Questions tagged [crystallography]

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

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Non-Equivalent T-Sites from a cif file

I am trying to find symmetrically inequivalent T-atoms in a crystal structure (zeolite). Does anyone happen to know any package that can help with that? I see that pymatgen does have options for ...
Saha_1994's user avatar
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How to make Pd(111) supercell (√3×√3)R30 via VESTA

How to make Pd(111) super-cell (√3×√3)R30 via VESTA or Avogadro software?
Rubi Agrawal's user avatar
4 votes
1 answer
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Can a tool “Set space group” be useful?

In my program Chemcraft, a popular tool is the “Set point group” utility: it symmetrizes the molecule according to a specified point group, and then the symmetry of the molecule is correctly ...
Linkey's user avatar
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Having difficulty creating the β-tellurene structure in VESTA

I've recently started with VESTA and am having some trouble building the β-Tellurene structure (monoclinic, space group nº 12). I know that the lattice vectors are: $$\vec {a} = a\hat x \\ \vec {b} = ...
Gabriel Elyas's user avatar
5 votes
1 answer
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Color of isosurface in charge density visualization

I am trying to visualize the charge density of a crystal through VESTA. However the intersection surface of the isosurface and the boundary turns into blue, which is certainly not included in my ...
蕭力諶's user avatar
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Why am I getting a wrong lattice constant from these SIESTA calculations?

I am currently learning to perform calculations on solids and am attempting to manually optimize the size of a face-centered cubic (FCC) cell of Nickel (Ni) using SIESTA (v. 4.1.5) with the Perdew-...
user1420303's user avatar
3 votes
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Miller indices and periodic boundary conditions

I want to implement building the Miller indeces in my program Chemcaft. Currently I need to understand more the computations with periodic boundary conditions (PBC) needed for crystallographers. The ...
Linkey's user avatar
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VESTA using command line

Can anyone please show me how to make a supercell with VESTA using a single command line without opening a GUI.
hakou elhaj's user avatar
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What is convention of predefined coordination system for defining elastic constant of a specific material

I try to find the elastic constants of LiTaO3 from online databases. I did find a page that lists them https://www.roditi.com/SingleCrystal/Lithium-Tantalate/LiTaO3-Properties.html As I know, the ...
lsdragon's user avatar
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How easy is it to distinguish water from ions in xray crystallography?

I'm interested in bound ions in protein xray crystal structures. Of course a lot of structures include biologically significant ions, such as Mg2+ in the active site of an enzyme. But a lot of ...
Alex I's user avatar
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How can I properly plot this .cube file in Python?

Motivation for Post: I saw a question about how to plot a .cube file recently on the Mathematica & Wolfram Language Stack Exchange. It was marked "off-...
D_C's user avatar
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Energy of formation Vs Formation Energy Vs Heat of Formation Vs Energy Above Hull differences

I work in the field of materials science. While exploring the concepts related to material stability, I have come across terms such as "Energy of Formation," "Formation Energy," &...
hamza's user avatar
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Computing lattice coordinates starting from lengths and angles

I've been reading this interesting paper and I'm trying to understand the following: it is known that a crystal lattice can be represented by 6 parameters corresponding to lattice vectors lengths ($a,...
James Arten's user avatar
1 vote
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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
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How to transform a perturbed surface structure to a reference surface structure?

Say I have a bulk FCC Pt structure obtained from Materials Project with a lattice constant a = 3.94 Å. I first did DFT to relax the bulk structure, and the optimized lattice constant becomes for ...
Shaun Han's user avatar
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How to find the scaling factors for minimum image convention?

Suppose that we have an arbitrary (not necessarily cubic) unit cell with cell parameters $\mathbf{a}$, $\mathbf{b}$, $\mathbf{c}$ (lattice vectors) and $\alpha$, $\beta$, $\gamma$ (lattice angles). We ...
ado sar's user avatar
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Is it possible to find a cubic supercell for a non-cubic crystal structure?

Suppose that we have a crystal material with a non-cubic unit cell. E.g. $\alpha \neq \beta \neq \gamma \neq 90^{\circ}$. Is it possible to find a supercell such that $\alpha = \beta = \gamma = 90^{\...
ado sar's user avatar
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Do the Miller indices <100> and <001> represent different families of directions? [closed]

In Miller indices, <100> is known to represent a family of directions: Source Does the <001> notation represent a different set of directions? I often see <001> in reference to the ...
artist_and_not_EE_by_training's user avatar
3 votes
1 answer
364 views

Why the relaxation of my material in Quantum ESPRESSO wasn't achieved?

I did a vc-relax calculation using HSE by Quantum ESPRESSO and after 22h time WALL the job was complete and JOB DONE was mentionned in the end of the output file ...
Camilla's user avatar
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Is it a good idea to always read charge and orbitals if I am working on similar systems?

For example, if I am investigating of the elastic properties of a crystal by doing a lot of computations of crystals applied with small strain. Also, is it a good idea to read charge and orbitals when ...
蕭力諶's user avatar
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Why I got more atoms than expected when generating POSCAR from VESTA

I tried to generate a perovskite structure with VESTA, and the following are my settings: The generated structure seems to be correct. However, when I tried to export it as POSCAR I got the following:...
蕭力諶's user avatar
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What is the best method to compute crystal structures?

I am rather new to VASP and I have seen people using different methods to compute crystal structure: Using Birch-Murnaghan equation to find optimal lattice volume, and then adjust the structure ...
蕭力諶's user avatar
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2 votes
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How to generate pole figures from limited amounts of area detector X-ray diffraction from thin films (explain it like I'm five years old)

Historically powder X-ray diffraction was the go-to method for reconstructing crystal structure. X-ray sources were limited in intensity and emittance and so to collect data in a reasonable amount of ...
uhoh's user avatar
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What determines if a material tends to undergo transgranular or intergranular fracure? [closed]

As an example, why does glass tend to break by means of intergranular fracture? My analysis so far led me to believe that the tendency can be related to the intermolecular bond strength in a given ...
Len's user avatar
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9 votes
1 answer
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How to stack graphene and hBN on top of each other?

I read in papers (e.g. link) about AA stacking, where C atoms are above the B and N atoms, and AB stacking where one C atom is above the N or B atom, while the other C atom is above the h-BN hexagon. ...
Vladislav Gladkikh's user avatar
7 votes
0 answers
49 views

Database (or table) of functions obeying symmetry properties of space groups

I'm looking for a table or database containing mathematical functions that belong to crystallographic space groups by having the same symmetry elements. Imagine a 2D square planar lattice. It has a 4-...
Mika R.'s user avatar
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5 votes
0 answers
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What is the ibrav value of a rhombohedral structure? [closed]

I have a rhombohedral structure The SYSTEM and CELL_PARAMETERS blocks looks like this: &SYSTEM ibrav = 0 A = 6.058435171 ...
Camilla's user avatar
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3 votes
1 answer
191 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 ...
蕭力諶's user avatar
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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 ...
Camilla's user avatar
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4 votes
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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 ...
Saha_1994's user avatar
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7 votes
2 answers
337 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 ...
DaveS's user avatar
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5 votes
0 answers
111 views

Which crystal structure I have to choose for DFT calculations? [closed]

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 ...
Camilla's user avatar
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2 votes
1 answer
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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 ...
artist_and_not_EE_by_training's user avatar
4 votes
1 answer
69 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
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1 vote
0 answers
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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 ...
leire's user avatar
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4 votes
1 answer
241 views

Should this phenolic hydroxyl be rotatable?

Looking at nelfinavir, I get variable results from different compchem packages on whether the phenol hydroxyl oxygen should be rotatable (SP3) or non-rotatable (SP2). Which one is it? Feasibly, there ...
lewiso1's user avatar
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2 votes
0 answers
25 views

Difference and meaning of isopointal and isoconfigurational structures [closed]

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 ...
leire's user avatar
  • 183
5 votes
0 answers
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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? [closed]

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 ...
Ali's user avatar
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2 votes
1 answer
183 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: ...
leire's user avatar
  • 183
4 votes
1 answer
494 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. ...
rik's user avatar
  • 91
3 votes
1 answer
358 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 ...
James Arten's user avatar
4 votes
1 answer
462 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,...
rik's user avatar
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3 votes
0 answers
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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 ...
Chan's user avatar
  • 629
2 votes
0 answers
28 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:...
Zul Qarnian's user avatar
3 votes
0 answers
197 views

How to transform the conventional cell to primitive cell, by hand?

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 ...
Jack's user avatar
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3 votes
0 answers
36 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 ...
Jack's user avatar
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2 votes
0 answers
204 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 ...
UJM's user avatar
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5 votes
2 answers
285 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 ...
Chan's user avatar
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5 votes
0 answers
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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 ...
Jack's user avatar
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4 votes
0 answers
63 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 ...
uhoh's user avatar
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