Questions tagged [atomic-simulation-environment]

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

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26
votes
13answers
962 views

What are the freely available crystal-structure visualization softwares?

I use VESTA mostly for crystal structure visualizations. What other options are available?
16
votes
3answers
425 views

Computational tools for automatic creation of surface slab models of complex systems

I am looking for computational tools that can be used to automatize the generation surface slab models of latices of oxides, layered oxides, perovskites etc. I have found a promising Python package, ...
16
votes
1answer
415 views

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

I am aware of pyPROCAR and VASPKIT. Are there any other tools supporting VASP
13
votes
1answer
475 views

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.
12
votes
2answers
261 views

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 ...
11
votes
2answers
297 views

Moving from VASP to CASTEP for bulk crystal and surface calculations

Can someone that works with CASTEP and VASP explain to me how a workflow might change between the two programs? I am very familiar with VASP but have not used CASTEP before. As an example, assuming ...
11
votes
2answers
404 views

How to include individual PBC box dimensions in xyz file format compatible with VMD

I am using ASE to write an xyz file. Each frame in the file has a different PBC (periodic boundary condition). Currently, a frame starts like this: ...
11
votes
1answer
81 views

Best way to read forces and positions and energies into Atomic Simulation Environment (ASE)?

My current procedure is to create a .xyz file out of my MD run for a crystal structure. I can read the energy and also each atomic position. But I want to add forces. If I add forces as the additional ...
8
votes
1answer
70 views

Periodic Boundary Conditions in Atomistic Simulation Environment

Consider the following atoms object. atoms_al = ase.build.fcc111('Al', size=(1,2,2), vacuum=16.0, orthogonal=True) To set the periodic boundary conditions along the ...
8
votes
1answer
49 views

How to define the a, b, c vectors in the cut function in ASE

I am testing an example of the 'cut' function in ASE cut. In this example, the surface Al(111) is created using vectors (1, -1, 0) and (0, 1, -1) included in the "cut" function. But I am not ...
8
votes
0answers
112 views

ASE's fmax and FHI-AIMS's relax_geometry bfgs "tolerance". Are they same? [closed]

They look like the same thing, but their definitions are confusing. Additionally, while it's possible to use 'tolerance'< 0.05 in AIMS easily, in ASE, some structures never optimize if you choose ...
7
votes
2answers
129 views

Converting input file into XYZ format using ASE

Here is my code: ...
7
votes
1answer
172 views

How to sort using ase.build.sort?

I am trying to sort a set of Cu atoms in a fcc (non primitive) crystal structure according to their Z cordinate. I am using ase.build.sort to do this with the help ...
7
votes
1answer
458 views

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 ...
7
votes
1answer
115 views

problem using GPAW in Google Colab

I am trying to follow the following: https://peterschindler.github.io/ This is searchable on the internet and it shows how to use GPAW as an ASE calculator. The installation is done by ...
7
votes
1answer
58 views

How to discard molecules at the boundary in the Atomic Simulation Environment (ASE)?

When building a supercell for a molecular crystal with the Atomic Simulation Environment, it seems that the program takes into account periodic boundary conditions when replicating the unit cell. How ...
6
votes
1answer
73 views

Downloading ASE (Atomic Simulation Environment) on older versions of Python

I'm trying to install something called ASE that models atomic structures. I have ASE currently installed on python 3.7, however I need to run scripts that can import and recognize ASE in an older ...
6
votes
0answers
44 views

Constructing an anisotropic crystal in WulffPack

I am trying to create an LiFePO4 crystal in WulffPack. I have the surface energies of seven different surfaces from the paper [1]. When I input the same to WulffPack, it creates a structure comprising ...
5
votes
1answer
152 views

ASE: why do I get warnings about "monoclinic" and "orthorhombic" not being interpreted?

I am trying to use ASE (Atomic Simulation Environment) to build a supercell of some molecular crystals and then output the result to a file with the atoms given in a specified order for each molecule, ...
4
votes
1answer
38 views

Are all the atom tags equal to 0 for ase.build.surface() objects?

I'm looking to build a surface slab in Atomic Simulation Environment (ASE) for CeO2 (fluorite structure). Using ase.build.surface( ) allowed modelling the surface. I would now like to run a relaxation ...