[ase-users] Create POSCAR file with rectangluar unit cell

[Offermans Willem]

Hello Fabian and ASE friends,

I’m confused. Why would you read CONTCAR and not POSCAR?

The definition of your unit cell and atom positions is in the POSCAR file, if I remember correctly. So why would you read CONTCAR, if you want to alter unit cell and atom positions?


Met vriendelijke groeten,
Mit freundlichen Grüßen,


Willem Offermans
Researcher Electrocatalysis SCT
VITO NV | Boeretang 200 | 2400 Mol
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[cid:982BA063-B96A-4A1B-89AB-5A01CA9FC70D at vito.local]

On 28 Nov 2018, at 10:26, fabian via ase-users <ase-users at listserv.fysik.dtu.dk<mailto:ase-users at listserv.fysik.dtu.dk>> wrote:

Dear David,

Thank you for your reply!

But i am somehow stuck!

import ase.io.vasp
from ase import Atoms
from ase.constraints import FixAtoms
from ase.structure import molecule
from ase.utils.geometry import sort
from ase.io<http://ase.io/> import read, write


slab = ase.io.vasp.read_vasp("CONTCAR")

# What goes here?

write("CONTCAR_primitive", slab,direct=True,sort=True,format='vasp', vasp5=True)



Is what i have and the part in between is completely unintuitive for me. Would you be willing to give me a hint wich function i need to use and how?
I played arround with your suggestions but i could not really get it to work i am sorry.
All the best
Fabian





Am 27.11.2018 um 16:25 schrieb Ollodart, David Bernd:
Hello Fabian,

If the crystal structure which is non-rectangular is a primitive cell form of fcc, bcc, hcp, diamond, zincblende, rocksalt, cesiumchloride, or wurtzite, then in ase/build/bulk.py there are the algorithms for converting from a primitive cell to an orthorhombic (rectangular in 3-D) unit cell under _orthorhombic_bulk. Otherwise you can use the general tools in ase/build/supercells.py to transform from a primitive or other cell to a desired supercell.

Best,

David
________________________________
From: ase-users-bounces at listserv.fysik.dtu.dk<mailto:ase-users-bounces at listserv.fysik.dtu.dk> <ase-users-bounces at listserv.fysik.dtu.dk><mailto:ase-users-bounces at listserv.fysik.dtu.dk> on behalf of fabian via ase-users <ase-users at listserv.fysik.dtu.dk><mailto:ase-users at listserv.fysik.dtu.dk>
Sent: Tuesday, November 27, 2018 7:50:01 AM
To: ase-users at listserv.fysik.dtu.dk<mailto:ase-users at listserv.fysik.dtu.dk>
Subject: [ase-users] Create POSCAR file with rectangluar unit cell

Dear all

I have a set of computational results that were calculated with a non
rectangular unit cell, i.e the unit vectors are skewed 30 deg .

Is it possible to move the atoms of the substrate such that the unitcell
is rectangluar and equivalent?

Thank you in advance

Fabian

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