lost the last iteration

[huan...@mail.huji.ac.il]

Dear All,

I am writing a script to split a file into several files. The structure of the sample file is like follows,

       9       # the number of atoms

 i =    0     # the number of step

  N        X_00     Y_00     Z_00    # from this line to the followed 9 lines are the coordinates of each atom

  H        X_01     Y_01     Z_01

  H        X_02     Y_02     Z_02

  H        X_03     Y_03     Z_03

  H        X_04     Y_04     Z_04

  N        X_05     Y_05     Z_05

  H        X_06     Y_06     Z_06

  H        X_07     Y_07     Z_07

  H        X_08     Y_08     Z_08

       9

 i =    1

  N        X_10     Y_10     Z_10

  H        X_11     Y_11     Z_11

  H        X_12     Y_12     Z_12

  H        X_13     Y_13     Z_13

  H        X_14     Y_14     Z_14

  N        X_15     Y_15     Z_15

  H        X_16     Y_16     Z_16

  H        X_17     Y_17     Z_17

  H        X_18     Y_18     Z_18

       9

 i =    2

  N        X_20     Y_20     Z_20

  H        X_21     Y_21     Z_21

  H        X_22     Y_22     Z_22

  H        X_23     Y_23     Z_23

  H        X_24     Y_24     Z_24

  N        X_25     Y_25     Z_25

  H        X_26     Y_26     Z_26

  H        X_27     Y_27     Z_27

  H        X_28     Y_28     Z_28

...... repeat the blocks but the different coordinates.

The aim is to split the coordinates by each atoms and save them into 9 files according to atoms(lines). For example, the first file contains the coordinates of the first atom (the coordinates of the first line), the second file contains the coordinates of the second atom (the second line), and so forth. 

file0    # save the coordinates of the first lines of each step

X_00     Y_00     Z_00

X_10     Y_10     Z_10

X_20     Y_20     Z_20

……

file1   # save the coordinates of the second lines of each step

X_01     Y_01     Z_01

X_11     Y_11     Z_11

X_21     Y_21     Z_21

......

file2  # save the coordinates of the third lines of each step

X_02     Y_02     Z_02

X_12     Y_12     Z_12

X_22     Y_22     Z_22

......

I have finished my script and it worked except for missing the last iteration. For instance, there 10 steps in the sample file. As a result, each output files should have 10 lines of coordinates. However, in my results, only 9 lines of coordinates in each file.

My script is shown as follows,

#!/usr/bin/python

with open('sample.xyz','r') as fo:

    Natom = int(fo.next())

    line = fo.next()

    timestep = 0

    coords = []

    row = 0

    for line in fo:

        try:

            if row < Natom:

                info = line.split()

                coords.append(info[1:])

                row += 1

            else:

                for n in range(Natom):

                    with open('position%d.txt' %n, 'a+') as fw:

                        xyz = coords[n]

                        output = "%s, %s, %s" %(xyz[0], xyz[1], xyz[2])

                        fw.write(output + "\n")

                

                coords = []

                row = 0

                timestep += 1

                line = fo.next()

        except StopIteration:

           break

Enclosed please find the sample file (sample.xyz) and my script (split_test.py). Any suggestion would be greatly appreciated. 

Regards,

Huan

[ran an]

I've add a print to confirm the value of Natom, and I get a number '9', the same as you expected.
but consider that:
  if row < Natom:  # it only run 9 times from 0,1,2.....to 8.   and 9 is not inclusive.
  for n in range(Natom):
so it's not weird that you could only get nine lines each file with the range(Natom).
so recommend that you reconsider your Natom's value and could referenced at the red-marked lines below
hope that will helpful.

#!/usr/bin/python

with open('sample.xyz','r') as fo:

    Natom = int(fo.next())

       print Natom