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nbody_reorder_atoms.py
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Sat, May 11, 18:01

nbody_reorder_atoms.py
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#!/usr/bin/env python
"""
Reorder the atoms in the Angles section of a data file to make sure that
atoms have a "canonical order" (for example the first atom has a lower
id than the last atom, for angle and dihedral interactions.
(This helps us detect potential problems like dupicate Angle interactions.)
"""
import sys
from operator import itemgetter
g_program_name = __file__.split('/')[-1]
in_stream = sys.stdin
section_name = ''
if len(sys.argv) == 2:
section_name = sys.argv[1]
else:
sys.stderr.write('Usage Example:\n\n'
' '+g_program_name+' Angles < angles.txt > new_angles.txt\n\n'
' In this example \"angles.txt\" contains only the \"Angles\" section of\n'
' a LAMMPS DATA file. (Either a text-editor, or the \n'
' \"extract_lammps_data.py\" script can be used to select a section from\n'
' a LAMMPS DATA file\n\n'
'Error('+g_program_name+'): expected exactly one argument:\n'
' \"Angles\", \"Dihedrals\", or \"Impropers\"\n')
exit(-1)
# Ordering rules are defined in a seperate module named
# nbody_Angles.py, nbody_Dihedrals.py, nbody_Impropers.py
# Load that now.
module_name = 'nbody_'+section_name
g = __import__(module_name) #defines g.bond_pattern, g.canonical_order
# This module defines the graph representing the bond pattern for this type
# of interaction. (The number of vertices and edges for the graph corresponds
# to the number of atoms and bonds in this type of interaction.)
natoms = g.bond_pattern.GetNumVerts()
nbonds = g.bond_pattern.GetNumEdges()
for line_orig in in_stream:
line = line_orig.rstrip('\n')
comment = ''
if '#' in line_orig:
ic = line.find('#')
line = line_orig[:ic]
comment = ' '+line_orig[ic:].rstrip('\n')
tokens = line.strip().split()
swapped = False
if len(tokens) == 2+natoms:
all_integers = True
abids_l = [[0 for i in range(0, natoms)],
[0 for i in range(0, nbonds)]]
for i in range(0, natoms):
if not tokens[2+i].isdigit():
all_integers = False
if all_integers:
for i in range(0, natoms):
abids_l[0][i] = int(tokens[2+i])
else:
for i in range(0, natoms):
abids_l[0][i] = tokens[2+i]
abids = g.canonical_order( (tuple(abids_l[0]), tuple(abids_l[1])) )
for i in range(0, natoms):
tokens[2+i] = str(abids[0][i])
sys.stdout.write(' '.join(tokens)+comment+'\n')

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