Questions tagged [crystallography]
Questions concerning crystallography, the science of determining the arrangement of atoms in crystalline solids.
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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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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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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 ...
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What determines if a material tends to undergo transgranular or intergranular fracure?
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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What are the freely available crystal-structure visualization softwares?
I use VESTA mostly for crystal structure visualizations.
What other options are available?
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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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Convert XYZ coordinates to Z-matrix
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:
...
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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 showing the same symmetry elements.
Let me provide an example since it might at ...
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What is the ibrav value of a rhombohedral structure?
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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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 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 detail, I cut the slab with atomic ...
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How do I know if the reconstruction in the picture is a 2x2 reconstruction?
How do I know if the reconstruction in the picture is a 2x2 reconstruction or not?
I believe that this corresponds to a 2x2 reconstruction because there's an even ...
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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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Is there a robust and reliable software to change the lattice vectors of unit cells?
I am working with Heusler and Half Heusler materials on LAMMPS. Currently the study follows the properties in individual lattice directions such as [100] [110] etc. As of now, I am obtaining the unit ...
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Which crystal structure I have to choose for DFT calculations?
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 ...
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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 ...
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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 ...
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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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Difference and meaning of isopointal and isoconfigurational structures
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 ...
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Is there a free software to build a crystal shape that is cut with a specific angle plane (like 40 degrees), which is not implemented in Vesta?
I would like to cut $\ce{SrTiO3}$ with a specific angle of 40 degrees, or to choose an angle plane which is not implemented in the Vesta software.
Could you please recommend a free software to build ...
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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:
...
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How to transform lattice in VESTA
Can anyone please help me transform $\ce{LiCoO2}$ hexagonal cell ($a \times a \times c$) to orthorhombic cell ($a \times a \sqrt{3} \times 1$) and hexagonal cell ($a \sqrt{3} \times a \sqrt{3}\times 1$...
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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. ...
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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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What software should I use for an MD study of a temperature-dependent crystallographic phase transition?
I want to study the crystallographic phase transitions of crystals with increasing temperature. Which freely available MD package should I choose, which has easily available tutorials/example-input-...
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Tilting Octahedra of Perovskite structures in structure file
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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What does capital sigma followed by an integer (Σn) mean in the context of grain boundaries?
I've just run across a nomenclature for coincidence lattices at grain boundaries which uses a capital greek letter sigma followed by an integer. For example A.D. Rollett's 2016 Grain Boundary ...
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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.
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How to make idealized infinite alpha helix or beta sheet?
I'm interested in studying some simple periodic model systems representing proteins. For that I'd like to make pdb files of an alpha helix or beta sheet with idealized coordinates which is infinitely ...
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Stability using Phonon Calculation
While performing phonon calculation using finite difference method, we get normal modes printed in the outcar file. Now there is a distinction between two different types of modes in the outcar file.
...
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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:...
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How to transform the conventional cell to primitive cell?
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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How to transform the k coordinate into the k path used in the band structure?
When drawing the band structure, I need to transform the coordinate of k-points into a k-path, but I am not sure what the formula is.
I checked the result of siesta,...
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Confusion in primitive, conventional and supercell crystal structure
I am doing the DFT calculations in Quantum ESPRESSO code. I have 2 different pwscf input file of the same crystal. I am confused which one is representing primitive, conventional and supercell ...
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How does one make sure that the [hkl] direction in ab-inito calculations is the same as in experimental calculations?
I am currently looking at isotropic properties and let's say I want to determine my property in the [100] direction. Now, I basically want that my [100] direction be the same as the [100] direction in ...
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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 does one decide the directions in which they will calculate effective mass?
I have been working on trying to calculate the effective mass in different directions by fitting a parabola to the VBM and CBM and using the fitted parameters to calculate $\frac{d^2E}{dk^2}$. And ...
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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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How to determine the concrete value for the wavenumber in tight-binding approximation
As a simple problem setting,
consider a one-dimensional linear crystal of NaCl with only 1s orbitals,
where the atomic distance between Na and Cl is also assumed to be 0.5 Å
for simplicity (Fig. 1).
...
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How to fix outliers in Ramachandran plot using Coot [closed]
I have the following Ramachandran plot generated by Coot:
Notice that it has high outliers content (red dots). I want to manually drag those
red dots into some part of the region. Eventually, I ...
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Repository of Common Surfaces
Are there any repositories of crystal surfaces? Due to orientation / termination of surfaces, occasionally it is non-trivial to decide how exactly to cut a surface for things such as oxides. I ...
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Spacing issues about multiple-layer bcc structure
I am trying to make Hartree potential of bcc Tungsten(001).
My software is VASP.
5-layer should have 5 bound states.
But I don't have them
I heard it is a layer-layer spacing issue.
I built slab of ...
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Slab rotation with ASE, unexpected behaviour [closed]
I am trying to generate the $\sqrt{3}\times\sqrt{3}R30^\circ$ representation of a Pt111 slab, I start by generating the $1\times1$ using ASE:
...
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