Questions tagged [crystallography]
Questions concerning crystallography, the science of determining the arrangement of atoms in crystalline solids.
88
questions
7
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0answers
27 views
Crystallography: How to sample *unique* structures from configuration space? (binary alloy supercell)
I'm working with a binary alloy system (call it 'AB'), and I'd like to generate a few unique configurations for DFT purposes.
My primitive cubic unit cell consists of 4 atoms; i.e. 4 positions. Thus, ...
9
votes
0answers
29 views
How to generate a complete set of doped (substituted) structures?
I'm trying to analyse doping in a certain material in low concentrations. I'm approaching the problem by taking crystallographic unit cell of that material, then expanding that to a 2x2x2 supercell ...
5
votes
0answers
111 views
Straightforward formalism to get four sets of 2D hexagonal lattice vectors of fcc(111) planes that I can also cite?
I am simulating low energy electron diffraction (LEED) from a polyfaceted sample. Usually it's a single, well-defined flat crystalline surface.
Since low energy electrons (below a few hundred eV) only ...
10
votes
2answers
100 views
High throughput tool to quantify the similarity of crystal structures?
Quantifying the similarity of crystal structures is important to understand and predict the properties of less-studied crystals. For example, the inorganic crystal structure database (ICSD) contains ...
8
votes
0answers
41 views
Is there a script that will suggest (hkl) indices based on distances in an electron diffraction pattern for a known crystal structure?
I am looking for a script (preferably in Python) that will suggest (hkl) indices based on distances in an electron diffraction pattern. The crystal structure is known,i.e. I have the CIF file and know ...
6
votes
0answers
66 views
How to optimize the geometry of beta PHB in VASP?
I would like to calculate the elastic constants of beta PHB. From this paper. I know that it has P3221 space group. The beta PHB has upward and downward chains, which exist at one lattice site with 50%...
9
votes
1answer
76 views
Problems with finding the unit cell from a CIF file and extracting XYZ coordinates using a software
I got hold of a CIF file for a material that I am interested in. I am trying to isolate the xyz coordinates of the molecules. However, when I open the CIF file in VESTA, I get a near-infinite periodic ...
11
votes
1answer
76 views
Extracting molecular strucutre from CIF file using VESTA or Mercury
I am trying to extract XYZ coordinates from a CIF file for a molecule to use in DFT calculations. I have Mercury and Vesta installed on my computer. Whenever I open the files, I get the following ...
11
votes
3answers
2k views
How to make a python code that can read a .xyz file and find the distance between atoms?
I want to make a python script that will load an xyz file. From the xyz parameters, I need to find the distance between atoms, angle and dihedral between atoms.
The file xyz have this structure:
...
7
votes
1answer
53 views
How to discard molecules at the boundary in the Atomic Simulation Environment (ASE)?
When building a supercell for a molecular crystal with the Atomic Simulation Environment, it seems that the program takes into account periodic boundary conditions when replicating the unit cell. How ...
13
votes
1answer
147 views
Minimum image convention for non-orthorhombic unit cells
I am trying to take into account periodic boundary conditions for non-orthorhombic unit cells.
I have the atomic coordinates for a monoclinic super cell with the following lattice vectors output by ...
13
votes
1answer
425 views
How do you write an .xyz file in the Atomic Simulation Environment?
I built a supercell of a molecular crystal and wish to write an .xyz file in ASE. How do I do that? The molecule has three different types of elements, C, H, and N.
5
votes
1answer
84 views
How do I extract the wave function from a VASP calculation?
We can obtain a energy band structure of a crystal from a DFT calculation in Vasp. Each point in each band represents an energy eigenvalue with a corresponding wave function from the Schrödinger ...
10
votes
1answer
144 views
How to import a .cif file into Avogadro 2?
I downloaded the latest version of Avogadro2 (1.91.0), but it appears I can't open a .cif file in this software. Is there a way around this? In an earlier version of Avogadro, I remember being able to ...
12
votes
1answer
82 views
How to cut properly a slab from a cif file?
I am trying to do DFT calculations on ethanol adsorbed on Pd, both surfaces 111 and 100. I have the cif file from the database and also I have built the new unit ...
12
votes
2answers
255 views
How to sort a supercell for a molecular crystal?
I am trying to build a supercell of the following (below) molecular crystal from its .cif file. How do I sort a supercell here according to each molecule in the supercell? I'm not tethered to a ...
5
votes
1answer
126 views
ASE: why do I get warnings about “monoclinic” and “orthorhombic” not being interpreted?
I am trying to use ASE (Atomic Simulation Environment) to build a supercell of some molecular crystals and then output the result to a file with the atoms given in a specified order for each molecule, ...
6
votes
0answers
33 views
Atomic Packing Fraction [closed]
I need to calculate excess entropy of mixing for a particular system of alloy. The excess entropy of mixing is dependent on temperature and it takes into account this temperature dependence by using ...
4
votes
0answers
22 views
Doubt in how dynamic strain aging and static strain aging are different from each other in its effect and phenomenon
I do understand how static strain aging occurs and why the yield point comes back if ample time is allotted after a loading and unloading cycles primarily due to diffusion of substitutional and ...
5
votes
1answer
51 views
Order of diffraction pattern confusion in XRD experiment
Somewhere I came across this phrase:
"expected diffraction angle for first order reflection."
With respect to XRD do I take this as a rule of thumb that the diffraction will always be a ...
11
votes
3answers
126 views
Rotation of crystal structure to match another structure of the same compound/polymorph
Say, I have two crystal structures of a particular organic molecule, the crystal structures are basically identical, apart from a rotation and redefinition of the lattice vectors/angles, a simple ...
5
votes
1answer
103 views
Why does twinning take place in high rate of shock loading and low temperature?
To quote from a good textbook, which I don't remember:
"Twins which are produced by mechanical deformation are called mechanical twins. Mechanical twins are produced in bcc or hcp metals under ...
7
votes
1answer
121 views
How to build the [111] slab model of NiSe2 with different terminations with ASE tool?
The following figure is the bulk structure of NiSe$_2$ downloaded from the materials project database.
Now I want to study the properties of its [111] plane. In detial, I cut the slab with atomic ...
10
votes
1answer
166 views
Nematicity in superconductors
It seems to me that the definition of "nematic phase" is quite chamaleonic.
Quoting from its first definition [Nature 393, 550 (1998)] for a 2-dimensional square lattice "The nematic ...
8
votes
0answers
121 views
Can we calculate bond enthalpies for each bond in a supercell of a disordered AB crystal using DFT?
Apart from using Bader charge analysis or energy of formation estimation, I wonder if there is a way to compute the bond energy of constituent bonds in a crystal using density functional theory.
Let's ...
12
votes
0answers
106 views
How do I know if the reconstruction in the picture is a 2 x 2 reconstruction?
How do I know if the reconstruction in the picture is a 2 x 2 reconstruction or not?
I believe that this corresponds to a 2x2 reconstruction because there's an even ...
10
votes
1answer
87 views
How do I reconstruct the surface with known Miller indices?
I'm trying to reconstruct the surface $(1\bar{1}01)$ in an hexagonal material and the reconstruction is described by the matrix $\begin{pmatrix} \hspace{3mm}3 \hspace{2mm}1 \\-1 \hspace{2mm}2 \end{...
6
votes
0answers
60 views
How do I identify an oblique surface mesh?
I have drawn three surface meshes from a hexagonal material for the $(0001)$, $(1\bar{1}00)$ and $(1\bar{1}01)$.
The first one would be the top horizontal surface of the hexagonal structure, the ...
5
votes
1answer
90 views
How can I find the area of an overlayer structure?
What sources would you recommend (or if you could instead explain it to me that would be great). I have never studied crystallography but must do a module on it and in some of the questions we were ...
18
votes
4answers
1k views
How to explain Miller indices to someone outside nanomaterials?
I often find that when talking to experimentalists outside of the field of nanomaterials, it is nearly impossible to explain Miller indices concisely. As this often comes up during talks from other ...
12
votes
1answer
111 views
What does it mean to assign group operations to distinct sets for space groups?
I am trying to understand space groups in crystallography. In International tables for crystallography, for a nonsymmorphic space group, they list some symmetry operations. 8 of them are listed under ...
12
votes
1answer
164 views
Finite temperature crystal structure prediction
Crystal structure prediction codes like USPEX, use DFT calculated values of energy ($0$ K) to study the phase space (or potential energy surface or internal energy surface, I'm confused which is it). ...
12
votes
1answer
311 views
Suggestions for a good crystal structure visualization workflow
Following up on this question about freely available crystal structure visualization codes, I wish to know what procedures people follow from start to finish in preparing images of their materials for ...
9
votes
0answers
68 views
Have FDTD methods made inroads into dynamical simulation of electron and/or X-ray scattering by crystals?
I'm afraid this question might be too basic or too naive or both, but here goes!
For optical diffraction by periodic nano-structures (gratings, semiconductor manufacturing metrology) the rigorous ...
12
votes
1answer
427 views
Si energy band values are not matching with literature values
I have performed the DFT calculation for Silicon in Quantum ESPRESO. I have tried to calculate the electronic band structure, the shape of wiggles of bands are mostly matching but the energy values ...
6
votes
0answers
109 views
How to convert lab frame quaternions and plane normal to misorientation quaternion and crystal plane normal for grain boundaries?
Background
Let qA and qB represent unit, orientation quaternions of grain A and grain B of a grain boundary in the lab reference ...
9
votes
2answers
381 views
Creating a heterostructure in VESTA
I have two different crystal structure and I want to create a heterostructure but the problem is that the shape of their unit cell is different. I know how to combine them if their unit cell are same. ...
