Questions tagged [atomic-simulation-environment]

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

Filter by
Sorted by
Tagged with
3 votes
0 answers
56 views

Atomic Simulation Environment (ASE) is unable to read a big trajectory file

The problem that I face is the ASE software can't read the trajectory file and throws this error ValueError: buffer is smaller than requested size. My assumption is ...
user avatar
  • 715
5 votes
0 answers
33 views

Getting Internal Calculator Data in ASE

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 ...
user avatar
2 votes
0 answers
30 views

Using the Atomic Simulation Environment to analyze molecules in a trajectory file

How would you use the Atomic Simulation Environment (ase.io) module to analyze, for example, all atoms in each molecule in a configuration? The Trajectory module ...
user avatar
  • 1,309
4 votes
0 answers
56 views

Space group issue with XYZ, VASP formats in VESTA

I am facing an issue while converting .cif/.vesta files into .xyz and ...
user avatar
4 votes
0 answers
37 views

Error in Raman calculations with moderate k-mesh size

I have been trying to get Raman active modes using the SIESTA interface with PyNAO-ASE. So far the results have been very promising. I am currently facing a problem where I try to increase the number ...
user avatar
  • 1,181
6 votes
0 answers
53 views

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

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) ...
user avatar
  • 161
7 votes
1 answer
165 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 ...
user avatar
  • 1,427
5 votes
1 answer
62 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 ...
user avatar
  • 1,427
3 votes
1 answer
90 views

How could I generate the parameter of 'selective dynamics' in POSCAR with ASE?

I often use selective dynamics to do structure optimization in VASP, but I am not sure how to do it when using ASE, it seems I could use the constraint class to tell ASE what I want to do. My question ...
user avatar
  • 1,427
6 votes
0 answers
57 views

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

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 ...
user avatar
  • 61
7 votes
1 answer
122 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 ...
user avatar
  • 1,427
5 votes
0 answers
131 views

Why calculation of coordination numbers from Element-specific RDFs (ASE) doesn't make sense? [closed]

The link to the trajectory is here.I am using the module and similar code of the ASAP calculator from ASE. The problem is as follows, the running Coordination Number doesn't match the number of atoms ...
user avatar
  • 715
4 votes
1 answer
107 views

RAMAN calculation with SIESTA and ASE-SIESTA

I have been using the ASE-SIESTA-PyNAO module to attempt some RAMAN/IR mode calculations on graphene (if anyone has any experience with this please send me a message maybe we can chat about it). At no ...
user avatar
  • 1,181
10 votes
2 answers
269 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. (...
user avatar
  • 715
5 votes
2 answers
76 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, ...
user avatar
  • 715
7 votes
2 answers
484 views

Converting input file into XYZ format using ASE

Here is my code: ...
user avatar
  • 715
4 votes
1 answer
70 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 ...
user avatar
8 votes
1 answer
103 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 ...
user avatar
  • 1,450
11 votes
1 answer
195 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 ...
user avatar
  • 211
8 votes
0 answers
63 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 ...
user avatar
8 votes
1 answer
90 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 ...
user avatar
  • 133
6 votes
1 answer
186 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
8 votes
1 answer
255 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 ...
user avatar
  • 1,081
8 votes
1 answer
2k 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 ...
user avatar
  • 1,081
7 votes
1 answer
94 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
  • 1,309
14 votes
1 answer
750 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
  • 1,309
12 votes
2 answers
299 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
  • 1,309
5 votes
1 answer
260 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
  • 1,309
7 votes
1 answer
382 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 ...
user avatar
11 votes
2 answers
771 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: ...
user avatar
  • 1,083
8 votes
0 answers
147 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 ...
user avatar
  • 1,859
11 votes
2 answers
414 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 ...
user avatar
29 votes
16 answers
2k views

What are the freely available crystal-structure visualization softwares?

I use VESTA mostly for crystal structure visualizations. What other options are available?
user avatar
  • 8,362
17 votes
1 answer
632 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
user avatar
  • 8,362
16 votes
3 answers
623 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, ...
user avatar
  • 1,638