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Questions tagged [atomic-simulation-environment]

For questions about the Atomic Simulation Environment (ASE) tools and Python modules

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35 votes
20 answers

What are the freely available crystal-structure visualization softwares?

I use VESTA mostly for crystal structure visualizations. What other options are available?
Thomas's user avatar
  • 9,142
9 votes
1 answer

How to stack a nanocrystal on top of a graphene slab in ASE?

I'm trying to model a 2D TMD (transition metal dichalcogenide) nanocrystal on a graphene substrate. I know how to generate 2D TMDs through the MX2 module, and I certainly know how to make graphene on ...
the-bfg's user avatar
  • 91
22 votes
1 answer

What are the pre/post processing tools available for VASP?

I am aware of pyPROCAR and VASPKIT. Are there any other tools supporting VASP
Thomas's user avatar
  • 9,142
8 votes
1 answer

Read a data file into the atoms object in ASE

There isn't that many tutorials on Atomic Simulation Environment on the net and among those I saw, the atoms object is always built explicitly within Python. What if I have a data file containing the ...
jboy's user avatar
  • 1,151
15 votes
2 answers

How do you write an .xyz file in the Atomic Simulation Environment?

I built a supercell of a molecular crystal and wish to write an .xyz file in ASE. How do I do that? The molecule has three different types of elements, C, H, and N.
user avatar
12 votes
2 answers

How to sort a supercell for a molecular crystal?

I am trying to build a supercell of the following (below) molecular crystal from its .cif file. How do I sort a supercell here according to each molecule in the supercell? I'm not tethered to a ...
user avatar
6 votes
2 answers

Continuous Coordination Number Definition

I am interested in quantifying the coordination number of some atoms in metals and am curious what approaches to defining a coordination number are possible for an atom. In particular, I am curious ...
Tristan Maxson's user avatar
6 votes
0 answers

How to calculate the surface area of a stepped surface slab in a unit cell? [closed]

I am trying to calculate the surface energies of Ni fcc (111) and (311) surfaces, therefore I need to calculate the surface areas. I use periodic slabs to model these surfaces. For a flat fcc (111) ...
Shaun Han's user avatar
  • 1,930
3 votes
1 answer

ASE GPAW variable cell relaxation

Ive been trying to do a vc relax using GPAW and ASE on the BaTiO3 unitcell. The input file is as below: ...
Atom's user avatar
  • 1,005
2 votes
2 answers

How to run simulation box relaxation with EAM callculator in ASE

I am trying to use EAM calculator in ASE. I want to perform simulation box relaxation with EAM potential. The code is working fine with EMT but fails in EAM as stress property is not implemented with ...
Pranav kumar's user avatar
  • 4,278