Questions tagged [atomic-simulation-environment]
For questions about the Atomic Simulation Environment (ASE) tools and Python modules
136 questions
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What are the freely available crystal-structure visualization softwares?
I use VESTA mostly for crystal structure visualizations.
What other options are available?
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22
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1
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What are the pre/post processing tools available for VASP?
I am aware of pyPROCAR and VASPKIT. Are there any other tools supporting VASP
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17
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3
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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, ...
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16
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2
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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.
user2026
13
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2
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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 ...
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12
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2
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585
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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 ...
user2026
11
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2
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2k
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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:
...
- 1,083
11
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1
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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 ...
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11
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1
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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 ...
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3
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Is there a scriptable tool to determine whether two periodic structures are the same?
I'm doing some material search, in which I remove 2-4 atoms from a medium sized (~20 atoms) unit cell. I need to find all different combinations that are unique with respect to the translational, ...
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10
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3
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706
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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,...
- 1,003
10
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2
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2k
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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. (...
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9
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1
answer
562
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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 ...
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9
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1
answer
371
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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 ...
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8
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2
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4k
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8
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1
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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 ...
- 1,161
8
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1
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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 ...
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8
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1
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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 ...
- 133
8
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1
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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
...
- 1,161
8
votes
1
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245
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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 ...
- 2,107
8
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0
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120
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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 ...
- 81
8
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0
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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 ...
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7
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1
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646
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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 ...
- 437
7
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1
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303
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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 ...
- 24.2k
7
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1
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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
1
answer
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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 ...
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7
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1
answer
776
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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 ...
- 2,107
7
votes
1
answer
125
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ASE-driven NWChem: How to include a Mulliken charges calculation?
I want to include the calculation of Mulliken charges into ASE-driven NWChem.
This is the input file I am using.
giving this error:
...
- 423
7
votes
1
answer
790
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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 ...
Malena Rybacki
7
votes
1
answer
783
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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 ...
user2026
6
votes
2
answers
179
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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 ...
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6
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1
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311
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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 ...
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6
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1
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226
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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
- 617
6
votes
1
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98
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Placing an atom along the line of the dipole moment of another molecule in ASE/GPAW
I have a solvent molecule, ethylene carbonate (EC), that I have calculated the dipole moment of. I want to place a Na atom at an appropriate distance from EC along the line of the dipole moment (in ...
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6
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1
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179
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Build supercell in ASE with forces and stress
This is my configuration in extended xyz format
...
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6
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2
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53
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....
6
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0
answers
56
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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 ...
- 111
6
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0
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566
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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) ...
- 1,970
5
votes
1
answer
1k
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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:
...
- 2,207
5
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2
answers
227
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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,
...
- 999
5
votes
1
answer
88
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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.
...
- 617
5
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1
answer
944
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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, ...
user2026
5
votes
1
answer
103
views
Why does increasing the cell size affect the energy of molecules?
At the moment I'm performing various convergence tests of a cation-solvent-anion complex in ASE using the GPAW calculator, and found strange results for energy vs. vacuum padding as shown in the ...
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5
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1
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265
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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 ...
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5
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2
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653
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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:
...
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1
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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 ...
- 617
5
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1
answer
362
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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 ...
- 163
5
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1
answer
224
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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.
...
- 53
5
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1
answer
393
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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.
- 609
5
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1
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830
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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 ...
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