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neb_combine.py
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Tue, Jun 18, 11:02

neb_combine.py
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#!/usr/bin/env python
# make new dump file by combining snapshots from multiple NEB replica dumps
# Syntax: neb_combine.py -switch arg(s) -switch arg(s) ...
# -o outfile = new dump file
# each snapshot has NEB atoms from all replicas
# -r dump1 dump2 ... = replica dump files of NEB atoms
# can be in any order
# -b dumpfile = background atoms (optional)
# first 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_combine.py -o outfile -b backfile -r dump1 dump2 ..."
sys.exit()
if os.path.exists(outfile): os.remove(outfile)
# ntotal = total atoms in each snapshot
# reset IDs of atoms in each NEB dump file
ntotal = 0
d = []
for file in rfiles:
one = dump(file)
nnew = one.snaps[0].nselect
idvec = range(ntotal+1,ntotal+nnew+1)
one.setv("id",idvec)
ntotal += nnew
d.append(one)
# nback = additional atoms in each snapshot
# reset IDs of atoms in background file
if backfile:
back = dump(backfile)
t = back.time()
back.tselect.one(t[0])
nback = back.snaps[0].nselect
idvec = range(ntotal+1,ntotal+nback+1)
back.setv("id",idvec)
else: nback = 0
ntotal += nback
# write out each snapshot
# natoms = ntotal, by overwriting nselect
# add background atoms if requested
times = d[0].time()
for time in times:
d[0].tselect.one(time)
i = d[0].findtime(time)
hold = d[0].snaps[i].nselect
d[0].snaps[i].nselect = ntotal
d[0].write(outfile,1,1)
d[0].snaps[i].nselect = hold
for one in d[1:]:
one.tselect.one(time)
one.write(outfile,0,1)
if backfile: back.write(outfile,0,1)

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