#!/usr/bin/perl
# the above is the standard linux/unix path for perl: change if your computer is nonstandard

sub print_help{
    print STDERR <<EOF;

Syntax:  xyz_stretch [options] input_xyzfile

generate an xyz file stretched by a factor (optionally in a given direction)

Options:
-f stretching factor (default: $stretch)
-a ax ay az  (stretching direction - if unspecified stretch uniformly
							by Nick 23 Oct 2014
EOF
    return;
}

$BIG=99.e99;
$stretch=2;

@a=(0.,0.,0.);
while($p=shift(@ARGV)){
    if($p=~/^[^\-]/){ # all command line options start with "-", otherwise it a filename
        if(-e $p){
            push(@inputfiles,$p);
        }else{
            print STDERR "ERROR: file $p does not exist\n";
        }
        next;
    }
    if($p eq "-f"){ # factor
	$stretch=shift(@ARGV)+0;
	next;
    }
    if($p eq "-a"){
	$x=shift(@ARGV)+0.; $y=shift(@ARGV)+0.; $z=shift(@ARGV)+0.;
	@a=($x,$y,$z);
	next;
    }
    if($p eq "-h"){ # help
	print_help;
	die "\n";
    }
    print_help;
    die "invalid option $p\n";
}

if($#inputfiles<0){
    push(@inputfiles,"-");      #       adds stdio for lack of arguments
}

$norm=$a[0]*$a[0]+$a[1]*$a[1]+$a[2]*$a[2];
$norm=sqrt($norm);
if($norm!=0.){
    for($i=0;$i<3;$i++){
	$a[$i]=$a[$i]/$norm;
    }
}
while ($filename=shift(@inputfiles)){
    $natom=0;
    $count=0;
    $totp=0;
    $frames=0;
    open(INPUT, $filename) || die "Cannot open $filename\n";
    while(<INPUT>){
	s/^\s*//;	# remove leading spaces
	@li = split('\s+');
	if($#li==0 && $count!=1){
	    $count=0;
	    $frames++;
	    @ato=();
	    @atpo=();
	    $natom=$li[0]+0;
	    print;
	}
	if($count==1){
	    $comment=$_;
	    $comment=~s/\n//;;
	    print $comment," stretched by ",$stretch,"\n";
	}
	if($count>1){
	    if($norm==0.){
		print $li[0],"\t",$li[1]*$stretch,"\t",$li[2]*$stretch,"\t",$li[3]*$stretch,"\n";
	    }else{
		$pro=$li[1]*$a[0]+$li[2]*$a[1]+$li[3]*$a[2];
		print $li[0];
		for($i=0;$i<3;$i++){
		    print "\t",$li[$i+1]+$a[$i]*$pro*($stretch-1);
		}
		print "\n";
	    }
	}
	$count++;
    }
    close(INPUT);
}