getgeom-scan

#!/usr/bin/perl

if (@ARGV < 2) { die "Syntax: getgeom filename identifier rootname charge multiplicity\nPulls out optimised geometries from a PES scan and uses them to create a new set of com files [rootname]-[identifier value].com\nEdit script to change calc type, basis set, etc.\n" } 

$file = $ARGV[0];
$id = $ARGV[1];
$mol = $ARGV[2];
$c = $ARGV[3];
$m = $ARGV[4];
$read = "n";
$readgeom = "n";
$npt = 0;

    @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");

open (FILE, "<$file") || die "couldn't open $file for reading\n";
while ($line = <FILE>) {
 #   print "$line $read\n";
     if ($line =~ / Optimization completed./) { 
         $read = "y";
     } 
     if (($line =~ /$id/) && ($line =~ /-DE\/DX/) && ($read =~ /y/))  { 
         @tmp = split(/\s+/,$line);
         if ($tmp[3] =~/\d+\.\d+/) {
             $r[$npt] = $tmp[3];
         }
         else {
             $r[$npt] = $tmp[4];
         }
         printf "%6.4f   ", $r[$npt];
         printf "%12.6f    ", $E[$npt][0];
         print "\n";
         $val[$npt] = int($r[$npt]*10);
         $root = $mol."-".$val[$npt];
         $out = $mol."-".$val[$npt].".com";
         open(OUT, ">$out") || die "Can't open $out for writing.\n"; 
         print OUT "%chk=$root.chk\n";
         print OUT "#BP86/gen 5D SCF=(Tight) IOP(2/17=4) INT(grid=ultrafine) Opt geom=modredundant\n\n";
         print OUT "$root\n\n";
         print OUT "$c $m\n";
         for ($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];
             $stripped_geometry[$i] = "$symbo[$atom[$i]-1]\t$x[$i]\t$y[$i]\t$z[$i]";
         }
         $stripped_geometry = join("\n",@stripped_geometry);
         print OUT "$stripped_geometry\n"; 
         print OUT "\n 29 35 F\n\n";
         print OUT "C H O 0\ndef2svp\n****\nFe 0\ndef2tzvp\n****\n\n";
         print OUT "\n --Link1--\n";
         print OUT "%chk=$root.chk\n";
         print OUT "#BP86/gen 5D SCF=(Tight) IOP(2/17=4) INT(grid=ultrafine) geom=check gues=read Freq(NoRaman) \n\n";
         print OUT "$root\n\n";
         print OUT "$c $m\n\n";
         print OUT "C H O 0\ndef2svp\n****\nFe 0\ndef2tzvp\n****\n\n";
         close (OUT);
         $npt++;
         $read = "n";
     }
     if ($line =~ /SCF Done/)  { 
         @tmp = split(/\s+/,$line);
         $E[$npt][0] = $tmp[5];
     }
     if ($line =~ /Standard orientation/)  { 
         $readgeom = "y";
         $no = 0;
         
     }
     if ($readgeom =~ /y/) {
        if ($line =~ /^\s+\d+/) { 
            $last_geometry[$no] = $line;
            $no++;
            }
        if ($line =~ /Rot/) { 
            $readgeom = "n";
            } 
     }

}

close (FILE);