remove_duplicate_atoms.py
fadc25d704eflammm-devel

remove_duplicate_atoms.py
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			#!/usr/bin/env python

			"""
			Get rid of lines containing duplicate copies of the same atom in the "Atoms"
			section of a LAMMPS data file. Duplicate lines which occur later are
			preserved and the earlier lines are erased.
			The file is read from sys.stdin. This program does not parse the entire
			data file. The text from the "Atoms" section of the LAMMPS file must
			be extracted in advance before it is sent to this program.)

			"""

			import sys
			in_stream = sys.stdin
			f = None
			fname = None
			if len(sys.argv) == 2:
			fname = sys.argv[1]
			f = open(fname, 'r')
			in_stream = f

			atom_ids_in_use = set([])

			lines = in_stream.readlines()

			# Start at the end of the file and read backwards.
			# If duplicate lines exist, eliminate the ones that occur earlier in the file.
			i = len(lines)
			while i > 0:
			i -= 1
			line_orig = lines[i]
			line = line_orig.rstrip('\n')
			if '#' in line_orig:
			ic = line.find('#')
			line = line_orig[:ic]

			tokens = line.strip().split()
			if len(tokens) > 0:
			atom_id = tokens[0]
			if atom_id in atom_ids_in_use:
			del lines[i]
			else:
			atom_ids_in_use.add(atom_id)
			else:
			del lines[i]


			for line in lines:
			sys.stdout.write(line)

			if f != None:
			f.close()