#!/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_color_lattice [options] xyzfile

generate another xyz file with the atoms at higher energy chemically changed
relative to a hexagonal-lattice (W_3) potential (values from -1 to 0).

Options:
	-a lattice_spacing
	-t threshold  : set the energy threshold to change the atom kind
			by default threshold = -0.5
							by Nick 27 Aug 2021
EOF
    return;
}

$PI=3.14159265358979324;
$BIG=99.e99;
$a=1;
$thresh=-0.5;

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 "-a"){ # help
	$a=shift(@ARGV)+0;
	$a>0 or die "Invalid lattice parameter $a\n";
	next;
    }
    if($p eq "-t"){ # help
	$thresh=shift(@ARGV)+0;
	$thresh<=0 && $thresh>= -1 or print STDERR "xyz_color_lattice: Valid threshold had better be in the [-1 , 0] range\n";
	next;
    }
    if($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                     
}

$#inputfiles<2 or die "Can process 1 file only!\n";

$filename=$inputfiles[0];
$count=0;
$totp=0;
$frames=0;
$nold=-99999;
open(INPUT, $filename) || die "Cannot open $filename\n";

while(<INPUT>){
    s/^\s*//;	# remove leading spaces
    @li = split('\s+');
    if($#li==0 && $li[0]+0==$li[0] && $count!=1){
	$n=$li[0]+0;
	print;
	$frames++;
	$count=0;
    }elsif($count==1){
	print;
    }else{
	$x=$li[1];
	$y=$li[2];
#	$W= -0.5-0.25*(cos(2*$PI*$x/$a) + cos(2*$PI*$y/$a) ); # square version
	$W= -2. / 9. * (1.5 +2.*cos(2*$PI*$x/$a) *cos(2.*$PI*$y/(sqrt(3.)*$a)) + cos(4*$PI*$y/(sqrt(3.)*$a)) );
	if($W>$thresh){
	    print "Li	$li[1]	$li[2]	$li[3]\n";
        }else{
	    print;
        }
    }
    $count++;
}
close(INPUT);