[lammps-users] Vizualize results

Whether it takes long in Pizza.py probably depends on how fast your OpenGL implementation is. I have found that on my laptop, it's slow, but on my workstation, which has an NVIDIA card, it's much quicker. You can convert the dump file to a CFG file and view it with AtomEye, which I've found to be pretty quick even on my laptop. AtomEye does *not* use OpenGL. You can use Pizza.py to convert dump files to CFG, but so far as I've seen, the CFG files produced by Pizza.py have integer labels where element symbols should be. Maybe there is a way to fix this within Pizza.py, but so far I've used a little Perl as a workaround. This is the script I've written for a Ga-In-As system:

use warnings;
use strict;
use Tie::File;

foreach my $fileName (@ARGV) {
    tie my @fileLines, 'Tie::File', $fileName
        or die "Cannot open $fileName!\n";

    for (my $i = 0; $i < @fileLines; $i++) {
        $fileLines[$i] =~ s/^1\.0 1 /1.0 Ga/;
        $fileLines[$i] =~ s/^1\.0 2 /1.0 In/;
        $fileLines[$i] =~ s/^1\.0 3 /1.0 As/;

    untie @fileLines;

If you save the script as fix_cfg.pl, then you run it as follows:

perl fix_cfg.pl dump_file1 dump_file2 ...

You'll obviously have to modify this script to take into account the atom types that you are using, and I can only promise that the Perl script worked for me, not that it is robust.