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?
7
votes
2answers
129 views

Converting input file into XYZ format using ASE

Here is my code: ...
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 ...
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 ...
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 ...
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 ...
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 ...
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 ...
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 ...
7
votes
1answer
114 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 ...
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 ...
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.
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, ...
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 ...
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
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 ...
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 ...
16
votes
1answer
414 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
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, ...