Questions tagged [crystallography]
Questions concerning crystallography, the science of determining the arrangement of atoms in crystalline solids.
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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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How to fill in all atoms in unit cell starting from a CIF file?
I am trying to write code that builds a unit cell with all atoms explicitly specified, starting from a CIF file of a molecular crystal. The CIF files come from CSD. My first try was to use Gemmi to ...
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What are the specific differences between these two notations of supercell denoted by (√3×√3)R30∘ and (√3×√3)?
I am studying the super-cell structures in crystallography and came across two different notations:
(√3×√3)R30∘ and (√3×√3). I would like to understand whether these two notations represent the same ...
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Why does my POSCAR file say I have 4 Pd atoms when I actually have 14 based on my structure from a crystal database?
I am having trouble getting my geometry optimization to run, and I think it may be my POSCAR.
I downloaded a FCC Pd crystal structure from a crystal database. I downloaded the cif into materials ...
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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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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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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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Visualize variation of lattice parameters with temperature after MD
I am interested to plot lattice parameters vs temperature after Molecular Dynamics calculation in NPT ensemble to detect structural phase transition of my system, Ex- So, I am looking for python ...
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Can conventional unit cell have higher symmetry than primitive cell for the same crystal?
This question arises from the last sentence of the first paragraph (see here) of the section "Formalism". If primitive cell can have lower symmetry, why don't the DFT results using these two ...
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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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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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Is there any software or Python library for visualizing higher-order Brillouin Zones of standard lattices?
I am looking for a software or Python library to help me visualize higher-order Brillouin Zones (BZs) of standard lattices like FCC, BCC, etc. I have already plotted the first BZ of an FCC lattice ...
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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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Have I missed something? "Aluminum is even simpler than Silicon: one atom per unit cell in a fcc lattic"?
In this tutorial page 17, it says: "Aluminum is even simpler than Silicon: one atom per unit cell in a fcc lattic".
If it is FCC, then it should be the same as Silicon, two atoms per unit ...
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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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How to make a super cell for molecular crystal with PBC
I am trying to build a supercell for molecular crystals from a .cif file. With the ASE package, the supercell has the perfect PBC, but the atom sequence is very random and might be difficult to match ...
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Photorealistic Rendering: How To?
i have started computationally modelling materials from first principles recently, my code of choice being VASP [6.1.0].
Recently i have come across this paper in Nature: DOI:10.1038/s41567-023-01960-...
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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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Total energy calculation for an isolated atom
I tried calculating total energy using SCF calculations after optimization with quantum espresso. Still, I don't know how to optimize total energy in the standard state instead of isolated atoms.
If ...
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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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Non-Equivalent T-Sites from a cif file
I am trying to find symmetrically inequivalent T-atoms in a crystal structure (zeolite).
Does anyone happen to know any package that can help with that? I see that pymatgen does have options for ...
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How to make Pd(111) supercell (√3×√3)R30 via VESTA
How to make Pd(111) super-cell (√3×√3)R30 via VESTA or Avogadro software?
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Can a tool “Set space group” be useful?
In my program Chemcraft, a popular tool is the “Set point group” utility: it symmetrizes the molecule according to a specified point group, and then the symmetry of the molecule is correctly ...
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Having difficulty creating the β-tellurene structure in VESTA
I've recently started with VESTA and am having some trouble building the β-Tellurene structure (monoclinic, space group nº 12). I know that the lattice vectors are:
$$\vec {a} = a\hat x \\ \vec {b} = ...
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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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Why am I getting a wrong lattice constant from these SIESTA calculations?
I am currently learning to perform calculations on solids and am attempting to manually optimize the size of a face-centered cubic (FCC) cell of Nickel (Ni) using SIESTA (v. 4.1.5) with the Perdew-...
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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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VESTA using command line
Can anyone please show me how to make a supercell with VESTA
using a single command line without opening a GUI.
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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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How easy is it to distinguish water from ions in xray crystallography?
I'm interested in bound ions in protein xray crystal structures. Of course a lot of structures include biologically significant ions, such as Mg2+ in the active site of an enzyme. But a lot of ...
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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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Energy of formation Vs Formation Energy Vs Heat of Formation Vs Energy Above Hull differences
I work in the field of materials science. While exploring the concepts related to material stability, I have come across terms such as "Energy of Formation," "Formation Energy," &...
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Computing lattice coordinates starting from lengths and angles
I've been reading this interesting paper and I'm trying to understand the following: it is known that a crystal lattice can be represented by 6 parameters corresponding to lattice vectors lengths ($a,...
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How to model an interface between two solids
I have two solid surfaces that I want to combine to study the interface as seen in the attached image. What I know is the lower part of the bottom structure is fixed to mimic the bulk. However, do I ...
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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 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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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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Why the relaxation of my material in Quantum ESPRESSO wasn't achieved?
I did a vc-relax calculation using HSE by Quantum ESPRESSO and after 22h time WALL the job was complete and JOB DONE was mentionned in the end of the output file ...
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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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Why I got more atoms than expected when generating POSCAR from VESTA
I tried to generate a perovskite structure with VESTA, and the following are my settings:
The generated structure seems to be correct. However, when I tried to export it as POSCAR I got the following:...
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What is the best method to compute crystal structures?
I am rather new to VASP and I have seen people using different methods to compute crystal structure:
Using Birch-Murnaghan equation to find optimal lattice volume, and then adjust the structure ...
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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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What determines if a material tends to undergo transgranular or intergranular fracure? [closed]
As an example, why does glass tend to break by means of intergranular fracture?
My analysis so far led me to believe that the tendency can be related to the intermolecular bond strength in a given ...
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How to stack graphene and hBN on top of each other?
I read in papers (e.g. link) about AA stacking, where C atoms are above the B and N atoms, and AB stacking where one C atom is above the N or B atom, while the other C atom is above the h-BN hexagon.
...
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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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What is the ibrav value of a rhombohedral structure? [closed]
I have a rhombohedral structure
The SYSTEM and CELL_PARAMETERS blocks looks like this:
&SYSTEM
ibrav = 0
A = 6.058435171
...
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A Question about ISIF Tag in VASP
I apologize for asking this stupid question, but I am a bit confused with the ISIF tag.
Doesn't a cell's shape and cell's volume depend on the atoms' positions?
If so, why can the cell's volume/shape ...
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Why does my zincblende structure not look cubic?
The structure of my material is zincblende. So normally the structure is cubic. However, when I open the primitive cell with xcrysden it dosen't look 100% cubic. It's a little bit inclined. Also when ...
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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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Generate structure using atomic coordinates
I am trying to write a Python/C++ code that reads in a *.xyz file and varies the interatomic distances, angles etc. between distinct atoms in a molecule. In other words, a complete new structure with ...
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