#!/usr/bin/env python3

# Author: Andrew Jewett (jewett.aij at g mail)
# License: MIT License  (See LICENSE.md)
# Copyright (c) 2013

"""
   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()
