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/...
- 1,341
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 ...
- 2,304
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 ...
- 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.
- 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 ...
- 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 ...
- 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 ...
- 4,268
14
votes
Accepted
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.
...
- 9,801
14
votes
Accepted
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 ...
- 7,394
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 ...
- 18.5k
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,...
- 2,004
12
votes
Accepted
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, ...
- 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 ...
- 13.6k
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 ...
- 18.5k
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 ...
- 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/...
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 ...
- 641
10
votes
Accepted
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 ...
- 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:
...
- 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 ...
- 9,801
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: ...
- 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 ...
8
votes
Accepted
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 ...
- 1,724
8
votes
Accepted
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 ...
- 446
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 ...
- 798
7
votes
Accepted
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 ...
- 1,174
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: ...
- 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 ...
- 9,801
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 ...
- 1,341
Only top scored, non community-wiki answers of a minimum length are eligible