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#!/usr/bin/env 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_displacement [options] xyzfile1
write out another xyz file with
a) the displacements between subsequent frames of xyzfile1 (default behavior)
b) changed names of atoms moving more than a given threshold (when -t is set)
Options:
-t threshold : set the displacement threshold to change the atom name
by default threshold=0, so that output is displacements
by Nick 10 May 2017
EOF
return;
}
$BIG=99.e99;
$thresh=0;
while($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 xyz_displacement: file $p does not exist\n";
}
next;
}
if($p eq "-t"){ # help
$thresh=shift(@ARGV)+0;
$thresh>0 or die "Invalid threshold $thresh\n";
next;
}
if($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 either 1 file only!\n";
$filename=$inputfiles[0];
$count=0;
$totp=0;
$frames=0;
$nold=-99999;
$threshq=$thresh*$thresh;
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;
if($n==$nold){
print;
}elsif($nold!=-99999){
print STDERR "ERROR xyz_displacement: file $filename has frames with different numbers of particles: $n, $nold\n";
}
$frames++;
$count=0;
}elsif($count==1){
$t=1. *$li[1];
if($t==$li[1]){
$tnow=$t;
if($n==$nold){
if($thresh>0){
print "#intermediate_time= ",0.5*($tnow+$told),"\n";
}else{
print "#deltat= ",$tnow-$told,"\n";
}
}
}else{
if($n==$nold){print;}
}
$told=$tnow;
}else{
if($n==$nold){
$dx=$li[1]-$oldx[$count];
$dy=$li[2]-$oldy[$count];
$dz=$li[3]-$oldz[$count];
if($thresh>0){
$delta=$dx*$dx+$dy*$dy+$dz*$dz;
if($delta>$threshq){
print "Rb $li[1] $li[2] $li[3]\n";
}else{
print;
}
}else{
print "$li[0] $dx $dy $dz\n";
}
}
$oldx[$count]=$li[1];
$oldy[$count]=$li[2];
$oldz[$count]=$li[3];
if($count==$n+1){
$nold=$n;
}
}
$count++;
}
close(INPUT);
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