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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
13k views

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
22 votes
1 answer
2k 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
Thomas's user avatar
  • 9,142
17 votes
3 answers
1k 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, ...
Greg's user avatar
  • 1,807
15 votes
2 answers
2k 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.
user avatar
13 votes
2 answers
995 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 ...
Tristan Maxson's user avatar
12 votes
2 answers
536 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 ...
user avatar
11 votes
2 answers
2k 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: ...
fireball.1's user avatar
  • 1,083
11 votes
1 answer
1k views

How to build the [111] slab model of NiSe2 with different terminations with ASE tool?

The following figure is the bulk structure of NiSe$_2$ downloaded from the materials project database. Now I want to study the properties of its [111] plane. In detail, I cut the slab with atomic ...
Jack's user avatar
  • 15.2k
11 votes
1 answer
1k 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 ...
DLV's user avatar
  • 211
10 votes
3 answers
643 views

Tool to extract rings from zeolite structures

I am trying to reproduce the work done in this paper https://doi.org/10.1021/acscatal.7b00588. In this direction, I have been successful in optimizing the unit cells of the zeolites. For further steps,...
ansonthms's user avatar
  • 991
10 votes
2 answers
2k views

ASE convesion of Trajectory file to XDATCAR

The issue here is while converting a TRAJ file to POSCAR, it works. But, for TRAJ to XDATCAR, it shows TypeError: images should be a sequence of Atoms objects. (...
Saha_1994's user avatar
  • 969
9 votes
1 answer
305 views

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
8 votes
1 answer
6k 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 ...
jboy's user avatar
  • 1,151
8 votes
1 answer
1k views

Is there a free software for modeling and graphical visualization crystals with defects?

At real situation, it can happen, that a crystal can have defects, for instance, some of them are point defects — Schottky, Frenkel defects, line defects — dislocations, planar defects — grain ...
SFriendly's user avatar
  • 967
8 votes
1 answer
340 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 ...
prananna's user avatar
  • 133
8 votes
1 answer
845 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 ...
jboy's user avatar
  • 1,151
8 votes
1 answer
231 views

What is the principle of generating INCAR tags in ASE?

I am wondering if there is a detailed explanation about how ASE chooses the INCAR tags, since VASP already provides default values for a lot of tags, does ASE choose the default values? There are a ...
Jack's user avatar
  • 2,057
8 votes
1 answer
476 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 ...
Binh Thien's user avatar
  • 2,137
8 votes
0 answers
108 views

Constructing an anisotropic crystal in WulffPack [closed]

I am trying to create an $\ce{LiFePO4}$ 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 ...
chatte22's user avatar
8 votes
0 answers
271 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 ...
Alfred's user avatar
  • 1,939
7 votes
1 answer
574 views

pyscf: Why should the choice of pseudopotential determine the total energy, and not the physics?

I have limited experience with DFT, but as an exercise I have written a DFT program of an atom (from scratch using nothing more than python built in functions and numpy) by following Richard Martin's ...
Mikke Mus's user avatar
  • 263
7 votes
2 answers
3k views

Converting input file into XYZ format using ASE

Here is my code: ...
Saha_1994's user avatar
  • 969
7 votes
1 answer
2k 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 ...
Nilabja Kanti Sarkar's user avatar
7 votes
1 answer
261 views

Better SIESTA workflows system?

Normally, I run all my SIESTA calculations manually and then go to post-processing the results, also manually. I would like to know which of the tools below is "better" (more complete?) in ...
Camps's user avatar
  • 23.6k
7 votes
1 answer
716 views

Translate INCAR to Python script using ASE

I am considering using ASE to translate my old work into a Python script. I already have the INCAR and POSCAR KPOINTS files. Is it possible to let ASE read these files and generate Python scripts that ...
Jack's user avatar
  • 2,057
7 votes
1 answer
703 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 ...
user avatar
7 votes
1 answer
690 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 ...
user avatar
6 votes
2 answers
156 views

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
1 answer
236 views

Clustering Algorithms with Periodic Boundary Conditions

I've been working on a project that involves the clustering of data with periodic boundary conditions. Like simulation of extra-framework water species. Specifically, I am looking for clustering ...
Saha_1994's user avatar
  • 969
6 votes
1 answer
1k views

Atomic Simulation Environment (ASE) Modelling. Adding additional layer

Beginners here, to ASE. I've create a 2x2x2 supercell of TiO2 from unit cell (.cif file obtained from LegacyMaterialsProject ) using ASE. The script code is attached as follows. The outcome is shown ...
ASA's user avatar
  • 63
6 votes
1 answer
185 views

How to convert MoO3 bulk structure to MoO3 (010) plane surface via VESTA software?

Convert MoO3 bulk structure to MoO3 (010) plane surface via VESTA
Rubi Agrawal's user avatar
6 votes
1 answer
115 views

Build supercell in ASE with forces and stress

This is my configuration in extended xyz format ...
Pranav kumar's user avatar
  • 4,278
6 votes
0 answers
54 views

Getting Internal Calculator Data in ASE [closed]

I am using the framework ASE to do computational chemistry calculations. I am using the calculator GPAW with it. How do I extract data that is internal to the calculator? I mostly want to get the ...
user9725's user avatar
  • 111
6 votes
0 answers
498 views

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
5 votes
1 answer
743 views

How to build a unit cell in ASE?

As a basic example, I want to build a defect MgO unit cell within ASE. From VASP the input is simple: ...
Wychh's user avatar
  • 2,167
5 votes
2 answers
207 views

How to calculate displacement in each coordinate and wrap w.r.t. lattice parameter?

The problem is my box is not orthorhombic (base angles different than 90 degrees). So, I am getting wrong results with the formula, ...
Saha_1994's user avatar
  • 969
5 votes
1 answer
71 views

How to convert all structure coordinates in .traj file to separate .txt files (e.g. POSCAR format files)?

I am using the ACAT code for generating the structures. ...
Rubi Agrawal's user avatar
5 votes
1 answer
830 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, ...
user avatar
5 votes
1 answer
129 views

problem calculating formation energy per atom using vasp

Using the below code I am trying to calculate the formation energy per atom and bandgap given the cif file. the values that are present in the material project. but I got these values which are wrong ...
harsh's user avatar
  • 223
5 votes
2 answers
205 views

How to make Quantum espresso input file from Vesta?

here is the CIF file of CaCO3 (http://www.crystallography.net/cod/1010962.html). I have opened it using Vesta and get the following data: ...
Muhammad Hasan's user avatar
5 votes
1 answer
79 views

How can one create various arrangements of two or more types of atoms (like O, N etc.) with distinct coverages on a metal surface?

How can I modify the procedure described in this answer to achieve adsorption of two or more types of atoms on a surface, each with distinct coverages? Is there an extension to the described method ...
Rubi Agrawal's user avatar
5 votes
1 answer
181 views

How to use ase gui to visualize the geometry optimization (through graphs and animation)?

How can I visualize the geometry optimization? I want to see the plot of potential energy through various iterations to reach the minimum value. I would also like to see the animation of the atoms ...
sachin hegde's user avatar
5 votes
1 answer
176 views

How to read multiple Atoms objects from a single file using ASE

I am trying to read Atoms objects from the file "data.txt", which contains multiple configurations. Each configuration has a different cell. ...
user174967's user avatar
5 votes
1 answer
246 views

Fix layers of a slab

How do you fix the bottom layers of a slab to mimic a bulk material in ASE? Any functional that takes the slab object and writes a POSCAR with selective dynamics will be deeply appreciated. Thank you.
Nana Kofi Boakye's user avatar
5 votes
1 answer
690 views

The standard format and parser of VASP output files

I see a lot of post-processing tools for VASP, including ASE, VASPKIT,Pymagten and some other customized codes. They all read the VASP output files like a normal text file. Sometimes I would meet ...
Jack's user avatar
  • 2,057
5 votes
2 answers
135 views

ASE: How to plot the irreducible Brillouin zone and this bandpath from a bandpath object

I am using ASE (Atomic Simulation Environment) for theoretical chemistry and I see an option to plot the irreducible Brillouin zone and this bandpath but I can't figure out how. I'm not a programmer. ...
Samaray's user avatar
  • 61
5 votes
1 answer
728 views

Visualise bonds in ASE

I want to visualize an MD trajectory produced with ASE. ase.visualize.view produces an output for atoms and trajectories. I am not able to show the bonds between atoms. For atoms, I can use this in ...
Marco Di Gennaro's user avatar
5 votes
2 answers
30 views

BCC issues Iron Slab in ase

I've been having issues trying to optimise a 3x3 bcc slab of iron in ase. When modelled as an fcc struture it isn't problematic but given that iron is bcc it's naturally important I have it run as bcc....
Keyan O'Donnell's user avatar
5 votes
0 answers
71 views

Problem with using VASP with ase on a GPU

I am a newbie using VASP, currently I am trying to calculate the formation energy per atom and pre bandgap using DFT with VASP on a GPU machine. I wrote the following script for calculating the ...
harsh's user avatar
  • 223
5 votes
0 answers
33 views

How can calculate length or coordinate of any molecule in different quantum state [like (rotational quantum state)j=2] with any software or code?

How can one determine the bond length of a diatomic or tri-atomic molecule(rot. state J=3 and vib. state v=2) from its ground state bond length (x angstrom) using computational tools or programming ...
Rubi Agrawal's user avatar