26 votes

Can a highly-cited published paper have this type of error?

Many published papers, even extremely highly cited ones by what you call "serious" authors, have issues like these. Consider for example this one which currently has 862 Google Scholar ...
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  • 27.8k
22 votes

Is the number of possible Bravais lattices a mathematical fact?

Quasicrystals were known well before 2015. The recent developments is in showing that such crystals exist naturally, rather than just in synthesized samples. The first (nowadays generally accepted) ...
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  • 3,938
19 votes
Accepted

How to explain Miller indices to someone outside nanomaterials?

You can see it with VESTA software. For example, we can see the different lattice planes of NaCl crystal. [001] plane of NaCl: [101] plane of NaCl: [111] plane of NaCl:
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  • 13.6k
15 votes

Can a highly-cited published paper have this type of error?

I was actually going to provide this as a comment as this in itself is not a proper answer. But since this got a bit too lengthy for a comment, I am providing this as an answer. It is possible for a ...
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  • 2,454
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. ...
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13 votes

How to explain Miller indices to someone outside nanomaterials?

Assuming a generic chemistry background I wouldn't assume that knowledge of crystal structure would be too in depth at an undergraduate level. It is definitely encountered, but depending on the type ...
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12 votes

Labeling of high symmetry points in Brillouin zone

I think the naming conventions are standardized and people computing band structures employ them directly. I will break down the high-symmetry points for a 2-D brillouin zone and post very good ...
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  • 2,172
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 ...
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  • 4,268
10 votes
Accepted

Get fractional coordinates from special Wyckoff positions

From that reference, what we got is the bond length from the atomic positions. One easy way is to look for a CIF file with the crystal information. From the CIF49801 bellow, we get the following info: ...
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  • 18.5k
10 votes
Accepted

How to extract the crystal symmetry from VASPs POSCAR/CONTCAR file?

There are multiple programs that can do this. As far as I know, all the open source codes use the excellent spglib package by Atsushi Togo "under the hood" for space group perception, ...
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9 votes

What does capital sigma followed by an integer (Σn) mean in the context of grain boundaries?

The $\Sigma$ values represent the volume of the Coincident Site Lattice (CSL) of the grain boundary in terms of the volume of the unit cell of the crystal. In general, grain boundaries with higher ...
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  • 1,274
9 votes

Nematicity in superconductors

Yes, nematic order is an alignment of rotational degrees of freedom without spatial structure. One good example of a nematic phase occurs in a liquid crystal composed of elongated molecules. The ...
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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 ...
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  • 331
9 votes
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High throughput tool to quantify the similarity of crystal structures?

As Thomas mentioned, there are tools from Materials Project that we use for structure similarity. See for example this paper, with code available in pymatgen. This works by creating local environment &...
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  • 1,411
8 votes

Rotation of crystal structure to match another structure of the same compound/polymorph

If you know which atoms correspond to each other in the two structures, you can use a structural superposition method. Least-squares superposition methods find the rotation matrix and translation that ...
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  • 1,485
8 votes

High throughput tool to quantify the similarity of crystal structures?

Not sure what your input files are, but there's a technique based on spherical harmonics that is relevant described here: High Throughput Profiling of Molecular Shapes in Crystals https://doi.org/10....
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  • 753
8 votes
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Could we predict all possible forms of carbon Allotropes?

One of the software I know is able to search/generate new structures is USPEX. From their site, USPEX means: USPEX (Universal Structure Predictor: Evolutionary Xtallography...and in Russian "...
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  • 18.5k
7 votes
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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 ...
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7 votes
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How to cut properly a slab from a cif file?

You can use ASE. For your case, I assume you are using the Pd crystal structure with space group 225. Cut the (111) surface with ASE: ...
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  • 13.6k
7 votes
Accepted

How do I reconstruct the surface with known Miller indices?

Cut a surface with ASE: ...
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  • 13.6k
7 votes

How to calculate the orthogonal representation of a HCP cell?

I understand that you are trying to implement cell lists. For orthogonal unit cell (or even better - cubic) the cells that subdivide the unit cell are nicely aligned with the unit cell. Wikipedia has ...
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  • 1,485
7 votes

Looking for crystal generator library

Please feel free to contribute to Open Babel. I'm sure people would use it! Probably the easiest C++ code to adapt would be from Avogadro 1, which directly used the Open Babel API. For example the &...
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7 votes

Which formalism is better suited to model a crystal with defects: Hartree–Fock, Kohn–Sham, or something else?

Let me first clarify a few things. Whether a calculation is Kohn-Sham or Hartree-Fock has nothing to do with whether the calculation is periodic or not. In fact, both Kohn-Sham and Hartree-Fock can ...
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  • 6,398
6 votes

CuO (monoclinic) crystallographic plane and their relaxed surface energy

I recommend that you calculate directly. You can use a package like ASE to generate terminations of a given surface using the build module. For the treatment of surface energies I would refer you to ...
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6 votes
Accepted

How can I find the area of an overlayer structure?

The 0001 facet area will be only dependent on the $a$ lattice constant. To solve for the area of that surface, you will just need to find the area of a rhombus with a $60^{\circ}$ angle. To read the ...
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6 votes

How to sort a supercell for a molecular crystal?

I don't know if this is exactly what you want to do, but pymatgen may be able to help (disclosure, I am a developer of this package). See this example code below ...
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  • 1,411
6 votes
Accepted

How do I extract the wave function from a VASP calculation?

It seems you are looking for a package to compute the irreducible representation of electronic states computed by VASP. This has been recently developed: J. Gao J, Wu Q, Persson C, Z. Wang. Irvsp: to ...
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6 votes

How to import a .cif file into Avogadro 2?

tldr; Try one of the [nightly builds](https://nightly.link/OpenChemistry/avogadrolibs/workflows/build_cmake/master) Avogadro uses Open Babel to read CIF files, and unfortunately, OB versions before v3 ...
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6 votes

Proposing a 2D quasicrystal; what are the necessary and sufficient conditions? (If it looks like a duck and quacks like a duck, or...?)

Independent of facing a 3D sample, or one of 2D/2.5D, IUCr's definition applies to both of them when stating «There are two definitions of the notion of quasicrystal. A quasicrystal is an aperiodic ...
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  • 1,457
6 votes

Which formalism is better suited to model a crystal with defects: Hartree–Fock, Kohn–Sham, or something else?

I would like to add a few aspects to the answer of wzkchem5. Considering local or semilocal xc functionals for the KS equations, one difference between HF and KS is that HF is computationally more ...
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