#!perl
#=========================================================
# Author: Andrea Minoia
# Date: 03/09/2010
#
# Rename all the atoms in the given structure files
# as "Atomic_Symbol"-N, where N is the position
# of the atom in the structure (e.g. C-1, C-2, H-10,...)
#
# The script has to be in the same directory of the
# structure to modify and the user has to update the
# variable $filename (line 20) according to the name of the
# file containing the atomic structure.
#

use strict;
use MaterialsScript qw(:all);

#open the structure file or die
my $filename="octane.xsd";
my $doc = $Documents{$filename}; 
if (!$doc) {die "no document";}
my $atoms=$doc->Atoms;

#init atomic intex
my $atomindex=0;
# now loop over the atoms
foreach my $atom (@$atoms) {
    $atomindex++;
    #assign newname
    my $newname=$atom->ElementSymbol.'-'.$atomindex;
    $atom->Name=$newname;
}

print "Atom names have been uptaded for all atoms in ". $filename

#end