Questions tagged [crystal-structure]

For questions about crystal structure.

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7
votes
2answers
662 views

How to make a python code that can read a .xyz file and find 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: ...
10
votes
1answer
90 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
votes
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
votes
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, ...
6
votes
0answers
29 views

Atomic Packing Fraction

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 ...
5
votes
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
votes
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 ...
7
votes
1answer
92 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
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 ...
18
votes
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
votes
1answer
110 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
votes
1answer
146 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
votes
1answer
295 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 ...
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 ...
12
votes
1answer
384 views

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 ...
5
votes
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 ...
9
votes
2answers
279 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
91 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 ...
11
votes
1answer
109 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 ? ...
12
votes
2answers
446 views

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 ...
9
votes
0answers
188 views

“The executable package.exe aborted with system error code 1073740940” in ABAQUS with the following VUMAT for crystal plasticity

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 ...
11
votes
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 ...
10
votes
1answer
142 views

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 ...
9
votes
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 ...
11
votes
6answers
1k views

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 ...
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 ...
20
votes
2answers
496 views

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 ...
12
votes
1answer
217 views

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 ...
13
votes
3answers
513 views

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)
13
votes
4answers
356 views

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 ...
11
votes
2answers
291 views

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 ...
14
votes
2answers
448 views

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. ...
15
votes
1answer
59 views

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 ...
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
votes
2answers
98 views

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 ...
16
votes
1answer
138 views

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 ...
26
votes
11answers
565 views

What are the freely available crystal-structure visualization softwares?

I use VESTA mostly for crystal structure visualizations. What other options are available?
13
votes
1answer
77 views

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 ...
17
votes
2answers
232 views

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·...
22
votes
3answers
160 views

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 ...
22
votes
4answers
268 views

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 ...
17
votes
2answers
136 views

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 ...
26
votes
1answer
166 views

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 ...
52
votes
7answers
724 views

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?