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neb_final.py
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Sat, Nov 9, 23:18

neb_final.py
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#!/usr/bin/env python
# make new dump file from final snapshots from multiple NEB replica dumps
# Syntax: neb_final.py -switch arg(s) -switch arg(s) ...
# -o outfile = new dump file
# snapshots numbered 1 to M = # of replicas
# -r dump1 dump2 ... = replica dump files of NEB atoms
# must be in correct sequence
# -b dumpfile = background atoms (optional)
# last snapshot in this file used as static non-NEB atoms
import sys,os
path = os.environ["LAMMPS_PYTHON_TOOLS"]
sys.path.append(path)
from dump import dump
# parse args
outfile = ""
backfile = ""
rfiles = []
argv = sys.argv
iarg = 1
narg = len(argv)
while iarg < narg:
if argv[iarg] == "-o":
outfile = argv[iarg+1]
iarg += 2
elif argv[iarg] == "-b":
backfile = argv[iarg+1]
iarg += 2
elif argv[iarg] == "-r":
ilast = iarg + 1
while ilast < narg and argv[ilast][0] != '-': ilast += 1
rfiles = argv[iarg+1:ilast]
iarg = ilast
else: break
if iarg < narg or not outfile or not rfiles:
print "Syntax: neb_final.py -o outfile -b backfile -r dump1 dump2 ..."
sys.exit()
if os.path.exists(outfile): os.remove(outfile)
# nback = additional atoms in each snapshot
if backfile:
back = dump(backfile)
t = back.time()
back.tselect.one(t[-1])
nback = back.snaps[-1].nselect
else: nback = 0
# write out each snapshot
# time = replica #
# natoms = ntotal, by overwriting nselect
# add background atoms if requested
n = 1
for file in rfiles:
neb = dump(file)
t = neb.time()
neb.tselect.one(t[-1])
hold = neb.snaps[-1].nselect
neb.snaps[-1].nselect = hold + nback
neb.snaps[-1].time = n
neb.write(outfile,1,1)
neb.snaps[-1].nselect = hold
if backfile: back.write(outfile,0,1)
n += 1

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