29 votes
Accepted

What are the freely available crystal-structure visualization softwares?

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.dk/...
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21 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 ...
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20 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 ...
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  • 1,274
18 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.
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  • 1,560
18 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 ...
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  • 3,804
17 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 ...
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  • 1,485
16 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 ...
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  • 4,268
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. ...
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14 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 ...
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14 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 ...
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13 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,...
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12 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, ...
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  • 6,852
12 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 ...
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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 ...
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11 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 ...
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  • 223
10 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/...
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10 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 ...
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10 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 ...
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  • 348
9 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: ...
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  • 1,341
8 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 ...
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8 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: ...
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  • 1,363
8 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 ...
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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 ...
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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 ...
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7 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 ...
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  • 798
7 votes
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ASE: why do I get warnings about "monoclinic" and "orthorhombic" not being interpreted?

As far as I understand, this warning can be safely ignored. While parsing a cif structure, the get_spacegroup() function in the cif parser of ASE, checks whether ...
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7 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: ...
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  • 71
7 votes

problem using GPAW in Google Colab

I hope it's okay to "self-answer". So I also posted this question in the GPAW mailing list and one of the users in the mailing list who go by the handle mazay0 offered a different means of ...
7 votes

Converting input file into XYZ format using ASE

Here is a more concise way of doing the same thing. from ase.io import read bec = read("bec_replaced.vasp").write("bec_replaced.xyz") It is not ...
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6 votes

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

Camps is correct, VMD cannot directly parse the comment line of an xyz file because the extended ASE format is not recognized. You can, however, use a tcl-script to load the file and parse the comment ...
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