Questions tagged [crystallography]

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

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4
votes
0answers
29 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
142 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
393 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
61 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 ...
10
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1answer
89 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
72 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 ...
11
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2answers
219 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
votes
1answer
103 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, ...
4
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0answers
20 views

Doubt in how dynamic strain aging and static strain aging are different from each other in its effect and phenomenon

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
49 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 ...
11
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3answers
119 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
votes
1answer
103 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 ...
10
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1answer
163 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 ...
7
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0answers
110 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 ...
11
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0answers
95 views

How do I know if the reconstruction in the picture is a 2 x 2 reconstruction?

How do I know if the reconstruction in the picture is a 2 x 2 reconstruction or not?                                     I believe that this corresponds to a 2x2 reconstruction because there's an even ...
10
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1answer
85 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{...
6
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0answers
55 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 ...
5
votes
1answer
90 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 ...
8
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0answers
58 views

Have Finite Difference Time Domain 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 ...
5
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0answers
82 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 frame, respectively. Let qm be the misorientation quaternion of qA and ...
11
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1answer
108 views

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 Grain Boundary Engineering & ...
8
votes
1answer
136 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 ? ...
11
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1answer
82 views

CuO (monoclinic) crystallographic plane and their relaxed surface energy

I want to calculate wulff construction for CuO of space group C2/c. Can any one help me with its crystallographic plane/Miller indices and their corresponding relaxed surface energy? If you can ...
9
votes
1answer
214 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. ...
8
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0answers
44 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 ...
9
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1answer
46 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 ...
18
votes
1answer
997 views

Is the number of possible Bravais lattices a mathematical fact?

Almost anyone that has taken a Solid State Physics course will know, that any 3D crystal must be in one of the 14 Bravais lattices due to symmetry operations and space filling. In 2015, a paper was ...
12
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1answer
766 views

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 ...
12
votes
1answer
92 views

Overview of how self-consistent dynamical low-energy electron diffraction simulations are performed

A technique for deducing arrangements of atoms on crystal surfaces is Low Energy Electron Diffraction or LEED. For a flat crystal surface aligned to a low-order plane with perhaps a 2D periodic ...
16
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1answer
43 views

Does the thermal evolution of molecular structures critically affect the validity of the calculated magnetic anisotropy?

This is a particular aspect I'm interested in, from the more generic question "Does the thermal evolution of chemical structures critically affect the validity of the calculated physical properties?". ...