geomconvert

#!/usr/bin/perl -w

    @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");

    $in = $ARGV[0];
    $out = $in.".xyz";
    open(LOG, $in) || die "Can't open $in for reading.\n";
    open(OUT, ">$out") || die "Can't open $out for writing.\n";
    while (<LOG>){
        $line = $_;
        if ($line =~ /^\s+$/) { last }
        push @last_geometry, $line;
    }
    close LOG;
    for ($i = 0 ;$i <= $#last_geometry ; $i++){
        @crap= split(/\s+/,$last_geometry[$i]);
        $atom[$i] = $crap[2];
        $x[$i] = $crap[4];
        $y[$i] = $crap[5];
        $z[$i] = $crap[6];
        push @stripped_geometry, "$symbo[$atom[$i]-1]\t$x[$i]\t$y[$i]\t$z[$i]";
    }
    $stripped_geometry = join("\n",@stripped_geometry);
    print OUT "$stripped_geometry\n";