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?
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
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
17
votes
Accepted
How to build matter modeling models with appropriate tools?
Atomic Simulation Environment (Surfaces)
I am going to narrowly cover surface models in this answer since ASE is more than capable of handling a wide range of models from nanoparticles, surfaces, 2D ...
- 9,801
17
votes
Accepted
How to calculate diffraction pattern from a model of unit cell?
Perhaps the easiest solution is to use VESTA, which can read in a CIF (and many other crystalline structure formats) and produce a powder diffraction pattern ("Utilities" > "Powder Diffraction Pattern"...
- 6,852
17
votes
Accepted
How can I create a .CIF file from x-ray diffraction data in a paper, for compound not found in crystallographic database
You can use the free software VESTA for creating a new structure by following steps
From the file menu choose New structure
Go to Unit cell panel and choose the space group of the structure
Enter ...
- 8,362
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
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
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
12
votes
Extracting molecular structure from CIF file using VESTA or Mercury
VESTA
I'm an avid user of VESTA and haven't quite used Mercury. So I'll the steps to do it in VESTA (it's quite easy though)
Step 1: Open your file in VESTA
Step 2: Choose the selection tool in the ...
- 4,268
11
votes
How may I create a CIF for a core-shell nanostructure? Is it possible in VESTA, or elsewhere?
Well, to answer properly this question first we would need a clarification about the nature of the CIF file. This type of file is Crystallographic Information File, which means that it is devoted to ...
- 1,560
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/...
9
votes
Accepted
acceptable range of stretching of a lattice unit cell when we do the heterostructure
I would like to add to Jack's answer that beyond the raw numbers of what an acceptable amount of strain may be, it can also be important to consider the physical situation of interest when matching ...
- 10k
9
votes
Problems with finding the unit cell from a CIF file and extracting XYZ coordinates using a software
If you haven't figured it out yet here is what I would've done using mercury to get the xyz file of the dimer. There is some disorder in the crystal structure which I think means that there are ...
- 331
8
votes
How can I create a .CIF file from x-ray diffraction data in a paper, for compound not found in crystallographic database
The journal requires that the data is deposited in CCDC, ICSD or CRYSTMET.
This one was apparently deposited in ICDC with the depository number CSD-417100 (the number is given in the paper, I don't ...
- 1,485
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
Creating a heterostructure in VESTA
Since the constituent monolayers have generally differing lattice constants, special care is needed in the construction of the atomic models in such a way that the strain is minimized.
Let us denote ...
- 13.6k
8
votes
How may I create a CIF for a core-shell nanostructure? Is it possible in VESTA, or elsewhere?
Two things are mixed in the question.
How to create atomistic model of a core-shell nanoparticle?
Are both the core and the shell assumed to be crystalline?
Most likely you will need is to write a ...
- 1,485
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
acceptable range of stretching of a lattice unit cell when we do the heterostructure
There are lots of papers about the strain engineering of two-dimensional materials. For example:
Strain-Engineering of Band Gaps in Piezoelectric Boron Nitride Nanoribbons
Tuning Electronic and ...
- 13.6k
7
votes
Accepted
Extracting the coordinates of a super cell in Vesta or Avogadro
One option is to use the Atomic Simulation Environment's sort function. The function ase.build.sort() takes a required Atoms ...
- 6,852
7
votes
Unit Cell Parameters for VASP Calculations
There some very important points to address here.
In a periodical structure, the atom coordinates and the cell parameters are not randomly selected. The crystal structure (atom positions, cell ...
- 18.5k
6
votes
How to calculate diffraction pattern from a model of unit cell?
You are looking for the calculation of structure factor. Basically the X-Ray spectra could be calculated as Fourier transform of your crystal lattice and the Intensity ($I(\mathbf{q})$) could be ...
- 2,784
5
votes
Accepted
Lattice representation: change of unit cell
I will start by re-stating your question to make sure I understand what you mean. You have a cell with lattice vectors written in Cartesian coordinates as follows:
$$
\begin{pmatrix}
\mathbf{a}=\hat{\...
- 10k
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