ASE scripts

ASE provides very convenient tool to manipulate the structures and convert them to different file formats.

Supercell

Below is a python script to read the structure from gen format (used in DFTB+) and then make a 333 supercell in gen and vasp format.

from ase.io import read, write

struc = read('h2o.gen',format='gen')
write('new.gen',struc*(3,3,3), format='gen')
write('POSCAR',struc*(3,3,3), format='vasp')

ASE could handle almost all file format in the major codes.

For more information, please visit the following link: https://wiki.fysik.dtu.dk/ase/ase/io/io.html

A more complicated case

Sometimes, one might wants to cut the crystal structure along some direction and then make the supercell. Below is an example of doing so.

from ase.io import read, write
from ase import geometry
from ase.build.supercells import make_supercell
import numpy as np

#Read structure from POSCAR, this is ase.atom object
struc = read('gra.vasp',format='vasp')

#make supercell here
P = np.array([[1,-1,0],[1,1,0],[0,0,1]])*2
gra1 = make_supercell(struc, P)

#After the lattice transformation
#the supercell might have unpleasant shape such as 
#[ 0, -1, 0]
#[ 1,  0, 0]
#[ 0,  0, 1]
#let's apply another transformation here

cell_par = gra1.get_cell_lengths_and_angles()
pos1 = gra1.get_scaled_positions()
cell1 = geometry.cell.cellpar_to_cell(cell_par)
gra1.set_cell(cell1)
gra1.set_scaled_positions(pos1)

#output in any format whichever you want
write('POSCAR',gra1, format='vasp')

Modify the orientation of surface structure

$ cat Pt_primitive.vasp
Ce1O2
1.000000000000000
22.95150000000000   0.000000000000000  0.000000000000000
11.47575000000000   19.87658205495854  0.000000000000000
17.78942000000002   10.27072642572731  29.05000121337461
 Ce O Pt C
180 360 19 0
Direct
9.611989863766990e-09 9.608114408254931e-09 0.1075147502183935
-0.0003887364393597298 -2.165967138571812e-05 0.2167485546162756
-0.001305103780566391 -0.0001492816586775858 0.3256709071579755
9.610177008345655e-09 0.1666666816113916 0.1075147502183935
-0.0004910138572741807 0.1664581574855210 0.2168893242489501
...
...

from ase.io import read
from ase.build.supercells import make_supercell
import numpy as np

at = read("Pt_primitive.vasp", format="vasp")
print(at.get_cell())
P = np.array([[1,-1,0],[1,1,0],[-1/2,-1/2,1]])
at1 = make_supercell(at, P)
print(at1.get_cell())
at1.write("2.vasp", format='vasp', vasp5=True, direct=True)

[22.9515  22.9515  35.57884 60.      60.      60.     ]
[22.9515     39.75316411 29.05760871 88.68889365 90.         90.        ]

Tips: Since some codes are changing their file formats from time to time in the development stage, one has to check if it works before using it as the script.