			#!/usr/local/bin/python

			# combine multiple NEB dump files into 1 dump file
			# Syntax: neb1.py dfinal itype dfile1 dfile2 ...
			# dfinal = new combined dump file
			# itype = atoms of this type are added to each snapshot
			# dfile1, dfile2, ... = NEB output dump files from each replica

			# assumes all N input files have same # of snapshots
			# for each snapshot time:
			# all dfile1 atoms are added to dfinal
			# only atoms of itype in dfile2,...,dfileN are added to dfinal

			import sys,os
			path = os.environ["LAMMPS_PYTHON_TOOLS"]
			sys.path.append(path)
			from dump import dump

			if len(sys.argv) < 5:
			print "Syntax: neb1.py dfinal itype dfile1 dfile2 ..."
			sys.exit()

			dfinal = sys.argv[1]
			itype = int(sys.argv[2])
			files = sys.argv[3:]

			tstr = "$type == %d" % itype

			ntotal = 0
			d = []
			for file in files:
			one = dump(file)
			one.sort()
			if d:
			one.aselect.test(tstr)
			nnew = one.snaps[0].nselect
			idvec = range(ntotal+1,ntotal+nnew+1)
			one.setv("id",idvec)
			ntotal += one.snaps[0].nselect
			d.append(one)

			if os.path.exists(dfinal): os.remove(dfinal)

			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(dfinal,1,1)
			d[0].snaps[i].nselec = hold
			for one in d[1:]:
			one.tselect.one(time)
			one.aselect.test(tstr)
			one.write(dfinal,0,1)

lammps/tools/python/neb1.py
b956107fc6f1lammm-master

neb1.py
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