Questions tagged [crystallography]
Questions concerning crystallography, the science of determining the arrangement of atoms in crystalline solids.
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questions with no upvoted or accepted answers
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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 ...
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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 ...
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Database (or table) of functions obeying symmetry properties of space groups
I'm looking for a table or database containing mathematical functions that belong to crystallographic space groups by having the same symmetry elements.
Imagine a 2D square planar lattice. It has a 4-...
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Straightforward formalism to get sets of lattice vectors of fcc (111), (110) and (100) facet surfaces 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 ...
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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 ...
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Color of isosurface in charge density visualization
I am trying to visualize the charge density of a crystal through VESTA. However the intersection surface of the isosurface and the boundary turns into blue, which is certainly not included in my ...
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How can I properly plot this .cube file in Python?
Motivation for Post: I saw a question about how to plot a .cube file recently on the Mathematica & Wolfram Language Stack Exchange. It was marked "off-...
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How to transform a perturbed surface structure to a reference surface structure?
Say I have a bulk FCC Pt structure obtained from Materials Project with a lattice constant a = 3.94 Å. I first did DFT to relax the bulk structure, and the optimized lattice constant becomes for ...
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How to find the most stable facet for a crystal?
I am trying to find the most stable facet for a crystal, but since there are many possible choices, like (1 0 0),(1 1 0),(1 1 1),(2 1 0), etc. My questions is:
I am wondering how should I determine ...
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Rich editing of ASE images
I want to produce some images related to graphene-like materials.
I was able to draw them using ASE visualize module after constructing the atomistic model. However ...
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answer
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Layer detection in a crystal structure
Context
I have two images from a Monte Carlo Basin Hopping where silicon (in yellow) is getting replaced by germanium (in blue). Both have 32 germanium atoms at Si/Ge = 2.5; only the Ge distribution ...
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Basic principles (and vocabulary) necessary to begin modeling the rate of atom surface diffusion and thermal planarization of ground metal surfaces?
Background:
Surface science experiments very often start with atomically smooth crystal surfaces as substrates. After one experiment ends the surface is sputter cleaned with cycles of keV energy argon ...
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How to choose a proper rotation matrix and apply it to rotate unit cell about Cartesian axis to align I-Cr-I bonds parallel to Cartesian axis
I was surveying this paper Remarkably enhanced Curie temperature in monolayer CrI3 by hydrogen and oxygen adsorption: A first-principles calculations, where they have rotated the unit cell (without ...
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How to choose the correct ibrav value and Identifying the 3-fold Axis
I'm trying to perform relaxation calculations for FeTiO3 with the ilmenite structure in Quantum Espresso. The documentation mentions two possible ibrav values for triagonal systems: 5 and -5. However, ...
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Atomic basin partitioning with electron density grid
I am performing Hirshfeld Atom Refinement (HAR) calculations with XRD data using aspheric atomic scattering factors, which are calculated from wavefunctions optimized in Orca. My crystal structure has ...
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How to model and compute the structure of high entropy alloys (HEAs) using SSOS methods with ATAT
I've recently been working on structural modeling of HEAs and got a little confused when I read about the SSOS approach. I would appreciate it if anyone is familiar with the SSOS method or MCSQS and ...
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Miller indices and periodic boundary conditions
I want to implement building the Miller indeces in my program Chemcaft. Currently I need to understand more the computations with periodic boundary conditions (PBC) needed for crystallographers.
The ...
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What is convention of predefined coordination system for defining elastic constant of a specific material
I try to find the elastic constants of LiTaO3 from online databases. I did find a page that lists them https://www.roditi.com/SingleCrystal/Lithium-Tantalate/LiTaO3-Properties.html
As I know, the ...
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Is it possible to find a cubic supercell for a non-cubic crystal structure?
Suppose that we have a crystal material with a non-cubic unit cell. E.g. $\alpha \neq \beta \neq \gamma \neq 90^{\circ}$. Is it possible to find a supercell such that $\alpha = \beta = \gamma = 90^{\...
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Is it a good idea to always read charge and orbitals if I am working on similar systems?
For example, if I am investigating of the elastic properties of a crystal by doing a lot of computations of crystals applied with small strain.
Also, is it a good idea to read charge and orbitals when ...
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How to generate pole figures from limited amounts of area detector X-ray diffraction from thin films (explain it like I'm five years old)
Historically powder X-ray diffraction was the go-to method for reconstructing crystal structure. X-ray sources were limited in intensity and emittance and so to collect data in a reasonable amount of ...
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390
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How to transform the conventional cell to primitive cell, by hand?
I am following this tutorial to transform a conventional cell to a primitive cell, but I am not sure how to determine the primitive copy of some atom in the conventional cell.
For example, in the ...
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How to visualize the basis in the unit cell of crystals?
Usually, the unit-cell of a crystal is made up of lattice points and basis, but all the crystallography software like VESTA doesn't show the basis, is there any ...
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A problem to simulate the kinetic energy operator using some field going through a crystal
We know about a differentiation and integration operations and also other ones can be simulated by an analog way using electric circuits with operational amplifiers (here are articles of the ...
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How to rotate Octahdrals locally along with unit cell axis
As the continuation of this discussion d orbitals PDOS analysis, I am curious about crystal field effects on a given atom by analysing $m_l$ projected DOS, the individual d-orbitals are given with ...
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Error in 2D Ewald sum for a multipolar expansion
I am attempting to calculate the potential of a particle at the center of an infinite two-dimensional lattice as per the following reference:
Reference: Lambin, PH & Senet, P. Ewald Summation of ...
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How to find the scaling factors for minimum image convention?
Suppose that we have an arbitrary (not necessarily cubic) unit cell with cell parameters $\mathbf{a}$, $\mathbf{b}$, $\mathbf{c}$ (lattice vectors) and $\alpha$, $\beta$, $\gamma$ (lattice angles).
We ...
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Surface atoms concentration
I have a bulk crystal that contains 4 different elements. I want to cut the crystal in such a way that the atoms at the surface still obey the concentration of each atom in the bulk. At least close. ...
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Code to build the monoclinic crystal lattice
Benzoic acid exists as a solid at room temperature. So, I want to build a monoclinic crystal structure of this molecule. Is there any code available to do that? Thanks.
Edit: Is there any way to build ...
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Unit conversion of q point (from iku to 1/a.u.) in yambo
Here are some necessary info about direct lattice and reciprocal lattice from yambo output file:
...
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