remove_duplicates_nbody.py
No OneTemporary
Actions

Subscribers

None

File Metadata

	#!/usr/bin/env python

	"""
	Get rid of lines containing duplicate bonded nbody interactions in the
	corresponding section of a LAMMPS data file (such as bonds, angles,
	dihedrals and impropers). Duplicate lines which occur later are
	preserved and the earlier lines are erased.
	(This program reads from sys.stdin. This program does not parse the entire
	data file. The text from the relevant section of the LAMMPS file should be
	extracted in advance before it is sent to this program.)

	"""

	import sys
	in_stream = sys.stdin

	if len(sys.argv) == 2:
	n = int(sys.argv[1])
	if (len(sys.argv) != 2) or (n < 1):
	sys.stderr.write('Error (remove_duplicates_nbody.py): expected a positive integer argument.\n')
	sys.exit(-1)

	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) == 2+n:
	atom_ids = tuple(tokens[2:2+n])
	if atom_ids in atom_ids_in_use:
	del lines[i]
	else:
	atom_ids_in_use.add(atom_ids)
	elif len(tokens) == 0:
	del lines[i]

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