source: util/ReSequenceDX.pl.in@ 1ddebb

#! @PERL@ -w
#
# Project: ESPACK 
# Jan Hamaekers
# Frederik Heber
# 2007
#

use strict;

my ($Help, $Prefix, $Outputdir, $Inputdir, $bytes, $ions);
my $i;
use Getopt::Long;
use File::Copy;

GetOptions("help"    => \$Help,
        "prefix=s"     => \$Prefix,
        "inputdir=s"    =>      \$Inputdir,
        "outputdir=s",   => \$Outputdir);
if ($Help) { usage(); }

sub usage {
    print STDERR <<"EOF";
Usage: $0 [OPTIONS]
Recreates the .dx files for OpenDX in a desired sequence from given .doc and .data files
  --prefix <prefix>             read data from file prefixed with this
  --inputdir <inputdir> read data from this directory
  --outputdir <outputdir> put the resequenced field into this dir 
  --help                        this help
EOF
    exit 1;
}

# open new .dx files and copy standard ones files
if (!defined $Outputdir) {
        if (defined $Inputdir) {
          $Outputdir="$Inputdir/view";
        } else {
                $Outputdir="./view";
        }
}
mkdir $Outputdir;
open(ELECTRONS_DX, ">$Outputdir/$Prefix.density.dx") or die "could not open $Outputdir/$Prefix.density.dx: $!";
open(IONS_DX, ">$Outputdir/$Prefix.ions.dx") or die "could not open $Outputdir/$Prefix.ions.dx: $!";

if (defined $Prefix && defined $Inputdir) {
        copy("$Inputdir/$Prefix.density.doc","$Outputdir/$Prefix.density.doc") or die "could not copy $Inputdir/$Prefix.density.doc to $Outputdir/: $!";
        copy("$Inputdir/$Prefix.ions.datZ","$Outputdir/$Prefix.ions.datZ") or die "could not copy $Inputdir/$Prefix.ions.datZ to $Outputdir/: $!";
        copy("$Inputdir/$Prefix.ions.doc","$Outputdir/$Prefix.ions.doc") or die "could not copy $Inputdir/$Prefix.ions.doc to $Outputdir/: $!";
} else {
        print "Need to know a prefix and inputdir for all OpenDX files!\n";
        exit 1;
}


# copy first the lines or so for the box
open(INPUT ,"<$Inputdir/$Prefix.density.dx");
my $buffer;
for ($i=1;$i<=11;$i++) {
        $buffer = <INPUT>;
        print ELECTRONS_DX "$buffer";
}
while (<INPUT>) {
        if ( /object "dat.0000"/ ) {
                my @linebuffer = split(/[ \t]+/);
                $bytes = $linebuffer[9];
        }
}
print "Found $bytes per data file\n";
close(INPUT);
open(INPUT ,"<$Inputdir/$Prefix.ions.dx");
for ($i=1;$i<=4;$i++) {
        $buffer = <INPUT>;
        print IONS_DX "$buffer";
}
while (<INPUT>) {
        if ( /object "ionpos.0000"/ ) {
                my @linebuffer = split(/[ \t]+/);
                $ions = $linebuffer[11];
        }
}
print "Found $ions per data file\n";
close(INPUT);

# add per object the referencing and copy the .data file
my ($source, $dest);
for($i=0;$i<=$#ARGV;$i++) {
        $source = sprintf("%04d",$ARGV[$i]);
        $dest = sprintf("%04d",$i);
        copy("$Inputdir/$Prefix.density.data.$source","$Outputdir/$Prefix.density.data.$dest") or die "could not copy $Inputdir/$Prefix.density.data.$source to $Outputdir/$Prefix.density.data.$dest: $!";
        printf(ELECTRONS_DX "object \"dat.%04d\" class array type float rank 0 items %d lsb binary\n", $i, $bytes);
        printf(ELECTRONS_DX "data file $Prefix.density.data.%04d,0\n",$i);
        print (ELECTRONS_DX "attribute \"dep\" string \"positions\"\n\n");  # 0 - 8586755 Bytes\n\n");
        printf(ELECTRONS_DX "object \"obj.%04d\" class field\n",$i);
        printf(ELECTRONS_DX "component \"positions\" \"posdens\"\ncomponent \"connections\" \"gridcon\"\ncomponent \"data\" \"dat.%04d\"\n\n",$i);

        copy("$Inputdir/$Prefix.ions.force.$source","$Outputdir/$Prefix.ions.force.$dest") or die "could not copy $Inputdir/$Prefix.ions.force.$source to $Outputdir/$Prefix.ions.force.$dest:$!";
        copy("$Inputdir/$Prefix.ions.pos.$source","$Outputdir/$Prefix.ions.pos.$dest") or die "could not copy $Inputdir/$Prefix.ions.pos.$source to $Outputdir/$Prefix.ions.pos.$dest:$!";
        printf(IONS_DX "object \"ionpos.%04d\" class array type float rank 1 shape 3 items %d lsb binary\n", $i, $ions);
        printf(IONS_DX "data file $Prefix.ions.pos.%04d,0\n\n",$i);
        printf(IONS_DX "object \"iondatF.%04d\" class array type float rank 1 shape 3 items %d lsb binary\n",$i, $ions);
        printf(IONS_DX "data file $Prefix.ions.force.%04d,0\nattribute \"dep\" string \"positions\"\n\n",$i);
        printf(IONS_DX "object \"ionobjF.%04d\" class field\n",$i);
        printf(IONS_DX "component \"positions\" \"ionpos.%04d\"\n",$i);
        printf(IONS_DX "component \"data\" \"iondatF.%04d\"\n",$i);
        printf(IONS_DX "object \"ionobjZ.%04d\" class field\n",$i);
        printf(IONS_DX "component \"positions\" \"ionpos.%04d\"\ncomponent \"data\" \"iondatZ\"\n\n",$i);
}

# finialize with member list
print ELECTRONS_DX "object \"series\" class series\n";
print IONS_DX "object \"ionseriesF\" class series\n";
for($i=0;$i<=$#ARGV;$i++) {
        printf(ELECTRONS_DX "member %d \"obj.%04d\" position %d.000000\n",$i,$i,$i);
        printf(IONS_DX "member %d \"ionobjF.%04d\" position %d.000000\n",$i,$i,$i);
}
print ELECTRONS_DX "end\n";
print IONS_DX "\n";
print IONS_DX "object \"ionseriesZ\" class series\n";
for($i=0;$i<=$#ARGV;$i++) {
        printf(IONS_DX "member %d \"ionobjZ.%04d\" position %d.000000\n",$i,$i,$i);
}
print IONS_DX "end\n";

# end
exit 0