Questions tagged [crystallography]
Questions concerning crystallography, the science of determining the arrangement of atoms in crystalline solids.
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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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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 ...
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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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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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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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Can we calculate bond enthalpies for each bond in a supercell of a disordered AB crystal using DFT? [closed]
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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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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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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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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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 ...
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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 ...
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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 ...
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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). ...
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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 ...
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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 ...
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Si energy band values are not matching with literature values
I have performed the DFT calculation for Silicon in Quantum ESPRESO. I have tried to calculate the electronic band structure, the shape of wiggles of bands are mostly matching but the energy values ...
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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 ...
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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. ...
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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 ...
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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 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 ?
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What is Surface termination and how to make surface termination of a crystal structure?
I want to calculate the surface energy of CuO and for that, I've asked CuO (monoclinic) crystallographic plane and their relaxed surface energy. But for the lack of knowledge of the surface ...
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"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 ...
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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 ...
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How to automatically plot atomic structures with magnetic moments?
I work with magnetic materials and I haven't found a way to automatically plot structures with their corresponding magnetic moments. For this specific project I am using VASP. I am trying to plot ...
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Get fractional coordinates from special Wyckoff positions
I'm trying to get the fractional coordinates for $\ce{Mo}$ and $\ce{MoS_2-2H}$ in $\ce{MoS_2-2H}$, where 2H is the phase. $\ce{MoS_2-2H}$ is a bilayer, in which each layer is separated from each other ...
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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 ...
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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 ...
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How do I extract a molecular structure from a CIF file?
When I open a CIF file of a crystal structure in a typical molecular editor like Avogadro, then I just see a few symmetry-unique atoms scattered around the unit cell. But I don't see the full molecule ...
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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 ...
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Meaning of atomic positional parameters
I am trying to model some materials with DFT, so I intended to start out with the structure. However, some texts that present XRD data, use a term called atomic positional parameter. I can't seem to ...
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How does the atomic arrangement look like in a compound that has partial/mixed site occupancies
I am working on modelling of a material that has partial/mixed site occupancies. For example consider the tetragonal (P4mm) compound $\ce{(Ba_{0.67}Sr_{0.33})TiO3}$. Following is the atomic ...
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9 x 9 x 9 periodic xyz file to cif file format
I have a 9 x 9 x 9 periodic crystal structure in .xyz format and I would like to change it to .cif file format.
Does anyone know how to convert the file?
(e.g. 9 x 9 x 9 to unit cell then cif)
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How to analyze the space group of a relaxed structure that has fractional site occupancies
I am using VASP package to model a material that has fractional site occupancies. An appropriate supercell (cif) was generated using supercell package and converted ...
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Is the original structure invalid if it's found later that the material crystallises with a slightly different space group symmetry?
I am studying a material which was first discovered in the early 1960s. It was reported then that it crystallized in the hexagonal $P6_3/mmc$ space group. Recently the material was synthesized again ...
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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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Is there a performance difference when using fractional coordinates instead of Cartesian coordinates?
In general, the CIF file with the crystal structure uses fractional coordinates for setting the atoms positions. In this type of coordinates, the atom positions are relative to the cell parameters.
...
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What are good resources to study crystallographic defects in different dimensional systems and their topological dimensionality?
I wonder if there are any books or resources that may address one or more of the following questions:
What kinds of defects are important for topology? Especially crystallographic defects.
How do ...
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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 ...
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Is it necessary to optimize structures obtained from a cif file?
Crystallographic Information Files (CIF) are, in general, obtained from experimental measurements. Since the information originated from real samples, is it mandatory to relax the structure in order ...
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