos_linear_Tref');
add_default($nl, 'config_eos_linear_Sref');
add_default($nl, 'config_eos_linear_densityref');
##############################
# Namelist group: eos_wright #
##############################
add_default($nl, 'config_eos_wright_ref_pressure');
########################################
# Namelist group: split_timestep_share #
########################################
add_default($nl, 'config_n_ts_iter');
add_default($nl, 'config_n_bcl_iter_beg');
add_default($nl, 'config_n_bcl_iter_mid');
add_default($nl, 'config_n_bcl_iter_end');
#####################################
# Namelist group: split_explicit_ts #
#####################################
add_default($nl, 'config_btr_dt');
add_default($nl, 'config_n_btr_cor_iter');
add_default($nl, 'config_vel_correction');
add_default($nl, 'config_btr_subcycle_loop_factor');
add_default($nl, 'config_btr_gam1_velWt1');
add_default($nl, 'config_btr_gam2_SSHWt1');
add_default($nl, 'config_btr_gam3_velWt2');
add_default($nl, 'config_btr_solve_SSH2');
#####################################
# Namelist group: split_implicit_ts #
#####################################
add_default($nl, 'config_btr_si_preconditioner');
add_default($nl, 'config_btr_si_tolerance');
add_default($nl, 'config_n_btr_si_large_iter');
add_default($nl, 'config_btr_si_partition_match_mode');
#####################################
# Namelist group: ALE_vertical_grid #
#####################################
add_default($nl, 'config_vert_coord_movement');
add_default($nl, 'config_ALE_thickness_proportionality');
add_default($nl, 'config_vert_taper_weight_depth_1');
add_default($nl, 'config_vert_taper_weight_depth_2');
add_default($nl, 'config_use_min_max_thickness');
add_default($nl, 'config_min_thickness');
add_default($nl, 'config_max_thickness_factor');
add_default($nl, 'config_dzdk_positive');
####################################################
# Namelist group: ALE_frequency_filtered_thickness #
#####################################################
add_default($nl, 'config_use_freq_filtered_thickness');
add_default($nl, 'config_thickness_filter_timescale');
add_default($nl, 'config_use_highFreqThick_restore');
add_default($nl, 'config_highFreqThick_restore_time');
add_default($nl, 'config_use_highFreqThick_del2');
add_default($nl, 'config_highFreqThick_del2');
#########################
# Namelist group: debug #
#########################
add_default($nl, 'config_check_zlevel_consistency');
add_default($nl, 'config_check_ssh_consistency');
add_default($nl, 'config_filter_btr_mode');
add_default($nl, 'config_prescribe_velocity');
add_default($nl, 'config_prescribe_thickness');
add_default($nl, 'config_include_KE_vertex');
add_default($nl, 'config_check_tracer_monotonicity');
add_default($nl, 'config_compute_active_tracer_budgets');
add_default($nl, 'config_disable_thick_all_tend');
add_default($nl, 'config_disable_thick_hadv');
add_default($nl, 'config_disable_thick_vadv');
add_default($nl, 'config_disable_thick_sflux');
add_default($nl, 'config_disable_vel_all_tend');
add_default($nl, 'config_disable_vel_hadv');
add_default($nl, 'config_disable_vel_coriolis');
add_default($nl, 'config_disable_vel_pgrad');
add_default($nl, 'config_disable_vel_hmix');
add_default($nl, 'config_disable_vel_surface_stress');
add_default($nl, 'config_disable_vel_topographic_wave_drag');
add_default($nl, 'config_disable_vel_explicit_bottom_drag');
add_default($nl, 'config_disable_vel_vmix');
add_default($nl, 'config_disable_vel_vadv');
add_default($nl, 'config_disable_tr_all_tend');
add_default($nl, 'config_disable_tr_adv');
add_default($nl, 'config_disable_tr_hmix');
add_default($nl, 'config_disable_tr_vmix');
add_default($nl, 'config_disable_tr_sflux');
add_default($nl, 'config_disable_tr_nonlocalflux');
add_default($nl, 'config_disable_redi_k33');
add_default($nl, 'config_read_nearest_restart');
###########################
# Namelist group: testing #
###########################
add_default($nl, 'config_conduct_tests');
add_default($nl, 'config_test_tensors');
add_default($nl, 'config_tensor_test_function');
###################################
# Namelist group: transport_tests #
###################################
add_default($nl, 'config_transport_tests_vert_levels');
add_default($nl, 'config_transport_tests_temperature');
add_default($nl, 'config_transport_tests_salinity');
add_default($nl, 'config_transport_tests_flow_id');
#########################################
# Namelist group: init_mode_vert_levels #
#########################################
add_default($nl, 'config_vert_levels');
#########################################
# Namelist group: manufactured_solution #