27
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/ase/
Visual Molecular Dynamics (VMD) and XCrySDen are the two tools I personally work with the most time. They produce nice graphics and can visualize densities ...
19
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 pymatgen.vis.structure_vtk, and ASE, for example ase.visualize. Mostly I use them anyway to build up my problem. They have some features for analysing results as well, ...
17
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"). Behind the scenes, VESTA is using RIETAN-FP to do the calculation, which has a standalone version to download if you wanted.
Another way you could do this, ...
17
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 the lattice parameters in the same panel
Change to Structure parameters panel and enter x,y,z and Ueq of each atom one by one
Save the structure and after ...
16
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 layered materials, bulk 3D materials, etc.
Metal Surfaces
Pt(111) models for example can be easily created within the ase.build module as follows.
from ase.build ...
16
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 interface for those who would like to work with scripts.
16
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 modes. However, it lacks tools to construct a simulation cell, unlike some of the other options people have mentioned.
15
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 pressing keys on keyboard. Mouse can be used for rotation, selection, etc, but surprisingly many things can be done with keyboard only.
It could handle millions of ...
15
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.
12
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 constructing molecules, it's also useful for creating and visualizing unit cells and slabs.
These are some tutorials for constructing:
Unit-cells in Avogadro
Slabs ...
11
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 diagrams, define and visualize Miller planes, and take slices through a crystal in any direction.
Build and explore networks of intermolecular contacts to gain an ...
10
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 periodic, crystalline, and symmetric materials. In my opinion a core-shell nanostructure (CNS) is not fullfilling this requirements.
In particular, the symmetry ...
10
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 left panel. (highlighted in
blue)
Step 3: Click and drag to select the atoms you want to manipulate;
Here the three top atoms
After selection they are ...
9
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 two different compounds in a heterostructure. This is particularly relevant for your point about "taking the average" of the lattice parameters of the ...
9
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,
Ambient occlusion and high-dynamic range rendering,
collage of structures, (transparent) adsorption surfaces, text-annotation,
cell replicas and supercells, ...
9
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/download.html
9
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 partial occupations of molecules/atoms at different positions so you need to delete them to get only one of set of the dimers in the xyz file.
8
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 be superimposed on crystalline structures and interactively rotated and manipulated. It runs on GNU/Linux. It also possesses some tools for analysis of ...
8
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 saving the image/animation.
Import of the following files is supported: DIAMDOC, DSF, EDF, DS1, CFG, CIF, CRY, CSD, DAT, PDB, ENT, INS, RES, DAT, IDF, KPL, XYZ, ...
8
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 have access to the database).
If you also don't have access to ICDC write an e-mail to the author asking for the CIF file. Most academics are happy to answer ...
8
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 the primitive cell basis vectors of a hexagonal 2D material $i$ as {$a_i$,$b_i$}. The supercell basis vector may be constructed as $n_ia_i$+$m_ib_i$, where $n_i$...
8
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 small program that generates the required configuration by calculating atomic positions.
You can create the first approximation of a (uniform) nanoparticle
by ...
7
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 Magnetic Properties of Early Transition-Metal Dichalcogenides via Tensile Strain
The tensile strain even up to $10\%$ is considered.
Can I take an average on the ...
7
One option is to use the Atomic Simulation Environment's sort function. The function ase.build.sort() takes a required Atoms object (e.g. the supercell of the original CIF) and an optional tags argument that allows you to sort however you wish. It's then just up to you to find out how to flag each individual molecule in the order that you'd like.
6
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 estimated as:
$$I(\mathbf{q}) = f^{2} \sum_{i=1}^{N} \exp{(-i \mathbf{q} \cdot \mathbf{R}_{i})}$$
Basically, $\mathbf{q}$ is the scattering vector and the X-Ray ...
5
I want to rotate the second structure $\theta=90^{\circ}$ about the x-axis. The rotation matrix is given as
$$R_x(90^{\circ})=\begin{pmatrix}1&0&0\\0&0&-1\\0&1&0\end{pmatrix}.$$
Start a new Vesta window:
New Structure-> Structure parameters -> Import
Import your first structure/origin unit cell. Maybe one have first to shift the ...
5
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{\mathbf{x}}-\hat{\mathbf{y}}-\hat{\mathbf{z}} \\
\mathbf{b}=\hat{\mathbf{x}}+\hat{\mathbf{y}}-\hat{\mathbf{z}} \\
\mathbf{c}=1.5\hat{\mathbf{x}}+2.5\hat{\mathbf{...
5
I used the structure manipulation scripts provided by AIRSS to generate the conventional cell associated with your primitive cell. I think AIRSS uses Spglib under the hood for this task, so you could probably use Spglib directly if you wanted.
Original cell
New cell
POSCAR file
POSCAR
1.0000000000000000
10.0886200000 0.0000000000 0.0000000000
0....
5
The reconstructed $(\sqrt{3} \times \sqrt{3})R30$ surface unit cell can be obtained by first applying the rotation matrix
$ \begin{pmatrix} 1.0 & 2.0 & 0.0 \\ -1.0 & 1.0 & 0.0 \\ 0.0 & 0.0 & 1.0
\end{pmatrix}$
to the primitive bulk unit cell, and then the reconstructed $(001)$ surface can be cleaved from this unit cell, or ...
5
This is a bit of a boring answer, but chances are you normally want to replace the current data and do nothing. The operation can be used to add or subtract densities to visualize charge differences, but if you just want to plot a spin density you can likely just use replace.
You also probably do not need to convert the units since most VASP-like tools tend ...
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