bin/pind

   1 #!/usr/bin/perl
   2
   3 use FindBin qw($Bin);
   4 use lib "$Bin/../lib";
   5
   6 # Don't edit the line below, it must look exactly like this.
   7 # Everything above this line will be replaced #
   8
   9 use PsN;
  10 use model;
  11 use tool::pind;
  12 use strict;
  13 use debug;
  14 use Getopt::Long;
  15 use common_options;
  16
  17 my $cmd_line = $0 . " " . join( " ", @ARGV );
  18
  19 ## Configure the command line parsing
  20 Getopt::Long::config("auto_abbrev");
  21
  22 my %options;
  23 ## Declare the options
  24
  25 my %required_options;
  26
  27 my %optional_options = ("lst:s"=>'',
  28                         "ind_param:s"=>''
  29                         );
  30
  31 my $res = GetOptions( \%options,
  32                       @common_options::get_opt_strings,
  33                       keys(%required_options),
  34                       keys(%optional_options) );
  35 exit unless $res;
  36
  37 common_options::set_globals( \%options, 'pind' );
  38 common_options::get_defaults( \%options, 'pind' );
  39 common_options::sanity_checks( \%options, 'pind' );
  40
  41 my %help_text;
  42
  43 $help_text{Pre_help_message} = <<'EOF';
  44   pind
  45
  46     Perl script for individual probabilities.
  47
  48   Usage:
  49 EOF
  50
  51 $help_text{Options} = <<'EOF';
  52     Options:
  53
  54       The options are given here in their long form. Any option may be
  55       abbreviated to any nonconflicting prefix. The -threads option
  56       may be abbreviated to -t(or even -thr) but -debug may not be
  57       abbreviated to -d because it conflicts with -debug_packages and
  58       -debug_subroutines.
  59
  60       The following options are valid:
  61 EOF
  62
  63 $help_text{-h} = <<'EOF';
  64       -h | -?
  65
  66       With -h or -? pind will print a list of options and exit.
  67 EOF
  68
  69 $help_text{-help} = <<'EOF';
  70       -help
  71
  72       With -help pind will print this, longer, help message.
  73 EOF
  74
  75 $help_text{-lst_file} = <<'EOF';
  76       -lst_file=<filename>
  77
  78       Optional, the lst-file from where to read initial parameter estimates.
  79       Default is the same name as the model file but with .mod replaced with .lst.
  80 EOF
  81
  82 $help_text{-ind_param} = <<'EOF';
  83       -ind_param=eta|theta
  84
  85       Optional, default eta. The parameter to set in individual ofv model files.
  86       Possibilities are eta or theta.
  87 EOF
  88
  89
  90 $help_text{Post_help_message} = <<'EOF';
  91       Also see 'execute -help' for a description of common options.
  92 EOF
  93
  94 common_options::online_help( 'pind', \%options, \%help_text, \%required_options, \%optional_options);
  95
  96 ## Check that we do have a model file
  97 if ( scalar(@ARGV) < 1 ) {
  98   print "A simulation model file must be specified. Use 'pind -h' for help.\n";
  99   exit;
 100 }
 101
 102 if( scalar(@ARGV) > 1 ){
 103   print "PIND can only handle one modelfile, you listed: ",join(',',@ARGV),". Use 'pind -h' for help.\n";
 104   exit;
 105 }
 106
 107 my $lst_file;
 108 if (defined $options{'lst_file'}){
 109   $lst_file=$options{'lst_file'};
 110 } else {
 111   #assume modelfile ends with .mod
 112   $lst_file = (substr ($ARGV[0],0,-3)).'lst'; #keep from beginning, skip last four characters
 113   unless ( -e $lst_file ){
 114     print "When option -lst_file is omitted, the name of the lst-file is assumed to be the same\n".
 115         "as the modelfile except that the last three letters are lst. Cannot find file $lst_file.\n";
 116     exit;
 117   }
 118 }
 119
 120 unless ( defined $options{'clean'} ){
 121   # Clean may be changed by default
 122   $options{'clean'} = 1;
 123 }
 124
 125 my $eval_string = common_options::model_parameters(\%options);
 126
 127 my $model = model -> new ( eval( $eval_string ),
 128                            extra_output                => ['fort.80'],
 129                            filename                    => $ARGV[0],
 130                            ignore_missing_output_files => 1 );
 131
 132 my $pind = tool::pind ->
 133     new ( eval( $common_options::parameters ),
 134           models             => [$model],
 135           lst_file           => $lst_file,
 136           ind_param           => $options{'ind_param'}
 137           );
 138
 139
 140 open(CMD, ">", $pind -> directory . "/command.txt");
 141 print CMD $cmd_line, "\n";
 142 close(CMD);
 143
 144 $pind -> run;
 145
 146 open( TMP, ">", 'ofv.done' );
 147 print TMP "1";
 148 close( TMP );
 149
 150
 151 #$pind -> prepare_results;
 152 #$pind -> print_results;
 153