Editing Sortcolumn.py

This script sorts the coordinates of the atoms in the POSCAR-file and outputs a sorted copy as '''POSCAR_sorted'''.<br />
POSCAR_sorted is ready to go, so it can be named POSCAR and run in VASP like that (though it's always advisable to perform a visual check yourself).<br />
The most important aspect in the sorting is to respect the groups of atom-types.

That's why the script takes first the column number to be sorted (from 1 to 3) and then the number of atoms per type in the right order (i.e. the line of atom numbers in the POSCAR).<br />
To obtain the script copy the full source code below into your favourite text-editor and call the file (preferably) "sortcolumn.py".<br />
Lastly make it executable with <code>chmod u+x</code>.

Disclaimer: ''Due to incompatibilities with Python versions older than Python 3, the script cannot be executed on Tekla2.''

==Source Code ''sortcolumn.py''==

 #!/usr/bin/env python
 
 ##Instructions list: by default operates on the POSCAR-file.
 ##The program yields a POSCAR_sorted as output,
 ##which is identical to the original but with one column
 ##sorted by increasing value and respecting the number of elements.
 ##
 ##Input in the terminal the column number (1,2 or 3) to be sorted
 ##and then the for each atomtype the number of atoms.
 
 import sys
 
 filelines = 1000
 offset = 2
 digits = "{0:.10f}"
 spaces = 8
 l = len(sys.argv) - offset
 
 if (l < offset):
     print("Give me axis and the number of atoms per type so I can split the sorting")
     sys.exit()
 
 def getKey(item = []):
          return item[int(sys.argv[1])-1]
 
 f = open('POSCAR', mode='r')
 s = open('POSCAR_sorted', mode='w')
 for i in range(filelines):
     temp = f.readline()
     s.write(temp)
     if (temp[0:3] == 'Car' or temp[0:3] == 'Dir'):
          break
 
 for j in range(offset, offset + l):
     data = []
     for i in range(int(sys.argv[j])):
          temp = f.readline().split(' ')
          temp = [x for x in temp if x != '' or x == '\n']
          temp[0:3] = [float(x) for x in temp[0:3]]
          data.append(temp)
 
     data = sorted(data, key=lambda x: x[int(sys.argv[1])-1])
     for i in range(0, len(data)-1):
          if len(data[i]) == 3:
              s.write(' '*spaces+str(digits.format(data[i][0]))+' '*spaces+str(digits.format(data[i][1]))+' '*spaces+str(digits.format(data[i][2]))+'\n')
          elif len(data[i]) == 6:
              s.write(' '*spaces+str(digits.format(data[i][0]))+' '*spaces+str(digits.format(data[i][1]))+' '*spaces+str(digits.format(data[i][2]))+" "+data[i][3]+" "+data[i][4]+" "+data[i][5])
          else:
              print("Check your coordinate format, buddy")
              sys.exit()
 
 for i in range(filelines):
     temp = f.readline()
     s.write(temp)
 
 f.close()
 s.close()
 
 ##Program written by N.Daelman on December the 1st 2016