#!/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_delete_atom [options] file.xyz

removes a single atom from a xyz file
options:
	-i or -a select the atom index (default = $index)
	-s Sy fixes the atomic symbol to Sy (default = $symbol)
						version 16/02/2018 by Nick
EOF
    return;
}

$BIG=9.999e200;

# defaults:
$index=1;
$symbol="Au";
$filename="-";

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" || $p eq "-i"){
        $index=shift(@ARGV)+0;
        $index>0 or die "Invalid index $index\n";
        next;
    }
    if($p eq "-s"){
        $symbol=shift(@ARGV);
        next;
    }
    if($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
}

$count=-1;
$actualframes=0;

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;
	    $index<=$natom or die "delete index $index > $natom\n";
	    print $natom-1,"\n";
	}
	if($count==1){
	    $comment=$_;
	    $comment=~s/\n//;;
	    print "$comment - deleted atom $index\n";
	}
	if($count>1){
	    if($count-1!=$index){
		print;
	    }else{
		shift @li;
		print $symbol,"\t@li","\n";
	    }
	}
	$count++;
    }
    close(INPUT);
}
















while(<INPUT>){
    s/^\s*//; @li = split('\s+');
    if($#li==0 && $li[0]+0==$li[0]){
	$count++;
	$natms = $li[0];
	$index <= $natms or die "index $index is not compatible with this xyz file, with $natms atoms only\n";
	$_=<INPUT>;
	s/^\s*//; @li = split('\s+');
	$time=$li[1]+0.;
	if($time<=0){
	    $time=$count;
	}
	for($i=1;$i<=$natms;$i++){
	    $_=<INPUT>;
	    if($i == $index){
		s/^\s*//; @li = split('\s+');
		print $time,"\t",$li[1],"\t",$li[2],"\t",$li[3],"\n",
	    }
	}
    }
}
close(INPUT);