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What are the freely available crystal-structure visualization softwares?

ASE The Atomic Simulation Environment (ASE) has visualization capabilities. It is a python environment that allows direct interaction with a lot of atomistic simulation tools. https://wiki.fysik.dtu....
Fabian's user avatar
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23 votes

What are the freely available crystal-structure visualization softwares?

pymatgen & ASE I'm a big fan of simplicity and integration in my python-based and Julia-based workflow. Therefore I typically directly use the visualisation features from pymatgen, such as ...
Michael F. Herbst's user avatar
22 votes

What are the freely available crystal-structure visualization softwares?

OVITO OVITO is a great tool for visualising supercells and simulation cells with a large number of atoms. There are plenty of modifications available that facilitate analysis, and it also has a Python ...
Mythreyi's user avatar
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20 votes

What are the freely available crystal-structure visualization softwares?

Jmol For visualisation there's also a standalone Java application Jmol, which has a GUI and a more powerful command-line "console". I particularly like it for quickly visualising vibrational ...
Phil Hasnip's user avatar
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20 votes

What are the freely available crystal-structure visualization softwares?

AtomEye My favorite for working with inorganic crystals. But I moved to biomolecules several years ago, so I don't know how it compares with newer programs. AtomEye has no menu. It is driven by ...
marcin's user avatar
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20 votes

What are the freely available crystal-structure visualization softwares?

OlexSys Olex2 For some applications there exists a elegant software called Olex2 which matches most of the crystallographic requirements of dealing with large systems like metal–organic frameworks.
SalvaCardona's user avatar
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18 votes

What are the freely available crystal-structure visualization softwares?

Avogadro Avogadro is generally considered to be a “molecular editor,” designed to construct and view molecules and materials in 3D. It's a cross-platform software. Even when its mainly used for ...
Anoop A Nair's user avatar
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17 votes
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What are the pre/post processing tools available for VASP?

The Atomic Simulation Environment (ASE) is a pretty big name missing from your list. It can read in a variety of VASP-generated output files and do several post-processing analyses. More importantly, ...
Andrew Rosen's user avatar
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16 votes

What are the freely available crystal-structure visualization softwares?

MERCURY Mercury is a specialized software to treat/manipulate crystal structures. It is part of the Cambridge Structural Database (CSD). From Mercury's site, it allows you to: Generate packing ...
Camps's user avatar
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15 votes
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Computational tools for automatic creation of surface slab models of complex systems

I highly recommend using pymatgen for this. I coded a surface slab generator for Avogadro and in addition to being slow (since it generates a supercell before ...
Geoff Hutchison's user avatar
15 votes

What are the freely available crystal-structure visualization softwares?

iRASPA fast & beautiful visualization of porous materials (but not only) Features according to https://iraspa.org/iraspa/ structure creation and editing, creating high-quality pictures and movies,...
leopold.talirz's user avatar
14 votes

What are the freely available crystal-structure visualization softwares?

XCrySDen Official website:http://www.xcrysden.org/XCrySDen.html XCrySDen is a crystalline and molecular structure visualization program aiming at the display of isosurfaces and contours, which can ...
Jack's user avatar
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14 votes
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How do you write an .xyz file in the Atomic Simulation Environment?

Assuming you have an atoms object, all you need to do is call the "write" function. ...
Tristan Maxson's user avatar
14 votes
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pyscf: Why should the choice of pseudopotential determine the total energy, and not the physics?

The energy of a system, be it a molecule or a material, is dependent on the energy reference (or energy zero point) you choose. Common energy references are: The state where all electrons (except for ...
wzkchem5's user avatar
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13 votes

What are the freely available crystal-structure visualization softwares?

VESTA You can try VESTA. It is good, lightweight and works on Windows and Linux platforms. It is good for viewing and production level image quality manipulation. https://jp-minerals.org/vesta/en/...
Pro's user avatar
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13 votes

What are the freely available crystal-structure visualization softwares?

Crystal Impact Diamond Crystal Impact Diamond, despite being a commercial product, offers a free demo-version. One can import a structure, adjust its appearance and use screen capturing software for ...
andselisk's user avatar
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13 votes

What are the freely available crystal-structure visualization softwares?

Beautiful Atoms Beautiful Atoms is a Python package for editing and rendering atoms and molecules objects using Blender. A Python interface that allows for automating workflows. Features: Model: ...
Xing's user avatar
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13 votes

Moving from VASP to CASTEP for bulk crystal and surface calculations

As the answer above mentioned, the biggest difference is perhaps CASTEP takes two input files with suffix "cell" and "param", other things are very similar. After all, both ...
bzbzbz's user avatar
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12 votes
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Moving from VASP to CASTEP for bulk crystal and surface calculations

The workflow transferring from VASP to CASTEP is quite similar. Within VASP, there are four main files that you need for a calculation: POSCAR – gives the positions of the atoms within the unit cell ...
benshi97's user avatar
  • 418
12 votes

Read a data file into the atoms object in ASE

Reading coordinates from a file is a very simple task with ASE. The following code reads the three different file types into an Atoms object: ...
Fabian's user avatar
  • 1,421
11 votes

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

That is a modification of the standard XYZ file format and is called extended XYZ format, and not all programs are compatible with it. From the VMD Molfile Plugin Documentation page, it looks that VMD ...
Camps's user avatar
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11 votes

What are the freely available crystal-structure visualization softwares?

MoleView Super lightweight Developed based on standard plotting library (Matplotlib) Very easy to install pip install moleview All-in-one command ...
High Performance Rangsiman's user avatar
10 votes

What are the freely available crystal-structure visualization softwares?

UnityMol Conceived with biological systems in mind, but relevant for any molecular system Modern interface: recent and still under active development Supported formats: ...
Hebo's user avatar
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10 votes

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

There is currently no tool built into ASE to do this sort of detective work on surface terminations. I highly suggest that you take the approach of trying to eliminate dangling bonds first (for ...
Tristan Maxson's user avatar
9 votes

How to sort using ase.build.sort?

The following code should create a Cu surface and sort it by z index. We do this by providing tags for the positions of the atoms. [:, 2] allows us to select the ...
Tristan Maxson's user avatar
8 votes

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

I have used ASE to create slaps of complex, anisotropic materials in the past. However, ase.lattice is not for creating slabs, it's a module containing functions ...
Fuzzy's user avatar
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8 votes

What are the freely available crystal-structure visualization softwares?

nglview and nvc Recently I found it hard to make the pymatgen structure_vtk visualization method to work. I believe it might be deprecated in favour of ...
Maurits Houck's user avatar
8 votes
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Periodic Boundary Conditions in Atomistic Simulation Environment

The PBC attribute in ASE is used for: finding nearest neighbours input for calculators that may use that information (dftd3, dmol, etc.) creation of surfaces finding the Bravais lattice certain ...
nickpapior's user avatar
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8 votes
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Translate INCAR to Python script using ASE

There seems to be a function to read INCAR files in ASE however in the code it mentions that the functions "are under early constructions". You can give it a try though and it might work ...
Peter Schindler's user avatar

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