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lammps/tools/reax/reaxc_bond.pl
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reaxc_bond.pl
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#!/usr/bin/perl
use Getopt::Long;
Getopt::Long::Configure ('bundling');
#################################################################
# #
# This script is designed to take the bond information from a #
# Lammps/reaxc *.trj file and output a molecular fraction file #
# for each frame. #
# #
# written by Mike Russo, PSU #
# modified by Aidan Thompson, 5/12/2011 #
# #
# The required .trj file is generated by running LAMMPS #
# with pair_style reax/c and the following settings in #
# the corresponding reax/c control file #
# write_freq 25 ! write trajectory after so many steps
# traj_compress 0 ! 0: no compression 1: uses zlib to compress trajectory output
# traj_title TATB ! (no white spaces)
# atom_info 0 ! 0: no atom info, 1: print basic atom info in the trajectory file
# atom_forces 0 ! 0: basic atom format, 1: print force on each atom in the trajectory file
# atom_velocities 0 ! 0: basic atom format, 1: print the velocity of each atom in the trajectory file
# bond_info 1 ! 0: do not print bonds, 1: print bonds in the trajectory file
# angle_info 0 ! 0: do not print angles, 1: print angles in the trajectory file
# #
#################################################################
#################################################################
# Setting up some default variables, and options for the user #
# to input. #
#################################################################
$in_file = "bonds.trj";
@test = qw(C H O N);
GetOptions ('f|file=s' => \$in_file, 'a|atoms=s' => \@atoms, 'h|help' => \$help);
if($help) {
print "Options for this program:\n-f --file for input file default= bonds.trj\n-a --atoms atom types (in correct order and input separately) default= @test\n";
exit;
}
open INPUT, "<$in_file" or die "Cannot open $in_file: $!";
open OUTPUT, ">frac.dat" or die "Cannot open output file: $!";
if(@atoms) {
@test = @atoms;
}
print "Input for this run:\n Input file = $in_file\n Atom types = @test\n";
#################################################################
#################################################################
# Main loop of the script. Goes through each frames bond list. #
#################################################################
$i = 0;
$section = 0;
$at_count = -1;
while(<INPUT>) {
if(/chars_to_skip_section/) {
$section++;
&bonds if($section > 2);
next;
}
next if($section <= 0); #skipping the header section
next if(/\s*[A-Za-z]/); #skip text lines
split;
if ($section == 1) {
$q = $_[0];
$temp = $_[1];
$q--;
$at_type[$q] = $temp;
next;
}
$_[0]--;
$_[1]--;
# Add i-j and j-i entries
push @{$list[$_[0]]}, $_[1];
push @{$list[$_[1]]}, $_[0];
$at_count++ if($section == 2);
}
$section++;
&bonds;
close(INPUT);
#################################################################
#################################################################
# Subroutine bonds: Uses the bond information to generate a #
# count for each species, put them into molecules, and then #
# count the number of each molecule type. #
#################################################################
sub bonds {
$flag = ();
$k = 0;
for(0..$#list) {
if($flag[$_] == 0) {
push @{$full_list[$k]}, $_;
foreach $atom (@{$full_list[$k]}) {
for($o = 0; $o <= $#{$list[$atom]}; $o++) {
unless(grep /^$list[$atom][$o]$/, @{$full_list[$k]}) {
push @{$full_list[$k]}, $list[$atom][$o];
$flag[$list[$atom][$o]] = 1;
}
}
}
} else {
next;
}
$k++;
}
### Output section ###
$frame = $section - 2;
open OUTPUT2, ">temp_$frame.dat" or die "Cannot open temp file: $!";
print OUTPUT2 "Frame # $frame\n";
for($m = 0; $m < $k; $m++) { #cycle through each molecule
foreach $atom ((@{$full_list[$m]})) { #for each atom in this molecule
${"$test[$at_type[$atom]]"} += 1; #Create variable named C,H,O, etc and set it to count
}
print OUTPUT2 "Mol $m = ";
foreach $atom (@test) {
print OUTPUT2 "$atom${$atom}" if(${$atom} > 0);
}
print OUTPUT2 "\n";
for($r = 0; $r <= $#test; $r++) {
${"$test[$r]"} = 0;
}
}
close (OUTPUT2); #close the temp file as output
open INPUT3, "<temp_$frame.dat" or die "Cannot open temp file: $!"; # opne it as input
while(<INPUT3>) {
next if(/Frame/);
split;
push @mol_list, $_[3] unless(grep /^$_[3]$/, @mol_list);
${"$_[3]"}++;
}
print OUTPUT "Frame # $frame\n";
foreach $mol (@mol_list) {
printf OUTPUT "%4d %s\n", ${"$mol"}, $mol;
${"$mol"} = 0;
}
@mol_list = ();
###
### Cleanup between frames ###
for(0..$at_count) {
@{$full_list[$_]} = ();
@{$list[$_]} = ();
}
###
}
#################################################################
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