# Tag Info

25

While there are undoubtedly other programs that do this, it's fairly easy to do in Avogadro. I start with a calculation on hexagonal SiC. As mentioned, it starts as $P_1$: Go to Crystallography -> Space Group -> Perceive Space Group The unit cell should update, including symmetrization if needed

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

Unlike non-periodical DFT codes, Quantum ESPRESSO uses planewave basis sets and pseudopotentials. There are many ways of writing your input file, and it all depends on what information you have or what you want to learn. Here is the skeleton of your input file: =============================================================================== &CONTROL ...

15

Let's imagine we have two different structures for the same compound, and that structure 1 has the lower energy and structure 2 has the higher energy. If you consider the potential energy surface of all potential atomic configurations, then each of these structures sits at a local minimum, and the minimum associated with structure 1 is lower in energy than ...

14

The question is too broad to be answered directly so I will provide a somewhat general scheme. Basically in an integral like $$\int d\mu A B C$$ one would seek to expand each part in irreducible representations of a given group, say for instance \begin{align} B=\frac{1}{\vert \mathbf{r}-\mathbf{r}^\prime\vert} =\frac{1}{r} \sum_{\ell} \left(\frac{r'}{r}\...

13

This can be done using PyMOL (which, while not free for general use, does have a free student license) via the set_symmetry argument, as documented here. This allows for a user-specified spacegroup and will update the CIF to match.

12

You can start with following this Quantum Espresso Tutorial. The tutorial includes Hands On: scf, Energy bands, eqn of state, Geometry, cell optimization, Magnetism, DFT + U, CPMD, TDDFT, GW, Phonos, Berry Phases, IR and Raman You can also follow Open online course on DFT, with simultaneous hands-on training on Quantum ESPRESSO. Available at any time for ...

11

Jmol/JSmol Did you consider Jmol/JSmol? It is freely available for Windows / Mac / Linux, scriptable, may export what is being displayed in formats relevant to chemistry (e.g., .pdb, .sdf), as image (e.g., .png, .pngj, [animated] .gif) and already is in use to teach symmetry in molecules and crystals. As an example, the interactive compilations by Symmetry@...

11

Regarding input file format, check this website: https://www.materialscloud.org/work/tools/qeinputgenerator Format from this website will provide you a starting point. But please remind that the result from this website IS NOT the ultimate solution and please do NOT regard the result from here as the "OK-button" solution. It seems that the example in your ...

9

First, you have to transform all the basis functions into the irreducible representations (irreps) of the point group of the molecule. You can do this with standard projection formulas. Once, you know the irreps of the basis functions, you have to look at the product table of the point group to find out whether the product of those four basis functions ...

9

spg-lib Another light-weight option is the spg-lib by Atsushi Togo and Isao Tanaka described here with multiple interfaces that can be found here. Especially, the tolerance parameters for the detection of symmetries are quite handy.

9

ASE The ASE python package can find the space group of a structure using the get_spacegroup function as follows. import ase.io as io from ase.spacegroup import get_spacegroup structure = io.read('path/to/POSCAR') sp = get_spacegroup(structure,symprec=1e-5) print(sp) I am not sure as to whether it can deal with fractional occupancies, but it seems it can ...

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

This is possible via ASE as well. There are modules which can handle space groups via spglib. I will focus on an application that hasn't been discussed yet. ASE has an advantage that you can enforce symmetry during an optimization of cell size / positions. Here is an example that can be run with GPAW which will load a geometry (POSCAR) and optimize the ...

8

Let's give it another go: In the monolayer you would place the inversion centre on the green atom. But this would reverse the direction of the trigonal prism formed by the yellow atoms. Hence, there can't be an inversion centre. In the bilayer the inversion centre is between the layers. Then the direction of the trigonal prism is reversed but it is also ...

8

Sometime the experiments can also be interpreted incorrectly. Namely, not all kinds of experiments are unambiguous; some require computational modeling to extract the structure. That is, even if the experiment were done correctly, the assignment can still be wrong if the interpretation is not correct. (I'm not sure this applies to crystal structure ...

6

This is standard output of bands.x which is a post-processing code to plot band structures used in QE under the PP folder.

6

When your lattice is primitive you have only the (0,0,0)+ set; when your lattice has some kind of centering (body- or face-centering) other sets are present, such as (1/2, 1/2, 1/2)+ or (1/2, 1/2, 0)+ It's not clear to me what you write. In the first page of the Internationl Tables you find all the symmetry operations that are listed with Roman numerals (1),(...

5

To start with, while it's not as necessary, you can apply symmetry arguments to one-electron integrals. Consider $\langle\mu|O_1|\nu\rangle$, where $O_1$ is some one-electron operator. If the molecule has some point group symmetry, we can form basis functions/operators that are irreducible representations of the group. Once we have the functions expressed in ...

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Bilbao Crystallographic Server You can take a look at the Bilbao Crystallographic Server. It has several tools for symmetry and structure analysis in the Solid State Theory Applications section.

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CCDC Mercury The Cambridge Crystallographic Data Centre (CCDC) provides a free-to-use visualization program Mercury that offers a wide variety of features for crystal structures including, perhaps not surprisingly crystallographic symmetry. The trick, of course, is to have appropriate crystal structures to illustrate points. CCDC does provide a free teaching ...

5

In order to get this question answered there are a variety of algorithms for determining symmetry. Here is what I've found Simple Algorithms for Determining the Molecular Symmetry -- not open access New computer program to calculate the symmetry of Molecules -- open access and with some matlab code snippets I've also found this link to a Researchgate page ...

4

These are some general comments about modelling disorder which I think address your question, but note I cannot provide specifics about the codes you are using. Imagine a simple configuration with only two sites for the discussion: Both atoms are of the same type (blue) so that this configuration has a mirror plane down the middle of the two atoms (dashed ...

4

Boy, you're not starting off easy. Proper implementation of symmetry is quite a job, especially since most systems of interest nowadays have no symmetry. For a reference, you can look at e.g. Dovesi's work on the use of symmetry in CRYSTAL, which is a periodic Hartree-Fock code using Gaussian orbitals. Symmetry is much more important in the periodic case, ...

2

FINDSYM Another useful tool to determine crystal symmetry is FINDSYM. It works with the .cif format exclusively, so you may have to convert your structural files to .cif before using it.

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