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Questions tagged [crystallography]

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

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35 votes
20 answers
13k views

What are the freely available crystal-structure visualization softwares?

I use VESTA mostly for crystal structure visualizations. What other options are available?
Thomas's user avatar
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57 votes
7 answers
2k 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?
Nike Dattani - No Free Time's user avatar
19 votes
2 answers
2k 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·...
ksousa's user avatar
  • 4,108
12 votes
1 answer
189 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 ...
uhoh's user avatar
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14 votes
1 answer
609 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 ...
Hitanshu Sachania's user avatar
11 votes
0 answers
129 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 ...
uhoh's user avatar
  • 2,034
3 votes
1 answer
105 views

How to model an interface between two solids

I have two solid surfaces that I want to combine to study the interface as seen in the attached image. What I know is the lower part of the bottom structure is fixed to mimic the bulk. However, do I ...
Nana Kofi Boakye's user avatar
31 votes
2 answers
4k views

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 ...
Barbaud Julien's user avatar
27 votes
4 answers
702 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 ...
epalos's user avatar
  • 4,869
20 votes
2 answers
719 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 ...
livars98's user avatar
  • 2,496
20 votes
7 answers
6k views

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: ...
Jose Pinto's user avatar
17 votes
2 answers
368 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 ...
Anibal Bezerra's user avatar
15 votes
2 answers
2k 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.
user avatar
14 votes
7 answers
4k 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 ...
Felix's user avatar
  • 1,431
13 votes
1 answer
698 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 ...
Jonny_92's user avatar
  • 133
13 votes
1 answer
133 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 ...
Thomas's user avatar
  • 9,132
13 votes
1 answer
2k views

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 ...
Collodial_machine 's user avatar
12 votes
2 answers
515 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 ...
user avatar
11 votes
1 answer
193 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 ...
Shafayet Rahat's user avatar
11 votes
2 answers
317 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 ...
Thomas's user avatar
  • 9,132
10 votes
1 answer
522 views

Proposing a 2D quasicrystal; what are the necessary and sufficient conditions? (If it looks like a duck and quacks like a duck, or...?)

Quasicrystals show repeating motifs or patterns but are not periodic. And yet their Fourier transforms invariably demonstrate a pattern of sharp peaks revealing that there is still an underlying... ...
uhoh's user avatar
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10 votes
0 answers
110 views

How to implement a toy DFT [duplicate]

I want to learn DFT for research purposes and I need to implement a toy DFT for pedagogical reasons. I would like some recommendations regarding resources like books, articles, or any other thing that ...
sinecosine's user avatar
9 votes
1 answer
140 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 ...
Hitanshu Sachania's user avatar
8 votes
3 answers
877 views

Cu FCC vc-relax method error

Reference: Density Functional Theory: A Practical Introduction, David Sholl, Janice A. Steckel, Chapter 2, Page No. 48 Section 2.2 The fcc Cu calculations in Fig. 2.3 used a cubic supercell with 4 Cu ...
147875's user avatar
  • 663
6 votes
2 answers
154 views

Continuous Coordination Number Definition

I am interested in quantifying the coordination number of some atoms in metals and am curious what approaches to defining a coordination number are possible for an atom. In particular, I am curious ...
Tristan Maxson's user avatar
4 votes
1 answer
78 views

Program to classify structures of different composition?

Is there a program to classify and compare structures with different composition? I want to compare e.g. structure_1 with composition [2,1,4] and structure_2 with composition [16,8,32]. Maybe both ...
leire's user avatar
  • 183