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lammps/tools/moltemplate/moltemplate/renumber_DATA_first_column.py
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renumber_DATA_first_column.py
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#!/usr/bin/env python
"""
renumber the integers at the beginning of ever line in the file
to make sure these numbers are contiguous.
The file is read from sys.stdin.
This program does not parse an entire LAMMPS data file.
The text from the "Atoms" section
(or "Bonds", or "Angles", or "Dihedrals", or "Impropers" sections)
of the LAMMPS file must be extracted in advance.
"""
import sys
from operator import itemgetter
def main():
in_stream = sys.stdin
f = None
fname = None
if len(sys.argv) == 2:
fname = sys.argv[1]
f = open(fname, 'r')
in_stream = f
lines = in_stream.readlines()
column1_iorig_columnsAfter1 = []
# Start at the end of the file and read backwards.
# If duplicate lines exist, eliminate the ones that occur earlier in the file.
i = 0
while i < len(lines):
line_orig = lines[i]
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()
if len(tokens) > 0:
if str.isdigit(tokens[0]):
column1 = int(tokens[0])
else:
column1 = tokens[0]
column1_iorig_columnsAfter1.append(
[column1, i, ' '.join(tokens[1:]) + comment])
i += 1
# Sort the list of lines by the first number on each line
column1_iorig_columnsAfter1.sort(key=itemgetter(0))
# Change all of these numbers so that they are consecutive starting at 1
for i in range(0, len(column1_iorig_columnsAfter1)):
column1_iorig_columnsAfter1[i][0] = i + 1
# Sort the list of lines so they are back in the original order
column1_iorig_columnsAfter1.sort(key=itemgetter(1))
for i in range(0, len(column1_iorig_columnsAfter1)):
column1 = column1_iorig_columnsAfter1[i][0]
columnsAfter1 = column1_iorig_columnsAfter1[i][2]
sys.stdout.write(str(column1) + ' ' + columnsAfter1 + '\n')
if f != None:
f.close()
return
if __name__ == '__main__':
main()
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