Questions tagged [crystallography]
Questions concerning crystallography, the science of determining the arrangement of atoms in crystalline solids.
178
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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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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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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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Extracting molecular structure 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 ...
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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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Labeling of high symmetry points in Brillouin zone
A Brillouin zone is defined as a Wigner~Secitz primitive cell in the reciprocal lattice [1,2].
The construction of the first Brillouin zone for two different 2D lattices are shown below:
The ...
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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 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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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 ...
CommunityBot
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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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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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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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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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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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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 ...
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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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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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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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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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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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Do the Miller indices <100> and <001> represent different families of directions? [closed]
In Miller indices, <100> is known to represent a family of directions:
Source
Does the <001> notation represent a different set of directions? I often see <001> in reference to the ...
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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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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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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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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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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? [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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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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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? [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 ...
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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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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 ...
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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? [closed]
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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