Questions tagged [crystallography]

Questions concerning crystallography, the science of determining the arrangement of atoms in crystalline solids.

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wurtzite unit cell of ZnO

am looking to draw wurtzite unit cell of ZnO, and i find two of them and the second one my questions is what is the difference between them? and how can i draw the first one in software like vesta?
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0answers
26 views

Space group will not change in vesta

I have one unit cell of 16 atoms (4 formula unit cells) 2x2x2 unit cells. I want to construct the supercell with 32 and 64 atoms. I went in the transform and I changed the rotation matrix 4x2x2 and ...
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1answer
49 views

1T and 1H CIF file for MoS2

On the COD website, only 2-layer hexagonal (2H) and 3-layer orthorhombic (3R) $\ce{MoS2}$ are available. I can't find the 1-layer tetragonal (1T) and 1H CIF for $\ce{MoS2}$. Where can I find them, or ...
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2answers
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How can I make a CIF file for Monoclinic MoO2?

A CIF file of Monoclinic $\ce{MoO2}$ is not available in the Crystallography Open Database website. How can I make it myself or find it elsewhere?
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0answers
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Crystallography: How to sample *unique* structures from configuration space? (binary alloy supercell)

I'm working with a binary alloy system (call it 'AB'), and I'd like to generate a few unique configurations for DFT purposes. My primitive cubic unit cell consists of 4 atoms; i.e. 4 positions. Thus, ...
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49 views

How to generate a complete set of doped (substituted) structures?

I'm trying to analyse doping in a certain material in low concentrations. I'm approaching the problem by taking crystallographic unit cell of that material, then expanding that to a 2x2x2 supercell ...
5
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0answers
124 views

Straightforward formalism to get four sets of 2D hexagonal lattice vectors of fcc(111) planes 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 ...
10
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2answers
105 views

High throughput tool to quantify the similarity of crystal structures?

Quantifying the similarity of crystal structures is important to understand and predict the properties of less-studied crystals. For example, the inorganic crystal structure database (ICSD) contains ...
9
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0answers
46 views

Is there a script that will suggest (hkl) indices based on distances in an electron diffraction pattern for a known crystal structure?

I am looking for a script (preferably in Python) that will suggest (hkl) indices based on distances in an electron diffraction pattern. The crystal structure is known,i.e. I have the CIF file and know ...
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75 views

How to optimize the geometry of beta PHB in VASP?

I would like to calculate the elastic constants of beta PHB. From this paper. I know that it has P3221 space group. The beta PHB has upward and downward chains, which exist at one lattice site with 50%...
9
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1answer
86 views

Problems with finding the unit cell from a CIF file and extracting XYZ coordinates using a software

I got hold of a CIF file for a material that I am interested in. I am trying to isolate the xyz coordinates of the molecules. However, when I open the CIF file in VESTA, I get a near-infinite periodic ...
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1answer
84 views

Extracting molecular strucutre 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 ...
11
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4answers
2k views

How to make a python code that can read a .xyz file and find the distance between atoms?

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: ...
7
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1answer
58 views

How to discard molecules at the boundary in the Atomic Simulation Environment (ASE)?

When building a supercell for a molecular crystal with the Atomic Simulation Environment, it seems that the program takes into account periodic boundary conditions when replicating the unit cell. How ...
13
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1answer
150 views

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 ...
13
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1answer
451 views

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.
5
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1answer
109 views

How do I extract the wave function from a VASP calculation?

We can obtain a energy band structure of a crystal from a DFT calculation in Vasp. Each point in each band represents an energy eigenvalue with a corresponding wave function from the Schrödinger ...
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1answer
182 views

How to import a .cif file into Avogadro 2?

I downloaded the latest version of Avogadro2 (1.91.0), but it appears I can't open a .cif file in this software. Is there a way around this? In an earlier version of Avogadro, I remember being able to ...
12
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1answer
99 views

How to cut properly a slab from a cif file?

I am trying to do DFT calculations on ethanol adsorbed on Pd, both surfaces 111 and 100. I have the cif file from the database and also I have built the new unit ...
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2answers
261 views

How to sort a supercell for a molecular crystal?

I am trying to build a supercell of the following (below) molecular crystal from its .cif file. How do I sort a supercell here according to each molecule in the supercell? I'm not tethered to a ...
5
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1answer
139 views

ASE: why do I get warnings about "monoclinic" and "orthorhombic" not being interpreted?

I am trying to use ASE (Atomic Simulation Environment) to build a supercell of some molecular crystals and then output the result to a file with the atoms given in a specified order for each molecule, ...
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0answers
34 views

Atomic Packing Fraction [closed]

I need to calculate excess entropy of mixing for a particular system of alloy. The excess entropy of mixing is dependent on temperature and it takes into account this temperature dependence by using ...
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0answers
31 views

What's the difference between dynamic and static strain aging?

I do understand how static strain aging occurs and why the yield point comes back if ample time is allotted after a loading and unloading cycles primarily due to diffusion of substitutional and ...
5
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1answer
59 views

Order of diffraction pattern confusion in XRD experiment

Somewhere I came across this phrase: "expected diffraction angle for first order reflection." With respect to XRD do I take this as a rule of thumb that the diffraction will always be a ...
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3answers
128 views

Rotation of crystal structure to match another structure of the same compound/polymorph

Say, I have two crystal structures of a particular organic molecule, the crystal structures are basically identical, apart from a rotation and redefinition of the lattice vectors/angles, a simple ...
5
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1answer
104 views

Why does twinning take place in high rate of shock loading and low temperature?

To quote from a good textbook, which I don't remember: "Twins which are produced by mechanical deformation are called mechanical twins. Mechanical twins are produced in bcc or hcp metals under ...
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1answer
143 views

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 detial, I cut the slab with atomic ...
10
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1answer
173 views

Nematicity in superconductors

It seems to me that the definition of "nematic phase" is quite chamaleonic. Quoting from its first definition [Nature 393, 550 (1998)] for a 2-dimensional square lattice "The nematic ...
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0answers
123 views

Can we calculate bond enthalpies for each bond in a supercell of a disordered AB crystal using DFT?

Apart from using Bader charge analysis or energy of formation estimation, I wonder if there is a way to compute the bond energy of constituent bonds in a crystal using density functional theory. Let's ...
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0answers
120 views

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 ...
10
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1answer
95 views

How do I reconstruct the surface with known Miller indices?

I'm trying to reconstruct the surface $(1\bar{1}01)$ in an hexagonal material and the reconstruction is described by the matrix $\begin{pmatrix} \hspace{3mm}3 \hspace{2mm}1 \\-1 \hspace{2mm}2 \end{...
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0answers
61 views

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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1answer
91 views

How can I find the area of an overlayer structure?

What sources would you recommend (or if you could instead explain it to me that would be great). I have never studied crystallography but must do a module on it and in some of the questions we were ...
18
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4answers
1k views

How to explain Miller indices to someone outside nanomaterials?

I often find that when talking to experimentalists outside of the field of nanomaterials, it is nearly impossible to explain Miller indices concisely. As this often comes up during talks from other ...
12
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1answer
113 views

What does it mean to assign group operations to distinct sets for space groups?

I am trying to understand space groups in crystallography. In International tables for crystallography, for a nonsymmorphic space group, they list some symmetry operations. 8 of them are listed under ...
12
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1answer
166 views

Finite temperature crystal structure prediction

Crystal structure prediction codes like USPEX, use DFT calculated values of energy ($0$ K) to study the phase space (or potential energy surface or internal energy surface, I'm confused which is it). ...
12
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1answer
323 views

Suggestions for a good crystal structure visualization workflow

Following up on this question about freely available crystal structure visualization codes, I wish to know what procedures people follow from start to finish in preparing images of their materials for ...
9
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0answers
74 views

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 ...