#!/usr/bin/env perl
#-----------------------------------------------------------------------------------------------
#
# build-namelist
#
# This script builds the namelists for the CICE configuration of CCSM4.
#
# build-namelist is designed to be used in conjuction with configure.  By default configure
# produces a config_cache.xml file that contains all information needed at build time to procduce
# a CICE library.  build-namelist reads this file to obtain information it needs to provide
# default values that are consistent with the CICE library.  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.  But if multiple runs are to made using the
# same executable, successive invocations of build-namelist will overwrite previously generated
# namelist files.  So generally the best strategy is to invoke build-namelist from the run
# directory and use the -config option to provide the filepath of the config_cache.xml file.
#
# Date        Contributor      Modification
# -------------------------------------------------------------------------------------------
# 2009-01-20  Vertenstein      Original version
# 2008-07-15  Sean Santos      Added -inputdata functionality
#--------------------------------------------------------------------------------------------

use strict;
#use warnings;
#use diagnostics;

use Cwd;
use English;
use Getopt::Long;
use IO::File;
#-----------------------------------------------------------------------------------------------

sub usage {
    die <<EOF;
SYNOPSIS
     build-namelist [options]
OPTIONS
     -config "filepath"    Read the given CICE configuration cache file. 
                           Default: "config_cache.xml".
     -csmdata "dir"        Root directory of CCSM input data.
                           Can also be set by using the CSMDATA environment variable.
     -dir "directory"      Directory where output namelist file will be
                           written, i.e., ice_in
                           Default: current working directory.
     -help [or -h]         Print usage to STDOUT.
     -infile "filepath"    Specify a file containing namelists to read values from.
     -inputdata "filepath" Writes out a list containing pathnames for required input datasets in
                           specified file.
     -namelist "namelist"  Specify namelist settings directly on the commandline by supplying 
                           a string containing FORTRAN namelist syntax, e.g.,
                              -namelist "&forcing_nml dt=1800 /"
     -silent [-s]          Turns on silent mode - only fatal messages issued.
     -verbose              Turn on verbose echoing of informational messages.
     -version [or -v]      Echo the SVN tag name used to check out this CICE distribution.
     -caseroot             CASEROOT directory variable
     -rundir               RUNDIR directory variable
     -scriptsroot          SCRIPTSROOT directory variable
     -inst_string          INST_STRING variable


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., -dir 
      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.
EOF
}

#-----------------------------------------------------------------------------------------------
# Set the directory that contains the CICE 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) { 
    $cfgdir = absolute_path($ProgDir);
} else {
    $cfgdir = $cwd;
}

my $cfg_cache = "config_cache.xml";       # Default name of configuration cache file
my $outdirname = ".";                     # Default name of output directory name

#-----------------------------------------------------------------------------------------------
# Process command-line options.

my %opts = ( config      => $cfg_cache,
	     csmdata     => undef,
	     help        => 0,
	     dir         => $outdirname,
	     silent      => 0,
	     caseroot    => undef,
	     rundir      => undef,
	     scriptsroot => undef,
	     inst_string => undef,
	    );

GetOptions(
    "config=s"      => \$opts{'config'},
    "csmdata=s"     => \$opts{'csmdata'},
    "d|dir=s"       => \$opts{'dir'},
    "h|help"        => \$opts{'help'},
    "infile=s"      => \$opts{'infile'},
    "inputdata=s"   => \$opts{'inputdata'},
    "namelist=s"    => \$opts{'namelist'},
    "s|silent"      => \$opts{'silent'},
    "v|verbose"     => \$opts{'verbose'},
    "version"       => \$opts{'version'},
    "caseroot=s"    => \$opts{'caseroot'},
    "rundir=s"      => \$opts{'rundir'},
    "scriptsroot=s" => \$opts{'scriptsroot'},
    "inst_string=s" => \$opts{'inst_string'},	   
)  or usage();

# Give usage message.
usage() if $opts{'help'};

# Echo version info.
version($cfgdir) if $opts{'version'};    

# 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 (default)
# 2 - verbose
my $print = 1;
if ($opts{'silent'})  { $print = 0; }
if ($opts{'verbose'}) { $print = 2; }
my $eol = "\n";

if ($print>=2) { print "Setting CICE configuration script directory to $cfgdir$eol"; }

# Check that configuration cache file exists.
(-f $opts{'config'})  or  die <<"EOF";
** $ProgName - Cannot find configuration cache file: \"$opts{'config'}\" **
EOF

if ($print>=2) { print "Using CICE configuration cache file $opts{'config'}$eol"; }

my $CASEROOT;
my $SCRIPTSROOT;      
my $INST_STRING;
my $RUNDIR;
if ( defined $opts{'caseroot'} ) {
    $CASEROOT    = $opts{'caseroot'}; 
    $SCRIPTSROOT = $opts{'scriptsroot'};       
    $INST_STRING = $opts{'inst_string'}; 
    $RUNDIR      = $opts{'rundir'};
}

# Validate some of the commandline option values.
validate_options("commandline", \%opts);


#-----------------------------------------------------------------------------------------------
# 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 $perl5lib_dir = "$cfgdir/../../../../scripts/ccsm_utils/Tools/perl5lib";

# The XML::Lite module is required to parse the XML files.
(-f "$perl5lib_dir/XML/Lite.pm")  or  die <<"EOF";
** $ProgName - Cannot find perl module \"XML/Lite.pm\" in directory \"$perl5lib_dir\" **
EOF

# The Build::Config module provides utilities to access the configuration information
# in the config_cache.xml file
(-f "$perl5lib_dir/Build/Config.pm")  or  die <<"EOF";
** $ProgName - Cannot find perl module \"Build/Config.pm\" in directory \"$perl5lib_dir\" **
EOF

# The Build::NamelistDefinition module provides utilities to validate that the output
# namelists are consistent with the namelist definition file
(-f "$perl5lib_dir/Build/NamelistDefinition.pm")  or  die <<"EOF";
** $ProgName - Cannot find perl module \"Build/NamelistDefinition.pm\" in directory \"$perl5lib_dir\" **
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_dir/Build/NamelistDefaults.pm")  or  die <<"EOF";
** $ProgName - Cannot find perl module \"Build/NamelistDefaults.pm\" in directory \"$perl5lib_dir\" **
EOF

# The Build::Namelist module provides utilities to parse input namelists, to query and modify
# namelists, and to write output namelists.
(-f "$perl5lib_dir/Build/Namelist.pm")  or  die <<"EOF";
** $ProgName - Cannot find perl module \"Build/Namelist.pm\" in directory \"$perl5lib_dir\" **
EOF

# The namelist definition file contains entries for all namelist variables that
# can be output by build-namelist.
my $nl_definition_file = "$cfgdir/namelist_files/namelist_definition.xml";
(-f "$nl_definition_file")  or  die <<"EOF";
** $ProgName - Cannot find namelist definition file \"$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 $nl_defaults_file = "$cfgdir/namelist_files/namelist_defaults_cice.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 $cfgdir/perl5lib to the list of paths that Perl searches for modules
unshift @INC, "$perl5lib_dir";
require XML::Lite;
require Build::Config;
require Build::NamelistDefinition;
require Build::NamelistDefaults;
require Build::Namelist;

#-----------------------------------------------------------------------------------------------
# Create a configuration object from the CICE config_cache.xml file. 
my $cfg = Build::Config->new($opts{'config'});

# 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 CICE 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();

#-----------------------------------------------------------------------------------------------
my $TRUE  = '\.true\.';
my $FALSE = '\.false\.';

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

# 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'});

    # Validate input namelist -- trap exceptions
    my $nl_infile_valid;
    eval { $nl_infile_valid = $definition->validate($nl_infile); };
    if ($@) {
	die "$ProgName - ERROR: Invalid namelist variable in '-infile' $opts{'infile'}.\n $@";
    }

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

#-----------------------------------------------------------------------------------------------
# Get cice mode - not that cice_mode must be a configure time option since it sets
# NCAT which is a CPP variable

my $cice_mode = $cfg->get('cice_mode');
if ($cice_mode eq 'prescribed') {
    add_default($nl, 'prescribed_ice', 'val'=>'.true.');
} else {
    add_default($nl, 'prescribed_ice', 'val'=>'.false.');
}

#-----------------------------------------------------------------------------------------------
# Determine xml variables

my $inputdata_rootdir = undef;
my $CASE;
my $ICE_GRID;
my $ICE_DOMAIN_PATH; 
my $ICE_DOMAIN_FILE;
my $RUN_TYPE;
my $CONTINUE_RUN;
my $ICE_NCPL;
my $RUN_REFCASE;
my $RUN_REFDATE;
my $RUN_REFTOD;
my $SSTICE_GRID_FILENAME;
my $SSTICE_DATA_FILENAME;
my $SSTICE_YEAR_ALIGN;   
my $SSTICE_YEAR_START;   
my $SSTICE_YEAR_END;     
my $SSTICE_STREAM;       
my %xmlvars = ();
if ( defined $opts{'caseroot'} ) {
    my @files = <${CASEROOT}/*xml>;
    foreach my $file (@files) {
	my $xml  = XML::Lite->new( "$file" );
	my @e = $xml->elements_by_name('entry');
	while ( my $e = shift @e ) {
	    my %a = $e->get_attributes();
	    $xmlvars{$a{'id'}} = $a{'value'};
	}
    }
    foreach my $attr (keys %xmlvars) {
	if ( $xmlvars{$attr} =~ m/\$/ ) {$xmlvars{$attr} = expand_env_xml($xmlvars{$attr});}
	if ( $xmlvars{$attr} =~ m/\$/ ) {$xmlvars{$attr} = expand_env_xml($xmlvars{$attr});}
	if ( $xmlvars{$attr} =~ m/\$/ ) {$xmlvars{$attr} = expand_env_xml($xmlvars{$attr});}
	if ( $xmlvars{$attr} =~ m/\$/ ) {$xmlvars{$attr} = expand_env_xml($xmlvars{$attr});}
    }
    
    $ICE_GRID        = $xmlvars{'ICE_GRID'};
    $ICE_DOMAIN_PATH = $xmlvars{'ICE_DOMAIN_PATH'};
    $CASE            = $xmlvars{'CASE'};
    $ICE_DOMAIN_FILE = $xmlvars{'ICE_DOMAIN_FILE'};
    $ICE_NCPL        = $xmlvars{'ICE_NCPL'};
    $CONTINUE_RUN    = $xmlvars{'CONTINUE_RUN'};
    $RUN_TYPE        = $xmlvars{'RUN_TYPE'};
    $RUN_REFCASE     = $xmlvars{'RUN_REFCASE'};
    $RUN_REFDATE     = $xmlvars{'RUN_REFDATE'};
    $RUN_REFTOD      = $xmlvars{'RUN_REFTOD'};
    if ($cice_mode eq 'prescribed') {
	$SSTICE_GRID_FILENAME = $xmlvars{'SSTICE_GRID_FILENAME'};
	$SSTICE_DATA_FILENAME = $xmlvars{'SSTICE_DATA_FILENAME'};
	$SSTICE_YEAR_ALIGN    = $xmlvars{'SSTICE_YEAR_ALIGN'};
	$SSTICE_YEAR_START    = $xmlvars{'SSTICE_YEAR_START'};
	$SSTICE_YEAR_END      = $xmlvars{'SSTICE_YEAR_END'};
	$SSTICE_STREAM        = $xmlvars{'SSTICE_STREAM'};
    }

    # Check that the CCSM inputdata root directory has been specified.  This must be
    # a local or nfs mounted directory.
    if (defined($opts{'csmdata'})) {
	$inputdata_rootdir = $opts{'csmdata'};
    } else {
	$inputdata_rootdir = $xmlvars{'DIN_LOC_ROOT'};
    }
}
if ($print>=2) { print "CCSM inputdata root directory: $inputdata_rootdir$eol"; }

#-----------------------------------------------------------------------------------------------
# Add default values for required namelist variables that have not been previously set.
# This is done either by using the namelist default object, or directly with inline logic.

my $cam4 = $nl->get_value('cam4') =~ /$TRUE/io;

##################################
# namelist group: setup_nml      #
##################################

if ( defined $opts{'caseroot'} ) {
    if ( $RUN_TYPE eq 'startup' && $cice_mode ne 'prescribed') {
	my $ice_ic = get_default_value('ice_ic');
        if ($ice_ic =~ 'none') {
           add_default($nl, 'ice_ic', 'noprepend'=>'1');
        } else {
           add_default($nl, 'ice_ic');
        }
    }
    if ( $RUN_TYPE eq 'startup' && $cice_mode eq 'prescribed') {	
	add_default($nl, 'ice_ic', 'val'=>"default", 'noprepend'=>"1");
    }
    if ( $RUN_TYPE eq 'startup' && $cice_mode eq 'skl') {	
	add_default($nl, 'ice_ic', 'val'=>"default", 'noprepend'=>"1");
    }
    if ( $RUN_TYPE eq 'startup' && $cice_mode eq 'zbgc') {	
	add_default($nl, 'ice_ic', 'val'=>"default", 'noprepend'=>"1");
    }
    if ($RUN_TYPE eq 'branch' || $RUN_TYPE eq 'hybrid') {
	my $ice_ic;
        #standard cice filename
	$ice_ic = "${RUN_REFCASE}.cice.r.${RUN_REFDATE}-${RUN_REFTOD}.nc";
        #print "ice_ic 1 = ${ice_ic} $eol";
        #print "Check ${RUNDIR}/${RUN_REFCASE}_4lyr.cice5.r.${RUN_REFDATE}-${RUN_REFTOD}.nc $eol";
	if (-e "${RUNDIR}/${RUN_REFCASE}_4lyr.cice5.r.${RUN_REFDATE}-${RUN_REFTOD}.nc") {
	    $ice_ic = "${RUN_REFCASE}_4lyr.cice5.r.${RUN_REFDATE}-${RUN_REFTOD}.nc";
        }
        #print "ice_ic 2 = ${ice_ic} $eol";
        #print "Check ${RUNDIR}/${RUN_REFCASE}_4lyr.cice5${INST_STRING}.r.${RUN_REFDATE}-${RUN_REFTOD}.nc $eol";
	if (-e "${RUNDIR}/${RUN_REFCASE}_4lyr.cice5${INST_STRING}.r.${RUN_REFDATE}-${RUN_REFTOD}.nc") {
	    $ice_ic = "${RUN_REFCASE}_4lyr.cice5${INST_STRING}.r.${RUN_REFDATE}-${RUN_REFTOD}.nc";
        }
        #print "ice_ic = ${ice_ic} $eol";
	add_default($nl, 'ice_ic', 'val'=>"$ice_ic", 'noprepend'=>"1");
    }
# set by infodata in cesm
#    if ( $CONTINUE_RUN eq 'TRUE') {
#	add_default($nl, 'runtype', 'val'=>'continue');
#    } else {
#        if ( $RUN_TYPE eq 'branch') {
# 	    add_default($nl, 'runtype', 'val'=>'branch');
#        } else {
# 	    add_default($nl, 'runtype', 'val'=>'initial');
#	}
#    }
} else {
    # This is used for cam mode only
    add_default($nl, 'ice_ic', 'val'=>'default', 'noprepend'=>"1");
}

# set by infodata in cesm
#my $dt = 86400.0 / $ICE_NCPL;
#add_default($nl, 'dt', 'val'=>"$dt");
#add_default($nl, 'runid', 'val'=>"$CASE");
add_default($nl, 'ndtd');
add_default($nl, 'year_init');
add_default($nl, 'histfreq');
add_default($nl, 'histfreq_n');
add_default($nl, 'hist_avg');
add_default($nl, 'diagfreq');
add_default($nl, 'dumpfreq');
add_default($nl, 'dumpfreq_n');
add_default($nl, 'print_global');
add_default($nl, 'print_points');
add_default($nl, 'bfbflag');
add_default($nl, 'lonpnt');
add_default($nl, 'latpnt');
add_default($nl, 'lcdf64');
add_default($nl, 'restart_format');
add_default($nl, 'restart_ext');
add_default($nl, 'pointer_file');
add_default($nl, 'write_ic');
add_default($nl, 'cpl_bgc');

##################################
# namelist group: grid_nml       #
##################################

#if ($cice_mode eq 'prescribed' && $ICE_GRID ne 'ar9.*') {
#if ($cice_mode eq 'prescribed' && $ICE_GRID ne 'ar9v4') {
if ($cice_mode eq 'prescribed' && $ICE_GRID !~ /ar9v/) {
    add_default($nl, 'grid_type',  'val'=>'latlon');
    add_default($nl, 'grid_format','val'=>'nc');
    add_default($nl, 'grid_file',  'val'=>"$ICE_DOMAIN_PATH/${ICE_DOMAIN_FILE}" );
    add_default($nl, 'kmt_file',   'val'=>"$ICE_DOMAIN_PATH/${ICE_DOMAIN_FILE}" );
} else {
    add_default($nl, 'grid_type');
    add_default($nl, 'grid_format');
    add_default($nl, 'grid_file');
    add_default($nl, 'kmt_file');
}
add_default($nl, 'gridcpl_file');
add_default($nl, 'kcatbound');

##################################
# namelist group: forcing_nml    #
##################################

add_default($nl, 'formdrag');
add_default($nl, 'highfreq');
add_default($nl, 'natmiter');
add_default($nl, 'tfrz_option');
add_default($nl, 'fbot_xfer_type');
add_default($nl, 'l_mpond_fresh');

##################################
# namelist group: shortwave_nml  #
##################################

add_default($nl, 'shortwave');
add_default($nl, 'albedo_type');
add_default($nl, 'albicev');
add_default($nl, 'albicei');
add_default($nl, 'albsnowv');
add_default($nl, 'albsnowi');
add_default($nl, 'ahmax');
if ($cam4) {
    add_default($nl, 'R_ice'       , 'cam4'=>'.true.');
    add_default($nl, 'R_pnd'       , 'cam4'=>'.true.');
    add_default($nl, 'R_snw'       , 'cam4'=>'.true.');
    add_default($nl, 'dT_mlt'   , 'cam4'=>'.true.');
    add_default($nl, 'rsnw_mlt', 'cam4'=>'.true.');
} else {
    add_default($nl, 'R_ice'       );
    add_default($nl, 'R_pnd'       );
    add_default($nl, 'R_snw'       );
    add_default($nl, 'dT_mlt'   );
    add_default($nl, 'rsnw_mlt');
    add_default($nl, 'kalg');
}    


##################################
# namelist group: thermo_nml     #
##################################

add_default($nl, 'kitd');
add_default($nl, 'ktherm');
add_default($nl, 'conduct');
add_default($nl, 'a_rapid_mode');
add_default($nl, 'rac_rapid_mode');
add_default($nl, 'aspect_rapid_mode');
add_default($nl, 'dSdt_slow_mode');
add_default($nl, 'phi_c_slow_mode');
add_default($nl, 'phi_i_mushy');

##################################
# namelist group: dynamics_nml   #
##################################

add_default($nl, 'kdyn');
add_default($nl, 'revised_evp');
add_default($nl, 'ndte');
add_default($nl, 'advection');
add_default($nl, 'kstrength');
add_default($nl, 'krdg_partic');
add_default($nl, 'krdg_redist');
add_default($nl, 'mu_rdg');
add_default($nl, 'Cf');

##################################
# namelist group: ponds_nml      #
##################################

add_default($nl, 'hp1');
add_default($nl, 'hs0');
add_default($nl, 'hs1');
add_default($nl, 'dpscale');
add_default($nl, 'frzpnd');
add_default($nl, 'rfracmin');
add_default($nl, 'rfracmax');
add_default($nl, 'pndaspect');

##################################
# namelist group: zbgc_nml       #
##################################

add_default($nl, 'tr_brine');
add_default($nl, 'restart_hbrine');
add_default($nl, 'tr_zaero');
add_default($nl, 'modal_aero');
add_default($nl, 'skl_bgc');
add_default($nl, 'z_tracers');
add_default($nl, 'dEdd_algae');
add_default($nl, 'solve_zbgc');
add_default($nl, 'bgc_flux_type');
add_default($nl, 'restore_bgc');
add_default($nl, 'restart_bgc');
add_default($nl, 'scale_bgc');
add_default($nl, 'solve_zsal');
add_default($nl, 'restart_zsal');
add_default($nl, 'bgc_data_dir');
add_default($nl, 'sil_data_type');
add_default($nl, 'nit_data_type');
add_default($nl, 'fe_data_type');
add_default($nl, 'tr_bgc_Nit');
add_default($nl, 'tr_bgc_C');
add_default($nl, 'tr_bgc_chl');
add_default($nl, 'tr_bgc_Am');
add_default($nl, 'tr_bgc_Sil');
add_default($nl, 'tr_bgc_DMS');
add_default($nl, 'tr_bgc_PON');
add_default($nl, 'tr_bgc_hum');
add_default($nl, 'tr_bgc_DON');
add_default($nl, 'tr_bgc_Fe');
add_default($nl, 'grid_o');
add_default($nl, 'grid_o_t');
add_default($nl, 'l_sk');
add_default($nl, 'grid_oS');
add_default($nl, 'l_skS');
add_default($nl, 'phi_snow');
add_default($nl, 'initbio_frac');
add_default($nl, 'frazil_scav');
add_default($nl, 'ratio_Si2N_diatoms');
add_default($nl, 'ratio_Si2N_sp');
add_default($nl, 'ratio_Si2N_phaeo');
add_default($nl, 'ratio_S2N_diatoms');
add_default($nl, 'ratio_S2N_sp');
add_default($nl, 'ratio_S2N_phaeo');
add_default($nl, 'ratio_Fe2C_diatoms');
add_default($nl, 'ratio_Fe2C_sp');
add_default($nl, 'ratio_Fe2C_phaeo');
add_default($nl, 'ratio_Fe2N_diatoms');
add_default($nl, 'ratio_Fe2N_sp');
add_default($nl, 'ratio_Fe2N_phaeo');
add_default($nl, 'ratio_Fe2DON');
add_default($nl, 'ratio_Fe2DOC_s');
add_default($nl, 'ratio_Fe2DOC_l');
add_default($nl, 'fr_resp');
add_default($nl, 'tau_min');
add_default($nl, 'tau_max');
add_default($nl, 'algal_vel');
add_default($nl, 'R_dFe2dust');
add_default($nl, 'dustFe_sol');
add_default($nl, 'chlabs_diatoms');
add_default($nl, 'chlabs_sp');
add_default($nl, 'chlabs_phaeo');
add_default($nl, 'alpha2max_low_diatoms');
add_default($nl, 'alpha2max_low_sp');
add_default($nl, 'alpha2max_low_phaeo');
add_default($nl, 'beta2max_diatoms');
add_default($nl, 'beta2max_sp');
add_default($nl, 'beta2max_phaeo');
add_default($nl, 'mu_max_diatoms');
add_default($nl, 'mu_max_sp');
add_default($nl, 'mu_max_phaeo');
add_default($nl, 'grow_Tdep_diatoms');
add_default($nl, 'grow_Tdep_sp');
add_default($nl, 'grow_Tdep_phaeo');
add_default($nl, 'fr_graze_diatoms');
add_default($nl, 'fr_graze_sp');
add_default($nl, 'fr_graze_phaeo');
add_default($nl, 'mort_pre_diatoms');
add_default($nl, 'mort_pre_sp');
add_default($nl, 'mort_pre_phaeo');
add_default($nl, 'mort_Tdep_diatoms');
add_default($nl, 'mort_Tdep_sp');
add_default($nl, 'mort_Tdep_phaeo');
add_default($nl, 'k_exude_diatoms');
add_default($nl, 'k_exude_sp');
add_default($nl, 'k_exude_phaeo');
add_default($nl, 'K_Nit_diatoms');
add_default($nl, 'K_Nit_sp');
add_default($nl, 'K_Nit_phaeo');
add_default($nl, 'K_Am_diatoms');
add_default($nl, 'K_Am_sp');
add_default($nl, 'K_Am_phaeo');
add_default($nl, 'K_Sil_diatoms');
add_default($nl, 'K_Sil_sp');
add_default($nl, 'K_Sil_phaeo');
add_default($nl, 'K_Fe_diatoms');
add_default($nl, 'K_Fe_sp');
add_default($nl, 'K_Fe_phaeo');
add_default($nl, 'f_don_protein');
add_default($nl, 'kn_bac_protein');
add_default($nl, 'f_don_Am_protein');
add_default($nl, 'f_doc_s');
add_default($nl, 'f_doc_l');
add_default($nl, 'f_exude_s');
add_default($nl, 'f_exude_l');
add_default($nl, 'k_bac_s');
add_default($nl, 'k_bac_l');
add_default($nl, 'T_max');
add_default($nl, 'fsal');
add_default($nl, 'op_dep_min');
add_default($nl, 'fr_graze_s');
add_default($nl, 'fr_graze_e');
add_default($nl, 'fr_mort2min');
add_default($nl, 'fr_dFe');
add_default($nl, 'k_nitrif');
add_default($nl, 't_iron_conv');
add_default($nl, 'max_loss');
add_default($nl, 'max_dfe_doc1');
add_default($nl, 'fr_resp_s');
add_default($nl, 'y_sk_DMS');
add_default($nl, 't_sk_conv');
add_default($nl, 't_sk_ox');
add_default($nl, 'algaltype_diatoms');
add_default($nl, 'algaltype_sp');
add_default($nl, 'algaltype_phaeo');
add_default($nl, 'nitratetype');
add_default($nl, 'ammoniumtype');
add_default($nl, 'silicatetype');
add_default($nl, 'dmspptype');
add_default($nl, 'dmspdtype');
add_default($nl, 'humtype');
add_default($nl, 'doctype_s');
add_default($nl, 'doctype_l');
add_default($nl, 'dontype_protein');
add_default($nl, 'fedtype_1');
add_default($nl, 'feptype_1');
add_default($nl, 'zaerotype_bc1');
add_default($nl, 'zaerotype_bc2');
add_default($nl, 'zaerotype_dust1');
add_default($nl, 'zaerotype_dust2');
add_default($nl, 'zaerotype_dust3');
add_default($nl, 'zaerotype_dust4');
add_default($nl, 'ratio_C2N_diatoms');
add_default($nl, 'ratio_C2N_sp');
add_default($nl, 'ratio_C2N_phaeo');
add_default($nl, 'ratio_chl2N_diatoms');
add_default($nl, 'ratio_chl2N_sp');
add_default($nl, 'ratio_chl2N_phaeo');
add_default($nl, 'F_abs_chl_diatoms');
add_default($nl, 'F_abs_chl_sp');
add_default($nl, 'F_abs_chl_phaeo');
add_default($nl, 'ratio_C2N_proteins');


##################################
# namelist group: tracer_nml     #
##################################


add_default($nl, 'tr_lvl');
add_default($nl, 'tr_iage');
add_default($nl, 'tr_FY');
add_default($nl, 'tr_pond_cesm');
add_default($nl, 'tr_pond_lvl');
add_default($nl, 'tr_pond_topo');

my $ntr_aero = $cfg->get('ntr_aero');
if ($ntr_aero gt "0") {
   add_default($nl, 'tr_aero');
} else {
   add_default($nl, 'tr_aero', 'val'=>'.false.');
}

if ($cice_mode eq 'prescribed') {
   add_default($nl, 'restart_lvl', 'val'=>'.false.');
   add_default($nl, 'restart_age', 'val'=>'.false.');
   add_default($nl, 'restart_FY', 'val'=>'.false.');
   add_default($nl, 'restart_pond_cesm', 'val'=>'.false.');
   add_default($nl, 'restart_pond_lvl', 'val'=>'.false.');
   add_default($nl, 'restart_pond_topo', 'val'=>'.false.');
   add_default($nl, 'restart_aero', 'val'=>'.false.');
} else {
   add_default($nl, 'restart_lvl');
   add_default($nl, 'restart_age');
   add_default($nl, 'restart_FY');
   add_default($nl, 'restart_pond_cesm');
   add_default($nl, 'restart_pond_lvl');
   add_default($nl, 'restart_pond_topo');
   add_default($nl, 'restart_aero');
}

##################################
# namelist group: domain_nml     #
##################################

if (defined $xmlvars{'CICE_DECOMPSETTING'}) {
  add_default($nl, 'processor_shape', 'val'=>"$xmlvars{'CICE_DECOMPSETTING'}");
} else {
  add_default($nl, 'processor_shape');
}

if (defined $xmlvars{'CICE_DECOMPTYPE'}) {
    add_default($nl, 'distribution_type', 'val'=>"$xmlvars{'CICE_DECOMPTYPE'}");
} else {
    add_default($nl, 'distribution_type');
}
add_default($nl, 'distribution_wght'); 
my $distribution_wght = $nl->get_value('distribution_wght');
if ($distribution_wght =~ 'file') {
    add_default($nl, 'distribution_wght_file');
}
add_default($nl, 'ew_boundary_type');
add_default($nl, 'ns_boundary_type');
add_default($nl, 'maskhalo_dyn');
add_default($nl, 'maskhalo_remap');
add_default($nl, 'maskhalo_bound');

######################################
# namelist group: ice_prescribed_nml #
######################################

if ($cice_mode eq 'prescribed') {
    if ( defined $opts{'caseroot'} ) {
	if ($SSTICE_GRID_FILENAME eq 'UNSET') {
	    die "SSTICE_GRID_FILENAME must be set for cice prescribed mode \n";
	}
	if ($SSTICE_DATA_FILENAME eq 'UNSET') {
	    die "SSTICE_DATA_FILENAME must be set for cice prescribed mode \n"; 
	}
	if ($SSTICE_YEAR_ALIGN eq '-999') {
	    die "SSTICE_YEAR_ALIGN must be set for cice prescribed mode \n"; 
	}
	if ($SSTICE_YEAR_START eq '-999') {
	    die "SSTICE_YEAR_START must be set for cice prescribed mode \n"; 
	} 
	if ($SSTICE_YEAR_END eq '-999') {
	    die "SSTICE_YEAR_END must be set for cice prescribed mode \n"; 
	}
	my $stream_domxvarname;
	my $stream_domyvarname;
	if ($SSTICE_STREAM eq 'CAMDATA') {
	    $stream_domxvarname = "xc";  
	    $stream_domyvarname = "yc";
	} elsif ($SSTICE_STREAM eq 'WRFDATA') {
	    $stream_domxvarname = "xc";  
	    $stream_domyvarname = "yc";
	} else {       
	    $stream_domxvarname = "lon";  
	    $stream_domyvarname = "lat";
	}
	add_default($nl, 'model_year_align',  'val'=>"$SSTICE_YEAR_ALIGN");
	add_default($nl, 'stream_domtvarname','val'=>"time");
	add_default($nl, 'stream_domxvarname','val'=>"$stream_domxvarname");
	add_default($nl, 'stream_domyvarname','val'=>"$stream_domyvarname");
	add_default($nl, 'stream_domareaname','val'=>"area");
	add_default($nl, 'stream_dommaskname','val'=>"mask");
	add_default($nl, 'stream_domfilename','val'=>"$SSTICE_GRID_FILENAME");
	add_default($nl, 'stream_fldvarname' ,'val'=>"ice_cov");
	add_default($nl, 'stream_fldfilename','val'=>"$SSTICE_DATA_FILENAME");
	add_default($nl, 'stream_year_first' ,'val'=>"$SSTICE_YEAR_START");
	add_default($nl, 'stream_year_last'  ,'val'=>"$SSTICE_YEAR_END");
    } else {
	add_default($nl, 'model_year_align');
	add_default($nl, 'stream_domtvarname');
	add_default($nl, 'stream_domxvarname');
	add_default($nl, 'stream_domyvarname');
	add_default($nl, 'stream_domareaname'); 
	add_default($nl, 'stream_dommaskname');
	add_default($nl, 'stream_domfilename');
	add_default($nl, 'stream_fldvarname' );
	add_default($nl, 'stream_fldfilename');
	add_default($nl, 'stream_year_first' );
	add_default($nl, 'stream_year_last'  );
    }
    add_default($nl, 'prescribed_ice_fill', 'val'=>'.false.') ;
    add_default($nl, 'stream_mapread', 'val'=>'NOT_SET') ;
}

######################################
# namelist group: icefields_nml      #
######################################

add_default($nl, 'f_tmask');
add_default($nl, 'f_blkmask');
add_default($nl, 'f_tarea');
add_default($nl, 'f_uarea');
add_default($nl, 'f_dxt');
add_default($nl, 'f_dyt');
add_default($nl, 'f_dxu');
add_default($nl, 'f_dyu');
add_default($nl, 'f_HTN');
add_default($nl, 'f_HTE');
add_default($nl, 'f_ANGLE');
add_default($nl, 'f_ANGLET');
add_default($nl, 'f_bounds');
add_default($nl, 'f_NCAT');
add_default($nl, 'f_VGRDi');
add_default($nl, 'f_VGRDs');
add_default($nl, 'f_VGRDb');
add_default($nl, 'f_VGRDa');
add_default($nl, 'f_hi');
add_default($nl, 'f_hs');
add_default($nl, 'f_Tsfc');
add_default($nl, 'f_aice');
add_default($nl, 'f_uvel');
add_default($nl, 'f_vvel');
add_default($nl, 'f_uatm');
add_default($nl, 'f_vatm');
add_default($nl, 'f_fswdn');
add_default($nl, 'f_flwdn');
add_default($nl, 'f_snowfrac');
add_default($nl, 'f_snow');
add_default($nl, 'f_snow_ai');
add_default($nl, 'f_rain');
add_default($nl, 'f_rain_ai');
add_default($nl, 'f_sst');
add_default($nl, 'f_sss');
add_default($nl, 'f_uocn');
add_default($nl, 'f_vocn');
add_default($nl, 'f_sice');
add_default($nl, 'f_frzmlt');
add_default($nl, 'f_fswfac');
add_default($nl, 'f_fswabs');
add_default($nl, 'f_fswabs_ai');
add_default($nl, 'f_fswint_ai');
add_default($nl, 'f_albsni');
add_default($nl, 'f_alvdr');
add_default($nl, 'f_alidr');
add_default($nl, 'f_alvdf');
add_default($nl, 'f_alidf');
add_default($nl, 'f_alvdr_ai');
add_default($nl, 'f_alidr_ai');
add_default($nl, 'f_alvdf_ai');
add_default($nl, 'f_alidf_ai');
add_default($nl, 'f_albice');
add_default($nl, 'f_albsno');
add_default($nl, 'f_albpnd');
add_default($nl, 'f_coszen');
add_default($nl, 'f_flat');
add_default($nl, 'f_flat_ai');
add_default($nl, 'f_fsens');
add_default($nl, 'f_fsens_ai');
add_default($nl, 'f_fswup');
add_default($nl, 'f_flwup');
add_default($nl, 'f_flwup_ai');
add_default($nl, 'f_evap');
add_default($nl, 'f_evap_ai');
add_default($nl, 'f_Tair');
add_default($nl, 'f_Tref');
add_default($nl, 'f_Qref');
add_default($nl, 'f_congel');
add_default($nl, 'f_frazil');
add_default($nl, 'f_snoice');
add_default($nl, 'f_dsnow');
add_default($nl, 'f_meltt');
add_default($nl, 'f_melts');
add_default($nl, 'f_meltb');
add_default($nl, 'f_meltl');
add_default($nl, 'f_fresh');
add_default($nl, 'f_fresh_ai');
add_default($nl, 'f_fsalt');
add_default($nl, 'f_fsalt_ai');
add_default($nl, 'f_fhocn');
add_default($nl, 'f_fhocn_ai');
add_default($nl, 'f_fswthru');
add_default($nl, 'f_fswthru_ai');
add_default($nl, 'f_strairx');
add_default($nl, 'f_strairy');
add_default($nl, 'f_strtltx');
add_default($nl, 'f_strtlty');
add_default($nl, 'f_strcorx');
add_default($nl, 'f_strcory');
add_default($nl, 'f_strocnx');
add_default($nl, 'f_strocny');
add_default($nl, 'f_strintx');
add_default($nl, 'f_strinty');
add_default($nl, 'f_strength');
add_default($nl, 'f_divu');
add_default($nl, 'f_shear');
add_default($nl, 'f_sig1');
add_default($nl, 'f_sig2');
add_default($nl, 'f_dvidtt');
add_default($nl, 'f_dvidtd');
add_default($nl, 'f_daidtt');
add_default($nl, 'f_daidtd');
add_default($nl, 'f_dagedtt');
add_default($nl, 'f_dagedtd');
add_default($nl, 'f_mlt_onset');
add_default($nl, 'f_frz_onset');
add_default($nl, 'f_iage');
add_default($nl, 'f_FY');
add_default($nl, 'f_hisnap');
add_default($nl, 'f_aisnap');
add_default($nl, 'f_aicen');
add_default($nl, 'f_vicen');
add_default($nl, 'f_vsnon');
add_default($nl, 'f_snowfracn');
add_default($nl, 'f_trsig');
add_default($nl, 'f_icepresent');
add_default($nl, 'f_fsurf_ai');
add_default($nl, 'f_fcondtop_ai');
add_default($nl, 'f_fmeltt_ai');
add_default($nl, 'f_fsurfn_ai');
add_default($nl, 'f_fcondtopn_ai');
add_default($nl, 'f_fmelttn_ai');
add_default($nl, 'f_flatn_ai');
add_default($nl, 'f_fsensn_ai');
add_default($nl, 'f_keffn_top');
add_default($nl, 'f_Tinz');
add_default($nl, 'f_Sinz');
add_default($nl, 'f_Tsnz');
add_default($nl, 'f_a11');
add_default($nl, 'f_a12');
add_default($nl, 'f_e11');
add_default($nl, 'f_e12');
add_default($nl, 'f_e22');
add_default($nl, 'f_s11');
add_default($nl, 'f_s12');
add_default($nl, 'f_s22');
add_default($nl, 'f_yieldstress11');
add_default($nl, 'f_yieldstress12');
add_default($nl, 'f_yieldstress22');

######################################
# namelist group: icefields_pond_nml #
######################################

add_default($nl, 'f_apondn');
add_default($nl, 'f_apeffn');
add_default($nl, 'f_hpondn');
add_default($nl, 'f_apond');
add_default($nl, 'f_apond_ai');
add_default($nl, 'f_hpond');
add_default($nl, 'f_hpond_ai');
add_default($nl, 'f_ipond');
add_default($nl, 'f_ipond_ai');
add_default($nl, 'f_apeff');
add_default($nl, 'f_apeff_ai');

#########################################
# namelist group: icefields_mechred_nml #
#########################################

add_default($nl, 'f_ardg');
add_default($nl, 'f_vrdg');
add_default($nl, 'f_alvl');
add_default($nl, 'f_vlvl');
add_default($nl, 'f_dardg1dt');
add_default($nl, 'f_dardg2dt');
add_default($nl, 'f_dvirdgdt');
add_default($nl, 'f_opening');
add_default($nl, 'f_ardgn');
add_default($nl, 'f_vrdgn');
add_default($nl, 'f_dardg1ndt');
add_default($nl, 'f_dardg2ndt');
add_default($nl, 'f_dvirdgndt');
add_default($nl, 'f_aparticn');
add_default($nl, 'f_krdgn');
add_default($nl, 'f_aredistn');
add_default($nl, 'f_vredistn');
add_default($nl, 'f_araftn');
add_default($nl, 'f_vraftn');

######################################
# namelist group: icefields_drag_nml #
######################################

add_default($nl, 'f_Cdn_atm');
add_default($nl, 'f_Cdn_ocn');
add_default($nl, 'f_drag');

######################################
# namelist group: icefields_bgc_nml  #
######################################

add_default($nl, 'f_faero_atm');
add_default($nl, 'f_faero_ocn');
add_default($nl, 'f_aero');
add_default($nl, 'f_fbio');
add_default($nl, 'f_fbio_ai');
add_default($nl, 'f_zaero');
add_default($nl, 'f_bgc_S');
add_default($nl, 'f_bgc_N');
add_default($nl, 'f_bgc_C');
add_default($nl, 'f_bgc_DOC');
add_default($nl, 'f_bgc_DIC');
add_default($nl, 'f_bgc_chl');
add_default($nl, 'f_bgc_Nit');
add_default($nl, 'f_bgc_Am');
add_default($nl, 'f_bgc_Sil');
add_default($nl, 'f_bgc_DMSPp');
add_default($nl, 'f_bgc_DMSPd');
add_default($nl, 'f_bgc_DMS');
add_default($nl, 'f_bgc_DON');
add_default($nl, 'f_bgc_Fe');
add_default($nl, 'f_bgc_hum');
add_default($nl, 'f_bgc_PON');
add_default($nl, 'f_bgc_ml');
add_default($nl, 'f_upNO');
add_default($nl, 'f_upNH');
add_default($nl, 'f_bTin');
add_default($nl, 'f_bphi');
add_default($nl, 'f_iDi');
add_default($nl, 'f_iki');
add_default($nl, 'f_fbri');
add_default($nl, 'f_hbri');
add_default($nl, 'f_zfswin');
add_default($nl, 'f_bionet');
add_default($nl, 'f_biosnow');
add_default($nl, 'f_grownet');
add_default($nl, 'f_PPnet');
add_default($nl, 'f_algalpeak');
add_default($nl, 'f_zbgc_frac');

#-----------------------------------------------------------------------------------------------
# Write cice namelist file 

# Sea ice component 
my @groups = qw(setup_nml grid_nml tracer_nml thermo_nml dynamics_nml shortwave_nml ponds_nml forcing_nml domain_nml zbgc_nml icefields_bgc_nml icefields_drag_nml icefields_mechred_nml icefields_pond_nml icefields_nml ice_prescribed_nml);
my $outfile = "$opts{'dir'}/ice_in";
$nl->write($outfile, 'groups'=>\@groups);
if ($print>=2) { print "Writing sea ice component namelist to $outfile $eol"; }

#-----------------------------------------------------------------------------------------------
# Write cice input dataset list.
if ($opts{'inputdata'}) {
    check_input_files($nl, $inputdata_rootdir, $opts{'inputdata'});
}


#===============================================================================================
#===============================================================================================
# END OF MAIN SCRIPT
#===============================================================================================
#===============================================================================================

#===============================================================================================

sub add_default {

# Add a value for the specified variable to the specified namelist object.  The variables
# already in the object have the higher precedence, so if the specified variable is already
# defined in the object then don't overwrite it, just return.
#
# This method checks the definition file and adds the variable to the correct
# namelist group.
#
# The value can be provided by using the optional argument key 'val' in the
# calling list.  Otherwise a default value is obtained from the namelist
# defaults object.  If no default value is found this method throws an exception
# unless the 'nofail' option is set true.
#
# Additional optional keyword=>value pairs may be specified.  If the keyword 'val' is
# not present, then any other keyword=>value pairs that are specified will be used to
# match attributes in the defaults file.
#
# Example 1: Specify the default value $val for the namelist variable $var in namelist
#            object $nl:
#
#  add_default($nl, $var, 'val'=>$val)
#
# Example 2: Add a default for variable $var if an appropriate value is found.  Otherwise
#            don't add the variable
#
#  add_default($nl, $var, 'nofail'=>1)
#
#
# ***** N.B. ***** This routine assumes the following variables are in package main::
#  $definition        -- the namelist definition object
#  $inputdata_rootdir -- CCSM inputdata root directory

    my $nl = shift;     # namelist object
    my $var = shift;    # name of namelist variable
    my %opts = @_;      # options

    my $val = undef;

    # Query the definition to find which group the variable belongs to.  Exit if not found.
    my $group = $definition->get_group_name($var);
    unless ($group) {
	my $fname = $definition->get_file_name();
	die "$ProgName - ERROR: variable \"$var\" not found in namelist definition file $fname.\n";
    }

    # check whether the variable has a value in the namelist object -- if so then return
    $val = $nl->get_variable_value($group, $var);
    if (defined $val) {return;}

    # Look for a specified value in the options hash
    if (defined $opts{'val'}) {
	$val = $opts{'val'};
    }
    # or else get a value from namelist defaults object.
    # Note that if the 'val' key isn't in the hash, then just pass anything else
    # in %opts to the get_value method to be used as attributes that are matched
    # when looking for default values.
    else {
	$val = get_default_value($var, \%opts);
    }

    # if no value is found then exit w/ error (unless 'nofail' option set)
    unless (defined $val) {
	unless ($opts{'nofail'}) {
	    print "$ProgName - ERROR: No default value found for $var\n".
		"user defined attributes:\n";
	    foreach my $key (keys(%opts)) {
		if ($key ne 'nofail' and $key ne 'val') {
		    print "key=$key  val=$opts{$key}\n";
		}
	    }
	    die;
	}
	else {
	    return;
	}
    }

    # query the definition to find out if the variable is an input pathname
    my $is_input_pathname = $definition->is_input_pathname($var);

    # The default values for input pathnames are relative.  If the namelist
    # variable is defined to be an absolute pathname, then prepend
    # the CCSM inputdata root directory.
    # TODO: unless ignore_abs is passed as argument - and filename is not equal to 'default'  
    if ($is_input_pathname eq 'abs') {
	unless ($opts{'noprepend'}){
	    if ($val ne 'default') {
		$val = set_abs_filepath($val, $inputdata_rootdir);
	    }
	}
    }

    # query the definition to find out if the variable takes a string value.
    # The returned string length will be >0 if $var is a string, and 0 if not.
    my $str_len = $definition->get_str_len($var);

    # If the variable is a string, then add quotes if they're missing
    if ($str_len > 0) {
	$val = quote_string($val);
    }

    # set the value in the namelist
    $nl->set_variable_value($group, $var, $val);
}

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

sub get_default_value {

# Return a default value for the requested variable.
# Return undef if no default found.
#
# ***** N.B. ***** This routine assumes the following variables are in package main::
#  $defaults          -- the namelist defaults object
#  $uc_defaults       -- the use CASE defaults object

    my $var_name    = lc(shift);   # name of namelist variable (CASE insensitive interface)
    my $usr_att_ref = shift;       # reference to hash containing user supplied attributes

    # Check in the namelist defaults
    return $defaults->get_value($var_name, $usr_att_ref);

}

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

sub check_input_files {

# For each variable in the namelist which is an input dataset, check to see if it
# exists locally.
#
# ***** N.B. ***** This routine assumes the following variables are in package main::
#  $definition        -- the namelist definition object

    my $nl = shift;                 # namelist object
    my $inputdata_rootdir = shift;  # inputdata root directory
    my $outfile = shift;            # output file
    open(OUTFILE, ">$outfile") if defined $inputdata_rootdir;
    
    # Look through all namelist groups
    my @groups = $nl->get_group_names();
    foreach my $group (@groups) {
	
	# Look through all variables in each group
	my @vars = $nl->get_variable_names($group);
	foreach my $var (@vars) {
	    
	    # Is the variable an input dataset?
	    my $input_pathname_type = $definition->is_input_pathname($var);
	    
	    # If it is, check whether it exists locally and print status
	    if ($input_pathname_type) {
		
		# Get pathname of input dataset
		my $pathname = $nl->get_variable_value($group, $var);
		# Need to strip the quotes
		$pathname =~ s/[\'\"]//g;
		
                if ($pathname =~ m/unknown.+/) {
		    # skip file
                }
		elsif ($pathname =~ m/.*UNSET.*/) {
		    # skip file
                }
		elsif ($pathname =~ m/.*unset.*/) {
		    # skip file
                }
		elsif ($input_pathname_type eq 'stream') {
		    if ($pathname =~ m/.*(,).*/) {
			my @paths = split ",", $pathname, -1;   # The -1 prevents split from stripping trailing nulls
			foreach my $path (@paths) {
			    print OUTFILE "$var = $path\n";
			}
		    } else {
			print OUTFILE "$var = $pathname\n";
		    }			    
		    
		} 
		elsif ($input_pathname_type eq 'abs') {
		    if ($pathname ne 'default') {
			print OUTFILE "$var = $pathname\n";
		    }
		    elsif ($input_pathname_type =~ m/rel:(.+)/o) {
			# The match provides the namelist variable that contains the
			# root directory for a relative filename
			my $rootdir_var = $1;
			my $rootdir = $nl->get_variable_value($group, $rootdir_var);
			$rootdir =~ s/[\'\"]//g;
			$pathname = "$rootdir/$pathname";
			print OUTFILE "$var = $pathname\n";
		    }
		}
	    }
	}
    }
}

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

sub set_abs_filepath {

# check whether the input filepath is an absolute path, and if it isn't then
# prepend a root directory

    my ($filepath, $rootdir) = @_;

    # strip any leading/trailing whitespace
    $filepath =~ s/^\s+//;
    $filepath =~ s/\s+$//;
    $rootdir  =~ s/^\s+//;
    $rootdir  =~ s/\s+$//;

    # strip any leading/trailing quotes
    $filepath =~ s/^['"]+//;
    $filepath =~ s/["']+$//;
    $rootdir =~ s/^['"]+//;
    $rootdir =~ s/["']+$//;

    my $out = $filepath;
    unless ( $filepath =~ /^\// ) {  # unless $filepath starts with a /
        if ($filepath =~ m/unknown.+/ ) {
           $out = "$filepath";
       } else {
	   $out = "$rootdir/$filepath"; # prepend the root directory
       }
    }
    return $out;
}

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

sub absolute_path {
#
# Convert a pathname into an absolute pathname, expanding any . or .. characters.
# Assumes pathnames refer to a local filesystem.
# Assumes the directory separator is "/".
#
  my $path = shift;
  my $cwd = getcwd();  # current working directory
  my $abspath;         # resulting absolute pathname

# Strip off any leading or trailing whitespace.  (This pattern won't match if
# there's embedded whitespace.
  $path =~ s!^\s*(\S*)\s*$!$1!;

# Convert relative to absolute path.

  if ($path =~ m!^\.$!) {          # path is "."
      return $cwd;
  } elsif ($path =~ m!^\./!) {     # path starts with "./"
      $path =~ s!^\.!$cwd!;
  } elsif ($path =~ m!^\.\.$!) {   # path is ".."
      $path = "$cwd/..";
  } elsif ($path =~ m!^\.\./!) {   # path starts with "../"
      $path = "$cwd/$path";
  } elsif ($path =~ m!^[^/]!) {    # path starts with non-slash character
      $path = "$cwd/$path";
  }

  my ($dir, @dirs2);
  my @dirs = split "/", $path, -1;   # The -1 prevents split from stripping trailing nulls
                                     # This enables correct processing of the input "/".

  # Remove any "" that are not leading.
  for (my $i=0; $i<=$#dirs; ++$i) {
      if ($i == 0 or $dirs[$i] ne "") {
	  push @dirs2, $dirs[$i];
      }
  }
  @dirs = ();

  # Remove any "."
  foreach $dir (@dirs2) {
      unless ($dir eq ".") {
	  push @dirs, $dir;
      }
  }
  @dirs2 = ();

  # Remove the "subdir/.." parts.
  foreach $dir (@dirs) {
    if ( $dir !~ /\.\./ ) {
        push @dirs2, $dir;
    } else {
        pop @dirs2;   # remove previous dir when current dir is ..
    }
  }
  if ($#dirs2 == 0 and $dirs2[0] eq "") { return "/"; }
  $abspath = join '/', @dirs2;
  return( $abspath );
}

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

sub valid_option {

    my ($val, @expect) = @_;
    my ($expect);

    $val =~ s/^\s+//;
    $val =~ s/\s+$//;
    foreach $expect (@expect) {
	if ($val =~ /^$expect$/i) { return $expect; }
    }
    return undef;
}

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

sub validate_options {

    my $source = shift;   # text string declaring the source of the options being validated
    my $opts   = shift;   # reference to hash that contains the options

    my ($opt, $old, @expect);

}

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

sub quote_string {
    my $str = shift;
    $str =~ s/^\s+//;
    $str =~ s/\s+$//;
    unless ($str =~ /^[\'\"]/) {        #"'
        $str = "\'$str\'";
    }
    return $str;
}

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

sub expand_env_xml {

    my $value = shift;

    if ($value =~ /\$([\w_]+)(.*)$/) {
	my $subst = $xmlvars{$1};
	$value =~ s/\$${1}/$subst/g;
    }
    return $value; 
}