25
votes
Enforce a space group on a given crystal structure
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 -> ...
- 9,045
17
votes
Accepted
How to do periodic DFT calculations using Quantum ESPRESSO?
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 ...
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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 ...
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15
votes
Accepted
Is the original structure invalid if it's found later that the material crystallises with a slightly different space group symmetry?
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 ...
- 10.9k
14
votes
Accepted
How is group theory used to deduce which of these integrals are equal to 0?
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 ...
- 256
13
votes
Accepted
Enforce a space group on a given crystal structure
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 ...
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13
votes
How to do periodic DFT calculations using Quantum ESPRESSO?
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, ...
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12
votes
How to do periodic DFT calculations using Quantum ESPRESSO?
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 ...
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11
votes
What are good tools for visualizing glide planes and screw axes?
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 (...
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10
votes
Accepted
How to analyze the space group of a relaxed structure that has fractional site occupancies
ASE
The ASE python package can find the space group of a structure using the get_spacegroup function as follows.
...
- 1,124
9
votes
How is group theory used to deduce which of these integrals are equal to 0?
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 ...
- 1,431
9
votes
How to analyze the space group of a relaxed structure that has fractional site occupancies
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 ...
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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 ...
- 1,780
8
votes
Enforce a space group on a given crystal structure
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 ...
- 10.8k
8
votes
Is the original structure invalid if it's found later that the material crystallises with a slightly different space group symmetry?
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 ...
- 18k
8
votes
Accepted
Inversion symmetry in 2D materials
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 ...
- 1,431
7
votes
About LaCrO3 space group stability
First of all make sure both phases are stable or not, to check stability of any phase, find mechanical stability and dynamical stability. From mechanical stability, I am referring to stiffness matrix ...
- 3,921
7
votes
What does it mean to assign group operations to distinct sets for space groups?
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)+
...
- 651
6
votes
Accepted
How to analyze the band symmetry with Quantum ESPRESSO?
This is standard output of bands.x which is a post-processing code to plot band structures used in QE under the PP folder.
- 2,048
5
votes
What are good tools for visualizing glide planes and screw axes?
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 ...
- 9,045
5
votes
Accepted
Are there computational methods for the determination of the point group symmetry of a molecule of a given geometry?
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
...
- 7,957
5
votes
How is group theory used to deduce which of these integrals are equal to 0?
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 ...
- 15.2k
5
votes
How to analyze the space group of a relaxed structure that has fractional site occupancies
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.
- 22.3k
4
votes
How is group theory used to deduce which of these integrals are equal to 0?
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 ...
- 18k
4
votes
Accepted
Why does mcsqs change the space group of generated SQS?
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 ...
- 10.9k
4
votes
Accepted
Reciprocal lattice and k-lattice belong to different groups in VASP
The DFT code will typically reduce the number of Brillouin-zone sampling $k$-points to the irreducible Brillouin zone by applying point group operations. For this approach to work, the $k$-point grid ...
- 346
4
votes
How to determine the irreducible representation of an atomic orbital at a K point?
For VASP, you may try irvasp or irRep. Or for Quantum espresso, you can directly read the group representations from the output of bands.x.
- 2,048
4
votes
About high-symmetry points in the first Brillouin zone of space group R-3m
As described on the paper, the system presents a hexagonal unit cell. From the paper recommended by @MathJacky (if you don't have access to the published paper, there is an arXiv version), we have ...
- 22.3k
4
votes
Can a tool “Set space group” be useful?
Determining space group symmetry is really useful when going between a CIF (which typically only includes the symmetry-unique atoms) and a calculation (which typically includes all atoms in the unit ...
- 9,045
3
votes
Accepted
How to generate the remaining sites in a cubic lattice from a given POSCAR/cif in Python?
I sort of get what OP wants to achieve based on the comment section, but what a strange request! Nonetheless, this can be easily done by both pymatgen and the Atomic Simulation Environment (ASE).
The ...
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