Questions tagged [crystallography]
Questions concerning crystallography, the science of determining the arrangement of atoms in crystalline solids.
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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, ...
2
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1
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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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2
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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 ...
2
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1
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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 ...
4
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1
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How to make Pd(111) supercell (ā3×ā3)R30 via VESTA
How to make Pd(111) super-cell (ā3Ćā3)R30 via VESTA or Avogadro software?
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Can a tool āSet space groupā be useful?
In my program Chemcraft, a popular tool is the āSet point groupā 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 Ī²-tellurene structure in VESTA
I've recently started with VESTA and am having some trouble building the Ī²-Tellurene structure (monoclinic, space group nĀŗ 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 Ć
. 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:...
4
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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 ...
2
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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
...
3
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1
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225
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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 ...
7
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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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Which crystal structure I have to choose for DFT calculations? [closed]
I want to study the properties of NiO as a hole transporting material adapted for perovskite solar cells using Quantum ESPRESSO.
From Materials Project website, I saw that NiO can exist in different ...
2
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1
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How is it possible for amorphous metal to have good magnetic properties with randomly arranged atoms?
Cross-posted on Physics.SE.
It makes sense that something like grain-oriented electrical steel would have good magnetic properties (e.g., magnetic permeability). I'm envisioning magnetic field lines ...
4
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1
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Program to classify structures of different composition?
Is there a program to classify and compare structures with different composition?
I want to compare e.g. structure_1 with composition [2,1,4] and structure_2 with composition [16,8,32]. Maybe both ...
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Can CrystalFp library be used to compare structures with different number of atoms? [duplicate]
Can I use CrystalFp library to analyze different structures (e.g. of Ca2Si04) that don't have the same number of atoms?
I want to compare e.g. structure_1 with composition [2,1,4] and structure_2 with ...
4
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Should this phenolic hydroxyl be rotatable?
Looking at nelfinavir, I get variable results from different compchem packages on whether the phenol hydroxyl oxygen should be rotatable (SP3) or non-rotatable (SP2). Which one is it?
Feasibly, there ...
2
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Difference and meaning of isopointal and isoconfigurational structures [closed]
These are the meanings I`ve found, but I do not completely understand them.
Isopointal: Two structures that have the same space-group type or belong to a pair of enantiomorphic space groups. And that ...
2
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How do I know which is the asymmetric unit of a unit cell?
I need the number of independent atoms in the asymmetric unit
I have to introduce them in this form:
...
4
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1
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657
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Maximum bond length in Vesta
I need some cutoff radii to count bonds between different atoms in my system. When a .cif file is opened in Vesta, there are some default values of min and max bond lengths between two atomic species. ...
3
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1
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443
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How do the notions of Crystal structure, unit cell and supercell fit together?
I'm trying to fully understand the notion of crystal structures with some basic implications. I understand that it is conveniently described by a lattice which is the infinite repetition of points in ...
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Measuring distance with ASE
I wish to calculate the distance of all the atoms from a particular atom(atom A) in my cell. But I also want to include the atoms that might lie just beyond the periodic unit cell boundary.( In figure,...
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Tilting Octahedra of Perovskite structures in structure file [closed]
Perovskite materials form as a combination of $\ce{BX_6}$ octahdera along with A cation. Some perovskites display tilted octahedras. I am currently trying to run calculations for different tilted ...
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How to create doped possible structures for the calculation in VASP [duplicate]
I want to find the doped structure of a compound. So i need to know how we can find the possible structures after substitution or interstitial doping? for example i want the possible structures for 6:...
3
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254
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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 ...