ircscan

#! /usr/bin/perl 

@symbo=("","H","He",
        "Li","Be",                                                   "B", "C", "N", "O", "F","Ne",
        "Na","Mg",                                                  "Al","Si", "P", "S","Cl","Ar",
        "K","Ca","Sc","Ti", "V","Cr","Mn","Fe","Co","Ni","Cu","Zn","Ga","Ge","As","Se","Br","Kr",
        "Rb","Sr", "Y","Zr","Nb","Mo","Tc","Ru","Rh","Pd","Ag","Cd","In","Sn","Sb","Te", "I","Xe",
        "Cs","Ba",
        "La","Ce","Pr","Nd","Pm","Sm","Eu","Gd","Tb","Dy","Ho","Er","Tm","Yb","Lu",
        "Hf","Ta", "W","Re","Os","Ir","Pt","Au","Hg","Tl","Pb","Bi","Po","At","Rn",
        "Fr","Ra",
        "Ac","Th","Pa", "U","Np","Pu","Am","Cm","Bk","Cf","Es","Fm","Md","No","Lr");

$filename = $ARGV[0];
chomp($filename);
$filename =~ s/.log//;
$input =file2string($ARGV[0]);
$step=0;
@cm = split(/Charge/,$input);
@cm = split(/\s+/,$cm[1]);
if ($input =~/irc/i){
    print "this is an irc job\n";
    $job="irc";
}
elsif ($input =~/scan/i){
    @crap3 =split(/Scan/,$input);
    @startpoint =split(/\s+/,$crap3[0]);
    @stepsize =split(/\s+/,$crap3[1]);
    print "this is a scan job\n";
    $job="scan";
}

    

@crap = split(/Optimization /,$input);
open engfile, ">$filename.eng" or die $!;

for ($i=0;$i< $#crap;$i++){
    @crap1 = split(/Z-Matrix orientation:/,$crap[$i]);
    @geom = split(/Distance matrix/,$crap1[$#crap1]);
    @crap2 = split(/SCF Done:/,$crap[$i]);
    @eng = split(/\s+/,$crap2[$#crap2]);
    if($job eq "irc"){
        print engfile $step+1,"\t$eng[3]\n";
    }
    elsif($job eq "scan"){
        print engfile $step+1,"\t", $startpoint[$#startpoint]+$stepsize[2]*$i, "\t$eng[3]\n";
    }
    $optgeom[$step] = $geom[0];
    $step++;
}
close engfile ;

print "There are $step steps in $filename.log\n";

for ($i=0;$i<$step;$i++){
    $a = $i+1;
    open geomfile, ">$filename.$a.gin" or die $!;
    print geomfile "$cm[2]\t$cm[5]\n";
    @xyz=split(/\n/,$optgeom[$i]);
    for ($j=5;$j<$#xyz-1;$j++){
        @orient = split(/\s+/,$xyz[$j]);
        $A[$j] = $orient[2];
        $X[$j] = $orient[4];
        $Y[$j] = $orient[5];
        $Z[$j] = $orient[6];
        print geomfile "$symbo[$A[$j]]\t$X[$j]\t$Y[$j]\t$Z[$j]\n";
    }
    print geomfile "\n";
    close geomfile;
}

sub file2string {
    # file2string("filename") : gets a txt file, turns it into a string.
    local $/;

    open(INPUTFILE, $_[0]) ||die "Can't open $_[0] for reading.\n";
    undef $/;
    $file = <INPUTFILE>;
    close(INPUTFILE)|| die "Can't close $_[0].\n";
    return $file;
}

__END__