mirror of
https://github.com/nwchemgit/nwchem.git
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97f303e6f8
automatically be expanded to include useful information about the checkin (including the file's revision number). With the switch over to SVN this was lost because SVN only does this expansion if you explicitly ask for it (for every single file). I have added a script to the contrib directory that sets the appropriate property to get SVN to do this expansion. This script will make it easy to do this every time new source files are added. It is called svn_expand_Id, the script contains some comments that explain the issue and how it addresses this. This checkin sets this property for a subset of the relevant files (trying to commit all files at once failed with svn crashing). In future the script will only affect those files for which the property was not set before.
425 lines
14 KiB
Perl
425 lines
14 KiB
Perl
#
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# $Id$
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#
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#
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# perl script to parse nwchem output files
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#
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# The script is envoked with the command:
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# perl nwparse.pl [-h||-H||-help] [-d] [-q] [-s suffix] nwchem_output_file_1 [nwchem_output_file_2 ...]
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#
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#
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# Written: 4/21/97
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# By: Ricky A. Kendall
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# High Performance Computational Chemistry Group
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# Theory Modeling and Simulation Program
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# Environmental Molecular Sciences Laboratory
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# Pacific Northwest National Laboratory
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# P.O. Box 999
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# Richland, WA 99352-0999
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#
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$quiet = 0;
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$debug = 0;
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$num_argv = @ARGV;
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if ($num_argv == 0) {
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&Usage;
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die "fatal error: no file to parse\n";
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}
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$suffix = '.nwparse';
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#
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# parse optional arguments
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# 1) -d
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# 2) -s suffix
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# 3) -q
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@FILES_TO_PARSE = ();
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$get_suffix = 0;
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foreach $argument (@ARGV) {
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if ($get_suffix){
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$suffix = $argument;
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if (!($suffix =~ /^\./)) {$suffix = '.' . $suffix;}
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$get_suffix = 0;
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}
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elsif ($argument eq '-h' || $argument eq '-help' || $argument eq '-H'){
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&Usage; exit 0;}
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elsif ($argument eq '-d') {print "debug: debug turned on at command line\n";$debug = 1;}
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elsif ($argument eq '-s') {$get_suffix = 1;}
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elsif ($argument eq '-q') {$quiet = 1;}
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elsif ($argument =~ /^-/) {print "\n\nUnrecognized argument: $argument\n";die "fatal error";}
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else {push(@FILES_TO_PARSE,$argument);}
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}
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if ($debug) {$quiet =0;}
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if ($debug) {
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print "\ndebug:number of arguments: $num_argv\n\n";print "debug: arguments @ARGV";
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print "\ndebug: suffix is $suffix\n";
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print "\ndebug: files to parse @FILES_TO_PARSE";
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}
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foreach $filename (@FILES_TO_PARSE) {
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@atoms = ();
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@coords = ();
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@grads = ();
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if ($debug) {print "\ndebug: file to open is $filename\n";}
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open(FILE_TO_PARSE,$filename) || die "fatal error: Could not open file:$filename\n";
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$fileout = '>' . $filename . $suffix ;
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if ($debug) {print "\ndebug: file for parsed output is: $fileout\n";}
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open(FILE_OUTPUT,$fileout) || die "fatal error: Could not open file:$fileout\n";
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$selcipt_block = 0;
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$gradient_block = 0;
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$lines = 0 ;
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while (<FILE_TO_PARSE>){
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$lines ++;
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if ($selcipt_block && /^\s*$/) {
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$selcipt_block = 0;
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$num_energies = @ci_energy;
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$num_test = @pt_correc;
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if ($num_test != $num_energies) {
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die "number of ci+pt energies different than number of corrections\n";
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}
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$num_test = @cipt_ene;
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if ($num_test != $num_energies) {
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die "number of ci+pt energies different than number of summed ci+pt energies\n";
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}
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$num_test = @pt_norm;
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if ($num_test != $num_energies) {
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die "number of ci+pt energies different than number of pt norms\n";
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}
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if (! $quiet) {
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printf " ci energy pt correction ci+pt energy PT norm\n";
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printf " ---------- ------------- ------------ -------\n";
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}
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printf FILE_OUTPUT "ci energy pt correction ci+pt energy PT norm\n";
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printf FILE_OUTPUT "---------- ------------- ------------ -------\n";
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for ($itok = 0;$itok < $num_energies; $itok++){
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if (! $quiet){
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printf "%11.5f %13.5f %12.5f %7.3f\n",
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set_to_digits($ci_energy[$itok],5),
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set_to_digits($pt_correc[$itok],5),
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set_to_digits($cipt_ene[$itok],5),
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set_to_digits($pt_norm[$itok],3);
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}
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printf FILE_OUTPUT "%11.5f %13.5f %12.5f %7.3f\n",
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set_to_digits($ci_energy[$itok],5),
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set_to_digits($pt_correc[$itok],5),
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set_to_digits($cipt_ene[$itok],5),
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set_to_digits($pt_norm[$itok],3);
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}
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}
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if ($gradient_block && /^\s*$/) {
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$gradient_block = 0;
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$num_atoms = @atoms;
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$num_grads = @grads;
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$num_coords = @coords;
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if (($num_grads/3) != $num_atoms){
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print " num_grads = $num_grads\n";
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print " num_atoms = $num_atoms\n";
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die " fatal error ";
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}
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if (($num_coords/3) != $num_atoms){
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print " num_coords = $num_coords\n";
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print " num_atoms = $num_atoms\n";
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die " fatal error ";
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}
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if ($debug){
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print "debug: number of atoms: $num_atoms @atoms\n";
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print "debug: number of grads: $num_grads @grads\n";
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print "debug: number of coords: $num_coords @coords\n";
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}
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# SSSSSSSSSS FFFFFFFFFF FFFFFFFFFF FFFFFFFFFF
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if (! $quiet) {
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printf " Atoms Coordinates:\n";
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}
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printf FILE_OUTPUT " Atoms Coordinates:\n";
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for ($iatom=0;$iatom < $num_atoms; $iatom++){
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$indx1 = $iatom*3 ;
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$indx2 = $indx1 + 1;
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$indx3 = $indx1 + 2;
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if (! $quiet) {
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printf " %10s %10.4f %10.4f %10.4f\n",
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$atoms[$iatom],
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set_to_digits($coords[$indx1],4),
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set_to_digits($coords[$indx2],4),
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set_to_digits($coords[$indx3],4) ;
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}
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printf FILE_OUTPUT " %10s %10.4f %10.4f %10.4f\n",
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$atoms[$iatom],
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set_to_digits($coords[$indx1],4),
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set_to_digits($coords[$indx2],4),
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set_to_digits($coords[$indx3],4);
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}
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# SSSSSSSSSS FFFFFFFFFF FFFFFFFFFF FFFFFFFFFF
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if (! $quiet) {
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printf " Atoms Gradients:\n";
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}
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printf FILE_OUTPUT " Atoms Gradients:\n";
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for ($iatom=0;$iatom < $num_atoms; $iatom++){
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$indx1 = $iatom*3 ;
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$indx2 = $indx1 + 1;
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$indx3 = $indx1 + 2;
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if (! $quiet) {
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printf " %10s %10.4f %10.4f %10.4f\n",
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$atoms[$iatom],
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set_to_digits($grads[$indx1],4),
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set_to_digits($grads[$indx2],4),
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set_to_digits($grads[$indx3],4);
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}
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printf FILE_OUTPUT " %10s %10.4f %10.4f %10.4f\n",
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$atoms[$iatom],
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set_to_digits($grads[$indx1],4),
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set_to_digits($grads[$indx2],4),
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set_to_digits($grads[$indx3],4);
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}
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@atoms = ();
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@coords = ();
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@grads = ();
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}
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next if /^\s*$/;
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if (/failed/i || /warning/i) {
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print $_;
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}
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if (/^ Frequency/ || /^ P.Frequency/){
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if ($debug) {print "\ndebug: $_";}
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@line_tokens = split(' ');
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$num_line_tokens = @line_tokens;
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if ($debug) {
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print "debug:line_tokens: @line_tokens \n";
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print "debug:number : $num_line_tokens \n";
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}
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if (! $quiet) {
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printf "%s", @line_tokens[0];
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}
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printf FILE_OUTPUT "%s", @line_tokens[0];
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for($itok = 1;$itok < $num_line_tokens; $itok++){
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if (! $quiet) {
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printf "%10.0f ", set_to_digits(@line_tokens[$itok],0);
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}
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printf FILE_OUTPUT "%10.0f ", set_to_digits(@line_tokens[$itok],0);
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}
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if (! $quiet) {
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printf "\n";
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}
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printf FILE_OUTPUT "\n";
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}
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if (/Zero-Point Energy/) {
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if ($debug) {print "\ndebug: $_";}
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@line_tokens = split(' ');
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$num_line_tokens = @line_tokens;
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if ($debug) {
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print "debug:line_tokens: @line_tokens \n";
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print "debug:number : $num_line_tokens \n";
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}
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for($itok = 0;$itok < ($num_line_tokens-1); $itok++){
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if (! $quiet) {
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printf "%s ", @line_tokens[$itok];
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}
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printf FILE_OUTPUT "%s ", @line_tokens[$itok];
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}
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# *** Assumes $itok was incremented above
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if (! $quiet) {
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printf "%.5f\n", set_to_digits(@line_tokens[$itok],5);
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}
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printf FILE_OUTPUT "%.5f\n", set_to_digits(@line_tokens[$itok],5);
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}
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if (/nuclear/ && /repulsion/ && /energy/){
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if ($debug) {print "\ndebug: $_";}
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@line_tokens = split(' ');
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$num_line_tokens = @line_tokens;
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if ($debug) {
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print "debug:line_tokens: @line_tokens \n";
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print "debug:number : $num_line_tokens \n";
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}
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for($itok = 0;$itok < ($num_line_tokens-1); $itok++){
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if (! $quiet) {
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printf "%s ", @line_tokens[$itok];
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}
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printf FILE_OUTPUT "%s ", @line_tokens[$itok];
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}
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# *** Assumes $itok was incremented above
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if (! $quiet) {
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printf "%.4f\n", set_to_digits(@line_tokens[$itok],4);
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}
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printf FILE_OUTPUT "%.4f\n", set_to_digits(@line_tokens[$itok],4);
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}
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if (/Total/ && /energy/) {
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if (/SCF/ || /DFT/ || /CCSD/ || /MP2/ || /MCSCF/ || /RIMP2/ || /RISCF/ || /BAND/ || /PAW/ || /PSPW/ ) {
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if ($debug) {print "\ndebug: $_";}
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@line_tokens = split(' ');
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$num_line_tokens = @line_tokens;
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if ($debug) {
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print "debug:line_tokens: @line_tokens \n";
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print "debug:number : $num_line_tokens \n";
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}
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for($itok = 0;$itok < ($num_line_tokens-1); $itok++){
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if (! $quiet) {
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printf "%s ", @line_tokens[$itok];
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}
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printf FILE_OUTPUT "%s ", @line_tokens[$itok];
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}
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# *** Assumes $itok was incremented above
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if (! $quiet) {
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printf "%.5f\n", set_to_digits(@line_tokens[$itok],5);
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}
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printf FILE_OUTPUT "%.5f\n", set_to_digits(@line_tokens[$itok],5);
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}
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}
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if (/total/ && /energy/) {
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if ( /MBPT/ || /LCCD/ || /CCD/ || /LCCSD/ || /CCSD/ || /CCSDT/ || /CCSDTQ/ || /QCISD/ || /CISD/ || /CISDT/ || /CISDTQ/ ) {
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if ($debug) {print "\ndebug: $_";}
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@line_tokens = split(' ');
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$num_line_tokens = @line_tokens;
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if ($debug) {
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print "debug:line_tokens: @line_tokens \n";
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print "debug:number : $num_line_tokens \n";
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}
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for($itok = 0;$itok < ($num_line_tokens-1); $itok++){
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if (! $quiet) {
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printf "%s ", @line_tokens[$itok];
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}
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printf FILE_OUTPUT "%s ", @line_tokens[$itok];
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}
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# *** Assumes $itok was incremented above
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if (! $quiet) {
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printf "%.7f\n", set_to_digits(@line_tokens[$itok],7);
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}
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printf FILE_OUTPUT "%.7f\n", set_to_digits(@line_tokens[$itok],7);
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}
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}
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if (/Excitation energy/) {
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if ($debug) {print "\ndebug: $_";}
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@line_tokens = split(' ');
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$num_line_tokens = @line_tokens;
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if ($debug) {
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print "debug:line_tokens: @line_tokens \n";
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print "debug:number : $num_line_tokens \n";
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}
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for($itok = 0;$itok < ($num_line_tokens-1); $itok++){
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if (! $quiet) {
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printf "%s ", @line_tokens[$itok];
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}
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printf FILE_OUTPUT "%s ", @line_tokens[$itok];
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}
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# *** Assumes $itok was incremented above
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if (! $quiet) {
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printf "%.5f\n", set_to_digits(@line_tokens[$itok],5);
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}
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printf FILE_OUTPUT "%.5f\n", set_to_digits(@line_tokens[$itok],5);
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}
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if ($gradient_block == 2) {
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if ($debug) {print "debug:g3: $_";}
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@line_tokens = split(' ');
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$num_line_tokens = @line_tokens;
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if ($debug) {print "debug:num tok: $num_line_tokens\n"};
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if ($num_line_tokens == 8) {
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push(@atoms, $line_tokens[1]);
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push(@coords,@line_tokens[2..4]);
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push(@grads, @line_tokens[5..7]) ;
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if ($debug) {
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$num_atoms = @atoms;
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print " number of atoms: $num_atoms @atoms\n";
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$num_grads = @grads;
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print " number of grads: $num_grads @grads\n";
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$num_coords = @coords;
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print " number of coords: $num_coords @coords\n";
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}
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}
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else {print "possible bad gradient block\n";}
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}
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if (/atom coordinates gradient/){
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@atoms = ();
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@coords = ();
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@grads = ();
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$gradient_block = 1;
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if ($debug) {print "debug:g1: $_";}
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}
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if (/x y z x y z/){
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if ($debug) {print "debug:g2: gradient_block is $gradient_block\n";}
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if ($gradient_block == 1){
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$gradient_block++ ;
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if ($debug) {print "debug:g2: $_";}
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}
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}
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if ($selcipt_block == 2){
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if ($debug){print "debug:selci get info block: $_";}
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@line_tokens = split(' ');
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$num_line_tokens = @line_tokens;
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if ($debug) {print "debug:num tok: $num_line_tokens\n"};
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if ($num_line_tokens == 5){
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push(@ci_energy, $line_tokens[1]);
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push(@pt_correc, $line_tokens[2]);
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push(@cipt_ene, $line_tokens[3]);
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push(@pt_norm, $line_tokens[4]);
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}
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else {print "possible bad selci or selci+pt energy block\n";}
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}
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if (/^ EN\|/ || /^ MP\|/) {
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if ($selcipt_block == 1){
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@ci_energy = ();
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@pt_correc = ();
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@cipt_ene = ();
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@pt_norm = ();
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}
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$selcipt_block++ ;
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if ($debug) {print "debug:selcipt inc:$selcipt_block: line: $_";}
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}
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if (/^ Root/ && /final energy/){
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if ($debug) {print "\ndebug: $_";}
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@line_tokens = split(' ');
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$num_line_tokens = @line_tokens;
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if ($debug) {
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print "debug:line_tokens: @line_tokens \n";
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print "debug:number : $num_line_tokens \n";
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}
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for ($itok = 0; $itok < ($num_line_tokens - 1); $itok++){
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if ($itok == 1) {
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if (! $quiet) {printf "%4d ", @line_tokens[$itok];}
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printf FILE_OUTPUT "%4d ", @line_tokens[$itok];
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}
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else{
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if (! $quiet) {printf "%s ", @line_tokens[$itok];}
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printf FILE_OUTPUT "%s ", @line_tokens[$itok];
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}
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}
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if (! $quiet){printf "%.5f\n", set_to_digits(@line_tokens[$itok],5);}
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printf FILE_OUTPUT "%.5f\n", set_to_digits(@line_tokens[$itok],5);
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}
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}
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#
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#
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#
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if (! $quiet){
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print "nwparse.pl: parsed $lines in file $filename sent output to $fileout \n";
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}
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#
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# done close input and output files
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#
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close(FILE_TO_PARSE);
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close(FILE_OUPUT);
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}
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sub Usage
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{
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print "\n\nUsage: perl nwparse.pl [-h||-H||-help] [-d] [-q] [-s suffix] nwchem_output_file_1 [nwchem_output_file_2 ...]\n\n";
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print " -d := debug mode\n";
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print " -q := quiet mode (nothing to stdout) **\n";
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print " -s := override default suffix of .nwparse to user supplied 'suffix'\n";
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print " -h := prints this help message (equivalent to -help or -H)\n";
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print "\n **:Note: if -d is set -q is ignored\n";
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}
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sub set_to_digits
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{
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$value = shift;
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$digits = shift;
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for ($i = 0; $i < $digits ; $i++) {$value *= 10.0;}
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if ($value < 0.0) {$value -= 0.5;}
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else {$value += 0.5;}
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$value = int ($value);
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for ($i = 0; $i < $digits ; $i++) {$value /= 10.0;}
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if (abs($value) == 0.0) {$value = 0.0;}
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return $value;
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}
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