Questions tagged [crystallography]

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

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Continuous Coordination Number Definition

I am interesting 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 ...
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6 votes
1 answer
111 views

How to transform the k coordinate into the k path used in the band structure?

When drawing the band structure, I need to transform the coordinate of k-points into a k-path, but I am not sure what the formula is. I checked the result of siesta,...
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Any software for creating the atom configuration used in the siesta input file?

Is there any software that could generate the atom configurations used in the .fdf files? I am currently using wxDragon to convert the .cif file, but it would automatically reduce the atom number by ...
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3 votes
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Gold schmidt parameter calculation for perovskite materials

Gold schmidt parameter was created in order to see if a perovskite crystal structure would have crystal distortion in feasible range or not. This parameter has been extended to various other forms of ...
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4 votes
2 answers
535 views

Which formalism is better suited to model a crystal with defects: Hartree–Fock, Kohn–Sham, or something else?

Let’s suppose that (1) it’s required to calculate a crystal with certain parameters of a crystal lattice; (2) this crystal has some defects (let it be Frenkel defects for simplicity); (3) these ...
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How to create the vector image of crystal structure?

I am trying to create a vector image of TiO2 crystal because all journals require vector images. When I build the model for calculation, I use ...
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2 votes
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How to rotate layer of heterostructure and save it to fractional coordinate using VESTA?

I'm building multilayer structure. I build the heterostructure importing the the to phase of structure in VESTA File -> New structure -> Phase -> Import ...
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6 votes
1 answer
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Which atoms should be fixed when simulating metal oxides surface relaxation?

I am trying to model the surface relaxation on the TiO2(Anatase-101) surface, but it confuses me that when I try to set some atoms as fixed, unlike the crystal that only contains one element, there is ...
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10 votes
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How to extract the crystal symmetry from VASPs POSCAR/CONTCAR file?

VASPs POSCAR/CONTCAR file does not contain any direct information about the cell symmetry. If I run for example a calculation on simple TiN in space group 225, this symmetry is (should be) preserved. ...
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8 votes
2 answers
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Could we predict all possible forms of carbon Allotropes?

Suppose that I wanna make a program to predict possible forms of carbon's Allotropy. My idea is to use a structure search program to generate a lot of structures and calculate the Gibbs free energy to ...
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6 votes
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How to calculate the surface area of a stepped surface slab in a unit cell?

I am trying to calculate the surface energies of Ni fcc (111) and (311) surfaces, therefore I need to calculate the surface areas. I use periodic slabs to model these surfaces. For a flat fcc (111) ...
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3 votes
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1T phase MoS2 CIF File

The peak shift for XRD of the 1T and 2H phases of $\ce{MoS2}$ differs by a few degrees (just below 10 degrees for 1T, 14 degrees for 2H). In Rietveld Refinement, a standard CIF file can be used for ...
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6 votes
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Any Open-Source, Free Software That Can Be Used to Computationally Calculate Binding Affinity Between Two Molecules?

There are programs out there which calculate the binding affinity between a ligand and a target protein (Autodock 4, Autodock Vina, Chimera... etc). Is there any analogous program that can be used to ...
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10 votes
1 answer
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Recommendation of open source software that could build Heterostructure models visually?

I am looking for open-source software that could help me to build Heterostructure models visually, I've been working with BIOVIA Materials Studio before, but I got no valid license now, so I'd like to ...
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7 votes
1 answer
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XANES simulation software/code besides FEFF for Pt L3 edge?

I need to generate the XANES region spectra of the Pt L3 edge of a theoretical Pt6 crystal with adsorbed atoms/molecules, such as $\ce{Pt(H^*), Pt(O^*), Pt(OH^*),Pt(CO^*)}$. It is for generating ...
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6 votes
1 answer
60 views

How to determine the right k-points for the band structure of a slab?

I am trying to compare the band structure of a slab and the bulk phase, just like the example on the VASP wiki. In the example of VASP, it calculates the band structure of the slab of Ni metal. A slab ...
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6 votes
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Compute bulk electrical conducitivity from single-crystal measurements [closed]

If I have single-crystal measurements of electrical conductivity along 3D axes (considering for example anisotropic materials), is there any straightforward way to compute the bulk (global) electrical ...
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6 votes
1 answer
262 views

How to transform lattice in VESTA

Can anyone please help me transform $\ce{LiCoO2}$ hexagonal cell ($a \times a \times c$) to orthorhombic cell ($a \times a \sqrt{3} \times 1$) and hexagonal cell ($a \sqrt{3} \times a \sqrt{3}\times 1$...
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9 votes
1 answer
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Is it possible to do a collinear spin-orbit calculation in Quantum ESPRESSO?

In the presence of a 2D crystal and spin-orbit coupling, the SU(2) spin axial vector (Sx,Sy,Sz) decouples into an in-plane (Sx,Sy) and out-of-plane part Sz. For Quantum ESPRESSO, is there a way to ...
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8 votes
1 answer
160 views

How to choose a proper rotation matrix and apply it to rotate unit cell about Cartesian axis

In this paper, they have rotated the unit cell using a rotation matrix, so the axes are aligned with the atomic bonds. I would like to know how they calculated that rotation matrix, and which software ...
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2 votes
0 answers
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Visualizing Crystal Structures [duplicate]

I would like to know if there are any free alternatives to VESTA for visualizing crystal structures. Thanks
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9 votes
1 answer
356 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... ...
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10 votes
0 answers
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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 ...
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14 votes
1 answer
138 views

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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29 votes
2 answers
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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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5 votes
1 answer
56 views

Variable Cell Optimization of Halfnium Crystal

Reference: Density Functional Theory: A Practical Introduction, David Sholl, Janice A. Steckel, Chapter 2, Page No. 46 Hf is experimentally observed to be an hcp metal with c/a 1.58. Perform ...
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8 votes
3 answers
200 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 ...
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6 votes
0 answers
80 views

How to create a CIF using VESTA? [closed]

I am looking into double perovskite materials. One of the possible materials is $\ce{Cs4CuSb2Cl12}$. Now, although there are a few papers which have done ab intio calculations but none of the common ...
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5 votes
0 answers
34 views

DOS projection in alternate axis for eg and t2g contributions

I am studying doping in 0D and 2D perovskites which present tilted octahedra. It is important for me to analyze the contributions in the PDOS in terms of $e_g$ and $t_{2g}$ levels for d orbital in the ...
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4 votes
1 answer
41 views

wurtzite unit cell of ZnO

am looking to draw wurtzite unit cell of ZnO, and i find two of them and the second one how can I draw the first one in software like vesta?
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5 votes
1 answer
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1T and 1H CIF file for MoS2

On the COD website, only 2-layer hexagonal (2H) and 3-layer orthorhombic (3R) $\ce{MoS2}$ are available. I can't find the 1-layer tetragonal (1T) and 1H CIF for $\ce{MoS2}$. Where can I find them, or ...
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6 votes
2 answers
122 views

How can I make a CIF file for Monoclinic MoO2?

A CIF file of Monoclinic $\ce{MoO2}$ is not available in the Crystallography Open Database website. How can I make it myself or find it elsewhere?
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8 votes
0 answers
76 views

Crystallography: How to sample *unique* structures from configuration space? (binary alloy supercell) [closed]

I'm working with a binary alloy system (call it 'AB'), and I'd like to generate a few unique configurations for DFT purposes. My primitive cubic unit cell consists of 4 atoms; i.e. 4 positions. Thus, ...
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10 votes
0 answers
62 views

How to generate a complete set of doped (substituted) structures? [duplicate]

I'm trying to analyse doping in a certain material in low concentrations. I'm approaching the problem by taking crystallographic unit cell of that material, then expanding that to a 2x2x2 supercell ...
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6 votes
0 answers
171 views

Straightforward formalism to get four sets of 2D hexagonal lattice vectors of fcc(111) planes that I can also cite?

I am simulating low energy electron diffraction (LEED) from a polyfaceted sample. Usually it's a single, well-defined flat crystalline surface. Since low energy electrons (below a few hundred eV) only ...
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11 votes
2 answers
159 views

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 votes
0 answers
61 views

Is there a script that will suggest (hkl) indices based on distances in an electron diffraction pattern for a known crystal structure? [closed]

I am looking for a script (preferably in Python) that will suggest (hkl) indices based on distances in an electron diffraction pattern. The crystal structure is known,i.e. I have the CIF file and know ...
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6 votes
0 answers
92 views

How to optimize the geometry of beta PHB in VASP? [closed]

I would like to calculate the elastic constants of beta PHB. From this paper. I know that it has P3221 space group. The beta PHB has upward and downward chains, which exist at one lattice site with 50%...
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9 votes
1 answer
140 views

Problems with finding the unit cell from a CIF file and extracting XYZ coordinates using a software

I got hold of a CIF file for a material that I am interested in. I am trying to isolate the xyz coordinates of the molecules. However, when I open the CIF file in VESTA, I get a near-infinite periodic ...
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13 votes
1 answer
234 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 ...
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17 votes
6 answers
3k views

How to make a python code that can read a .xyz file and find the 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: ...
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7 votes
1 answer
131 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 ...
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  • 1,309
14 votes
1 answer
230 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 ...
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  • 1,309
14 votes
1 answer
797 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.
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5 votes
1 answer
297 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 ...
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  • 375
10 votes
1 answer
535 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 ...
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