Questions tagged [crystallography]

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

Filter by
Sorted by
Tagged with
1 vote
0 answers
10 views

A Question about ISIF Tag in VASP

I apologize for asking this stupid question, but I am a bit confused with the ISIF tag. Doesn't a cell's shape and cell's volume depend on the atoms' positions? If so, why can the cell's volume/shape ...
5 votes
1 answer
534 views

Why does my zincblende structure not look cubic?

The structure of my material is zincblende. So normally the structure is cubic. However, when I open the primitive cell with xcrysden it dosen't look 100% cubic. It's a little bit inclined. Also when ...
  • 875
3 votes
0 answers
84 views

Layer detection in a crystal structure

Context I have two images from a Monte Carlo Basin Hopping where silicon (in yellow) is getting replaced by germanium (in blue). Both have 32 germanium atoms at Si/Ge = 2.5; only the Ge distribution ...
  • 783
7 votes
2 answers
162 views

Generate structure using atomic coordinates

I am trying to write a Python/C++ code that reads in a *.xyz file and varies the interatomic distances, angles etc. between distinct atoms in a molecule. In other words, a complete new structure with ...
  • 73
5 votes
0 answers
69 views

Which crystal structure I have to choose for DFT calculations?

I want to study the properties of NiO as a hole transporting material adapted for perovskite solar cells using Quantum ESPRESSO. From Materials Project website, I saw that NiO can exist in different ...
  • 875
2 votes
1 answer
37 views

How is it possible for amorphous metal to have good magnetic properties with randomly arranged atoms?

Cross-posted on Physics.SE. It makes sense that something like grain-oriented electrical steel would have good magnetic properties (e.g., magnetic permeability). I'm envisioning magnetic field lines ...
1 vote
0 answers
37 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 ...
  • 153
1 vote
0 answers
25 views

Can CrystalFp library be used to compare structures with different number of atoms? [duplicate]

Can I use CrystalFp library to analyze different structures (e.g. of Ca2Si04) that don't have the same number of atoms? I want to compare e.g. structure_1 with composition [2,1,4] and structure_2 with ...
  • 153
2 votes
0 answers
17 views

Difference and meaning of isopointal and isoconfigurational structures

These are the meanings I`ve found, but I do not completely understand them. Isopointal: Two structures that have the same space-group type or belong to a pair of enantiomorphic space groups. And that ...
  • 153
5 votes
0 answers
44 views

Is there a free software to build a crystal shape that is cut with a specific angle plane (like 40 degrees), which is not implemented in Vesta?

I would like to cut $\ce{SrTiO3}$ with a specific angle of 40 degrees, or to choose an angle plane which is not implemented in the Vesta software. Could you please recommend a free software to build ...
  • 51
2 votes
1 answer
55 views

How do I know which is the asymmetric unit of a unit cell?

I need the number of independent atoms in the asymmetric unit I have to introduce them in this form: ...
  • 153
4 votes
1 answer
103 views

Maximum bond length in Vesta

I need some cutoff radii to count bonds between different atoms in my system. When a .cif file is opened in Vesta, there are some default values of min and max bond lengths between two atomic species. ...
  • 91
3 votes
1 answer
129 views

How do the notions of Crystal structure, unit cell and supercell fit together?

I'm trying to fully understand the notion of crystal structures with some basic implications. I understand that it is conveniently described by a lattice which is the infinite repetition of points in ...
4 votes
1 answer
147 views

Measuring distance with ASE

I wish to calculate the distance of all the atoms from a particular atom(atom A) in my cell. But I also want to include the atoms that might lie just beyond the periodic unit cell boundary.( In figure,...
  • 91
3 votes
0 answers
24 views

Tilting Octahedra of Perovskite structures in structure file

Perovskite materials form as a combination of $\ce{BX_6}$ octahdera along with A cation. Some perovskites display tilted octahedras. I am currently trying to run calculations for different tilted ...
  • 629
4 votes
0 answers
45 views

How to make idealized infinite alpha helix or beta sheet?

I'm interested in studying some simple periodic model systems representing proteins. For that I'd like to make pdb files of an alpha helix or beta sheet with idealized coordinates which is infinitely ...
  • 677
2 votes
0 answers
23 views

How to create doped possible structures for the calculation in VASP [duplicate]

I want to find the doped structure of a compound. So i need to know how we can find the possible structures after substitution or interstitial doping? for example i want the possible structures for 6:...
3 votes
0 answers
85 views

How to transform the conventional cell to primitive cell?

I am following this tutorial to transform a conventional cell to a primitive cell, but I am not sure how to determine the primitive copy of some atom in the conventional cell. For example, in the ...
  • 1,915
3 votes
0 answers
28 views

How to visualize the basis in the unit cell of crystals?

Usually, the unit-cell of a crystal is made up of lattice points and basis, but all the crystallography software like VESTA doesn't show the basis, is there any ...
  • 1,915
2 votes
0 answers
112 views

Confusion in primitive, conventional and supercell crystal structure

I am doing the DFT calculations in Quantum ESPRESSO code. I have 2 different pwscf input file of the same crystal. I am confused which one is representing primitive, conventional and supercell ...
  • 2,481
5 votes
2 answers
284 views

How does one make sure that the [hkl] direction in ab-inito calculations is the same as in experimental calculations?

I am currently looking at isotropic properties and let's say I want to determine my property in the [100] direction. Now, I basically want that my [100] direction be the same as the [100] direction in ...
  • 629
5 votes
0 answers
62 views

How to find the most stable facet for a crystal?

I am trying to find the most stable facet for a crystal, but since there are many possible choices, like (1 0 0),(1 1 0),(1 1 1),(2 1 0), etc. My questions is: I am wondering how should I determine ...
  • 1,915
4 votes
0 answers
59 views

Basic principles (and vocabulary) necessary to begin modeling the rate of atom surface diffusion and thermal planarization of ground metal surfaces?

Background: Surface science experiments very often start with atomically smooth crystal surfaces as substrates. After one experiment ends the surface is sputter cleaned with cycles of keV energy argon ...
  • 2,004
7 votes
1 answer
187 views

How does one decide the directions in which they will calculate effective mass?

I have been working on trying to calculate the effective mass in different directions by fitting a parabola to the VBM and CBM and using the fitted parameters to calculate $\frac{d^2E}{dk^2}$. And ...
  • 629
1 vote
1 answer
58 views

Is there a robust and reliable software to change the lattice vectors of unit cells?

I am working with Heusler and Half Heusler materials on LAMMPS. Currently the study follows the properties in individual lattice directions such as [100] [110] etc. As of now, I am obtaining the unit ...
  • 2,583
3 votes
1 answer
157 views

How to determine the concrete value for the wavenumber in tight-binding approximation

As a simple problem setting, consider a one-dimensional linear crystal of NaCl with only 1s orbitals, where the atomic distance between Na and Cl is also assumed to be 0.5 Å for simplicity (Fig. 1). ...
  • 1,709
3 votes
0 answers
231 views

How to fix outliers in Ramachandran plot using Coot [closed]

I have the following Ramachandran plot generated by Coot: Notice that it has high outliers content (red dots). I want to manually drag those red dots into some part of the region. Eventually, I ...
  • 1,644
4 votes
0 answers
33 views

Repository of Common Surfaces

Are there any repositories of crystal surfaces? Due to orientation / termination of surfaces, occasionally it is non-trivial to decide how exactly to cut a surface for things such as oxides. I ...
9 votes
1 answer
197 views

Stability using Phonon Calculation

While performing phonon calculation using finite difference method, we get normal modes printed in the outcar file. Now there is a distinction between two different types of modes in the outcar file. ...
  • 111
3 votes
1 answer
37 views

Spacing issues about multiple-layer bcc structure

I am trying to make Hartree potential of bcc Tungsten(001). My software is VASP. 5-layer should have 5 bound states. But I don't have them I heard it is a layer-layer spacing issue. I built slab of ...
2 votes
0 answers
59 views

Slab rotation with ASE, unexpected behaviour [closed]

I am trying to generate the $\sqrt{3}\times\sqrt{3}R30^\circ$ representation of a Pt111 slab, I start by generating the $1\times1$ using ASE: ...
  • 1,098
2 votes
0 answers
52 views

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 ...
6 votes
1 answer
291 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,...
  • 1,915
2 votes
1 answer
80 views

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 ...
  • 1,915
3 votes
0 answers
44 views

Gold schmidt parameter calculation for perovskite materials [closed]

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 ...
4 votes
2 answers
568 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 ...
  • 601
5 votes
1 answer
178 views

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 ...
  • 1,915
2 votes
0 answers
141 views

How to rotate layer of heterostructure and save it to fractional coordinate using VESTA? [closed]

I'm building multilayer structure. I build the heterostructure importing the the to phase of structure in VESTA File -> New structure -> Phase -> Import ...
  • 121
7 votes
1 answer
146 views

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 ...
  • 1,915
8 votes
1 answer
75 views

What software should I use for an MD study of a temperature-dependent crystallographic phase transition?

I want to study the crystallographic phase transitions of crystals with increasing temperature. Which freely available MD package should I choose, which has easily available tutorials/example-input-...
  • 181
10 votes
1 answer
242 views

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. ...
  • 403
8 votes
2 answers
758 views

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 ...
  • 1,915
6 votes
0 answers
203 views

How to calculate the surface area of a stepped surface slab in a unit cell? [closed]

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) ...
  • 161
3 votes
1 answer
119 views

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 ...
6 votes
0 answers
68 views

Any Open-Source, Free Software That Can Be Used to Computationally Calculate Binding Affinity Between Two Molecules? [closed]

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 ...
  • 211
10 votes
1 answer
287 views

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 ...
  • 1,915
7 votes
1 answer
70 views

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 ...
6 votes
1 answer
154 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 ...
  • 1,915
6 votes
0 answers
48 views

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 ...
7 votes
2 answers
1k 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 ($a \sqrt{3} \times a \sqrt{3}\times 1$...
  • 1,945