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lammps/tools/moltemplate/moltemplate/postprocess_input_script.py
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postprocess_input_script.py
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#!/usr/bin/env python
"""
Reorder the integer arguments to the commands in a LAMMPS input
file if these arguments violate LAMMPS order requirements.
We have to do this because the moltemplate.sh script will automatically
assign these integers in a way which may violate these restrictions
and the user has little control over this.
This script:
swaps the I and J integers in "pair_coeff I J ..." commands when I > J
Other features may be added later
"""
import sys
def main():
lines_orig = []
f = None
fname = None
num_lines_ignore = 0
# Lines from files passed as arguments are read and processed silently.
# (Why? Sometimes it's necessary to read the contents of previous input scripts
# in order to be able to understand a script command which appears later.
# I'm assuming these files will be processed by lammps in the same order. So I
# must insure that moltemplate.sh passes them to this program in that order.
# I'm too lazy to read the "include" commands in input scripts correctly.)
if len(sys.argv) > 1:
for fname in sys.argv[1:]:
f = open(fname, 'r')
in_stream = f
lines_orig += in_stream.readlines()
num_lines_ignore += len(lines_orig)
f.close()
# Lines read from the standard input are read, processed, and printed to stdout
in_stream = sys.stdin
lines_orig += in_stream.readlines()
pair_style_list = []
swap_occured = False
warn_wildcard = False
i = 0
while i < len(lines_orig):
# Read the next logical line
# Any lines ending in '&' should be merged with the next line before
# breaking
line_orig = ''
while i < len(lines_orig):
line_counter = 1 + i - num_lines_ignore
line_orig += lines_orig[i]
if ((len(line_orig) < 2) or (line_orig[-2:] != '&\n')):
break
i += 1
line = line_orig.replace('&\n', '\n').rstrip('\n')
comment = ''
if '#' in line_orig:
ic = line.find('#')
line = line_orig[:ic]
# keep track of comments (put them back later)
comment = line_orig[ic:].rstrip()
tokens = line.strip().split()
if ((len(tokens) >= 2) and (tokens[0] == 'pair_style')):
pair_style_list = tokens[1:]
if ((len(tokens) >= 3) and (tokens[0] == 'pair_coeff')):
if ((tokens[1].isdigit() and (tokens[2].isdigit())) and
(int(tokens[1]) > int(tokens[2]))):
swap_occured = True
tmp = tokens[2]
tokens[2] = tokens[1]
tokens[1] = tmp
if i >= num_lines_ignore:
# polite warning:
sys.stderr.write(
'swapped pair_coeff order on line ' + str(line_counter))
# if (fname != None):
# sys.stderr.write(' of file \"'+fname+'\"')
sys.stderr.write('\n')
# Deal with the "hbond/" pair coeffs.
#
# The hbond/dreiding pair style designates one of the two atom types
# as a donor, and the other as an acceptor (using the 'i','j' flags)
# If swapped atom types eariler, we also need to swap 'i' with 'j'.
#
# If "hbond/dreiding.." pair style is used with "hybrid" or
# "hybrid/overlay" then tokens[3] is the name of the pair style
# and tokens[5] is either 'i' or 'j'.
if len(pair_style_list) > 0:
if ((pair_style_list[0] == 'hybrid') or
(pair_style_list[0] == 'hybrid/overlay')):
if ((len(tokens) > 5) and (tokens[5] == 'i') and (tokens[3][0:6] == 'hbond/')):
tokens[5] = 'j'
sys.stderr.write(
' (and replaced \"i\" with \"j\")\n')
elif ((len(tokens) > 5) and (tokens[5] == 'j') and (tokens[3][0:6] == 'hbond/')):
tokens[5] = 'i'
sys.stderr.write(
' (and replaced \"j\" with \"i\")\n')
elif (pair_style_list[0][0:6] == 'hbond/'):
if ((len(tokens) > 4) and (tokens[4] == 'i')):
tokens[4] = 'j'
sys.stderr.write(
' (and replaced \"i\" with \"j\")\n')
elif ((len(tokens) > 4) and (tokens[4] == 'j')):
tokens[4] = 'i'
sys.stderr.write(
' (and replaced \"j\" with \"i\")\n')
sys.stdout.write(
(' '.join(tokens) + comment).replace('\n', '&\n') + '\n')
else:
if ((('*' in tokens[1]) or ('*' in tokens[2]))
and
(not (('*' == tokens[1]) and ('*' == tokens[2])))):
warn_wildcard = True
if i >= num_lines_ignore:
sys.stdout.write(line_orig)
else:
if i >= num_lines_ignore:
sys.stdout.write(line_orig)
i += 1
if swap_occured:
sys.stderr.write('\n'
' WARNING: Atom order in some pair_coeff commands was swapped to pacify LAMMPS.\n'
' For some exotic pair_styles such as hbond/dreiding, this is not enough. If you\n'
' use exotic pair_styles, please verify the \"pair_coeff\" commands are correct.\n')
if warn_wildcard:
sys.stderr.write('\n'
' WARNING: The use of wildcard characters (\"*\") in your \"pair_coeff\"\n'
' commands is not recommended.\n'
' (It is safer to specify each interaction pair manually.\n'
' Check every pair_coeff command. Make sure that every atom type in\n'
' the first group is <= atom types in the second group.\n'
' Moltemplate does NOT do this when wildcards are used.)\n'
' If you are using a many-body pair style then ignore this warning.\n')
return
if __name__ == '__main__':
main()
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