Questions tagged [crystallography]

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

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10
votes
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{...
10
votes
1answer
185 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 ...
9
votes
1answer
88 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 ...
9
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2answers
417 views

Creating a heterostructure in VESTA

I have two different crystal structure and I want to create a heterostructure but the problem is that the shape of their unit cell is different. I know how to combine them if their unit cell are same. ...
9
votes
1answer
250 views

Get fractional coordinates from special Wyckoff positions

I'm trying to get the fractional coordinates for Mo and S, for MoS$_2$-2H, where 2H means the phase. MoS$_2$-2H is a bilayer, in which each layer is separated from each other by Van der Waals forces. ...
9
votes
1answer
53 views

Does the Mermin-Wagner theorem influence the stability of graphene?

Prior to the discovery of graphene, the Mermin-Wagner theorem was used to argue that purely two-dimensional materials would not be stable as two-dimensional order would show logarithmic divergences at ...
9
votes
1answer
94 views

Partial density of states in random solid solutions

This question comes as a follow-up to https://mattermodeling.stackexchange.com/a/2214/116; nonetheless, it is relevant on its own as well. To designate a particular crystal structure to a random ...
9
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0answers
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 ...
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 ...
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 ...
9
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0answers
236 views

"The executable package.exe aborted with system error code 1073740940" in ABAQUS with the following VUMAT for crystal plasticity [closed]

I am new to crystal plasticity simulations and have been studying the concepts from "Introduction to Crystal Plasticity" in Mechanics of Microstructured Materials book. Additionally, I have ...
8
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1answer
164 views

How to calculate the orthogonal representation of a HCP cell?

I'm trying to write a program to calculate the neighbor lists of crystal systems. I found a few codes that are able to calculate it for orthogonal systems. How can I do it for non-orthogonal cells ? ...
8
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0answers
64 views

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, ...
8
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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 ...
8
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0answers
46 views

Symmetry of glide planes [closed]

I am trying to understand the symmetry elements of space group number 194 (P$6_3$/mmc), which is hexagonal and has 24 symmetry operations. In the table of symmetry operations it says that it has three ...
7
votes
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 ...
7
votes
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 ...
6
votes
2answers
74 views

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?
6
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0answers
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%...
6
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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 ...
6
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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 ...
6
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0answers
113 views

How to convert lab frame quaternions and plane normal to misorientation quaternion and crystal plane normal for grain boundaries?

Background Let qA and qB represent unit, orientation quaternions of grain A and grain B of a grain boundary in the lab reference ...
5
votes
1answer
140 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, ...
5
votes
1answer
111 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 ...
5
votes
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 ...
5
votes
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 ...
5
votes
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 ...
5
votes
1answer
50 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 ...
5
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0answers
125 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 ...
5
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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 ...
3
votes
1answer
29 views

wurtzite unit cell of ZnO

am looking to draw wurtzite unit cell of ZnO, and i find two of them and the second one how can I draw the first one in software like vesta?
2
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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 ...
0
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0answers
3 views

DOS projection in alternate axis for eg and t2g contributions

I am studying doping in 0D and 2D perovskites which present tilted octahedra. It is important for me to analyze the contributions in PDOS in terms of eg and t2g levels for d orbital in the transition ...

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