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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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) ...
- 4,656
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:
- 14.8k
17
votes
Convert XYZ coordinates to Z-matrix
ASE
The ASE library has an atom object with built-in get_angle, get_dihedral and ...
16
votes
Convert XYZ coordinates to Z-matrix
Easiest free tool to do this (no download necessary):
What you are describing, is the conversion from XYZ format to ZMAT format. How to do this, has been asked here on the Chemistry Stack Exchange, ...
- 33.1k
16
votes
Convert XYZ coordinates to Z-matrix
Open Babel
First, the command-line version:
obabel c60.xyz -oreport
Yields:
All interatomic distances
All bond angles
All connected torsions
Also, partial charges
...
- 8,655
15
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.
...
- 10.7k
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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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 ...
- 693
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 ...
- 2,312
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 ...
- 4,388
11
votes
Accepted
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 &...
- 1,501
10
votes
Accepted
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 ...
- 1,339
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:
...
- 21.9k
10
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 ...
- 361
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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10
votes
Accepted
Generate structure using atomic coordinates
To understand the new coordinates after altering the bond length of the C-O bonds you can use the below approach:
Let us first visualize the positions of all the atoms before and after altering the ...
- 2,875
9
votes
Accepted
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:
...
- 14.8k
9
votes
How to build the [111] slab model of NiSe2 with different terminations with ASE tool?
There is currently no tool built into ASE to do this sort of detective work on surface terminations. I highly suggest that you take the approach of trying to eliminate dangling bonds first (for ...
- 10.7k
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 ...
- 6,569
9
votes
Convert XYZ coordinates to Z-matrix
Maybe this comes a bit late. There are some tools which can do this. But I was also interested in doing such a calculation using python. I first started with an iterative process which was terribly ...
- 91
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 ...
- 1,750
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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8
votes
Accepted
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 "...
- 21.9k
8
votes
Accepted
Why does my zincblende structure not look cubic?
I think the premise of your question is mistaken. The structure you have shown in your question is the primitive cell of Zincblende. It is not cubic. The conventional structure has a face-centered ...
- 2,031
7
votes
Accepted
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 ...
- 1,134
7
votes
Accepted
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 ...
- 1,750
7
votes
Minimum image convention for non-orthorhombic unit cells
There is a nice explanation here outlining the difficulties for the minimum image convention in triclinic cells.
It describes an exact approach (edit: see discussion below), as well an approximate ...
- 1,873
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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