<< script to convert XYZ file to POSCARS (as used by USPEX) >>

[Camps]

Hello USPEXsers,

I have a lot (thousands) of structures in XYZ format.

I need to calculate the quase-entropy of all these structures. To do so, I need to convert all the XYZ files to the POSCARS format used by USPEX.

Does any one knows an script (aka xyz2vasp) that can accomplish that type of conversion?

Best regards,

Camps

[huy pham]

Dear Camps.

XYZ format doesn't has the information about the cell,

So I think you have to have this information, don't you?

If you have, you can write a small code to convert. I think it is not a big deal

Bests,

Huy

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Pham Cong Huy
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[I. Camps]

Dear Huy,

I have the cell info.

To be honest, my files correspond to single molecules that I artificially put in a cell/box (all the molecules will have the same "cell parameters"), and then, I need to calculate the quase-entropy to get an idea of the molecule order/disorder.

[]'s,

@mps

[bkappes]

Camps,

If you have python and the atomistic simulation environment (ASE, https://wiki.fysik.dtu.dk/ase/), then something like this should work (warning, it is untested)

Usage: xyz2vasp.py Lx Ly Lz file1.xyz [file2.xyz [...]]

=========

xyz2vasp.py

------------------

import sys

import numpy as np

from os.path import stripext

from ase.io import read, write

if len(sys.argv) < 5:

    print "Usage: xyz2vasp.py Lx Ly Lz file1.xyz [file2.xyz [...]]"

try:

    periodicLengths = [float(x) for x in sys.argv[1:4]]

    pv = np.diag(periodicLengths)

except ValueError:

    print "Usage: xyz2vasp.py Lx Ly Lz file1.xyz [file2.xyz [...]]"

for input in sys.argv[4:]:

    output = stripext(input)[0] + '.vasp'

    mol = read(input, format='xyz')

    mol.set_pbc(True)

    mol.set_cell(pv)

    write(output, mol, format='vasp')

------------------------

This will at least give you a place to start.

Cheers,

-Branden

[Prof. Dr. I. Camps]

Thank you very much!

[]'s,

---
Prof. Dr. Ihosvany Camps
Instituto de Ciências Exatas. Sala Q203-J
Universidade Federal de Alfenas. Unifal-MG
Rua Gabriel Monteiro da Silva, 700 Centro.  37130-000. Alfenas. MG. Brasil
Tel.  +55 (35) 3299-1260            Agenda: http://goo.gl/B9GoS9
Fax. +55 (35) 3299-1063           Skype: icamps              Twitter: @_icamps