Questions tagged [crystallography]
Questions concerning crystallography, the science of determining the arrangement of atoms in crystalline solids.
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Is there a database where we can find previously determined geometries of materials?
For small molecules, NIST has a database of experimentally determined geometries here, and ab initio geometries here. I wonder if there is something similar for materials?
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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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Can a highly-cited published paper have this type of error?
Related cross-network post: Have there been instances in physics where different scientists have interpreted the same data differently?
Here is my problem: I have been testing a force field published ...
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Available methods and codes for materials discovery / crystal structure prediction?
There are many open databases and projects that allow you to access computed crystal structures of experimentally known compounds, registered in the Inorganic Crystal Structure Database (ICSD). These ...
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How to map molecular vibrations into lattice phonons?
Let's assume I have already relaxed a molecular structure for a non-trivial molecule and obtained a geometry that is close to the one resulting from X-ray crystallography. This can be achieved in a ...
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Enforce a space group on a given crystal structure
If I have a CIF that is P1, is there a (preferably free) code that can map the structure to some user-specified space group? I know that there are ways to do similar things with molecular systems. For ...
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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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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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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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What are the differences between crystal structure file formats like CIF, XYZ, PDB etc.?
We come across many file formats like CIF, XYZ, PDB, INS, cc1, p1, POSCAR, FDF, struct etc. Why do we have so many file formats to store crystal structure information? Are they redundant? Can someone ...
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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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How can I create a .CIF file from x-ray diffraction data in a paper, for compound not found in crystallographic database
I tried to recover a .CIF file (Crystallographic Information File) with the crystal structure for the compound discussed in a paper by Reuter et. al.[1], strontium hydroxide octahydrate - $\ce{Sr(OH)2·...
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Extract coordination sphere from crystal structure
Some tools allow for a relatively inexpensive analysis of crystal field effects in metal complexes, starting from the coordination sphere. Additionally, there are multiple sources of crystal ...
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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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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.
user2026
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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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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?". ...
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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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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 ...
user2026
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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 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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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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Looking for crystal generator library
I am looking for a C or a C++ library that can do crystal generation, that is, multiply unit cells in one or more directions with symmetry information. (in other words, generate supercells).
I have ...
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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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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 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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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 ...
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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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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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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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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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How relevant are the displacement parameters in a crystal structure for materials modelling?
If I construct a crystal structure using lattice parameters and atomic coordinates as mentioned in a previous post, what difference does it make if I omit (or enter wrong parameters) for the ...
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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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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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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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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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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 ...
user2026
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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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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 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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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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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 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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