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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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A problem to simulate the kinetic energy operator using some field going through a crystal

We know about a differentiation and integration operations and also other ones can be simulated by an analog way using electric circuits with operational amplifiers (here are articles of the ...
SFriendly's user avatar
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5 votes
1 answer
67 views

Visualize variation of lattice parameters with temperature after MD

I am interested to plot lattice parameters vs temperature after Molecular Dynamics calculation in NPT ensemble to detect structural phase transition of my system, Ex- So, I am looking for python ...
Kratos1611's user avatar
5 votes
1 answer
71 views

Can conventional unit cell have higher symmetry than primitive cell for the same crystal?

This question arises from the last sentence of the first paragraph (see here) of the section "Formalism". If primitive cell can have lower symmetry, why don't the DFT results using these two ...
AbPhys's user avatar
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2 votes
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How to rotate Octahdrals locally along with unit cell axis

As the continuation of this discussion d orbitals PDOS analysis, I am curious about crystal field effects on a given atom by analysing $m_l$ projected DOS, the individual d-orbitals are given with ...
Kratos1611's user avatar
1 vote
0 answers
61 views

Code to build the monoclinic crystal lattice

Benzoic acid exists as a solid at room temperature. So, I want to build a monoclinic crystal structure of this molecule. Is there any code available to do that? Thanks. Edit: Is there any way to build ...
Roshan Shrestha's user avatar
7 votes
1 answer
234 views

Is there any software or Python library for visualizing higher-order Brillouin Zones of standard lattices?

I am looking for a software or Python library to help me visualize higher-order Brillouin Zones (BZs) of standard lattices like FCC, BCC, etc. I have already plotted the first BZ of an FCC lattice ...
Puspendu Rana's user avatar
2 votes
0 answers
27 views

Error in 2D Ewald sum for a multipolar expansion

I am attempting to calculate the potential of a particle at the center of an infinite two-dimensional lattice as per the following reference: Reference: Lambin, PH & Senet, P. Ewald Summation of ...
JasonC's user avatar
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7 votes
1 answer
91 views

Have I missed something? "Aluminum is even simpler than Silicon: one atom per unit cell in a fcc lattic"?

In this tutorial page 17, it says: "Aluminum is even simpler than Silicon: one atom per unit cell in a fcc lattic". If it is FCC, then it should be the same as Silicon, two atoms per unit ...
an offer can't refuse's user avatar
3 votes
0 answers
29 views

How to choose the correct ibrav value and Identifying the 3-fold Axis

I'm trying to perform relaxation calculations for FeTiO3 with the ilmenite structure in Quantum Espresso. The documentation mentions two possible ibrav values for triagonal systems: 5 and -5. However, ...
sankalpa's user avatar
2 votes
1 answer
116 views

How to make a super cell for molecular crystal with PBC

I am trying to build a supercell for molecular crystals from a .cif file. With the ASE package, the supercell has the perfect PBC, but the atom sequence is very random and might be difficult to match ...
Pradip Si's user avatar
4 votes
0 answers
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Photorealistic Rendering: How To?

i have started computationally modelling materials from first principles recently, my code of choice being VASP [6.1.0]. Recently i have come across this paper in Nature: DOI:10.1038/s41567-023-01960-...
F.N.'s user avatar
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3 votes
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Atomic basin partitioning with electron density grid

I am performing Hirshfeld Atom Refinement (HAR) calculations with XRD data using aspheric atomic scattering factors, which are calculated from wavefunctions optimized in Orca. My crystal structure has ...
Przemyslaw Dera's user avatar
4 votes
2 answers
180 views

Total energy calculation for an isolated atom

I tried calculating total energy using SCF calculations after optimization with quantum espresso. Still, I don't know how to optimize total energy in the standard state instead of isolated atoms. If ...
MALAK's user avatar
  • 43
3 votes
0 answers
28 views

How to model and compute the structure of high entropy alloys (HEAs) using SSOS methods with ATAT

I've recently been working on structural modeling of HEAs and got a little confused when I read about the SSOS approach. I would appreciate it if anyone is familiar with the SSOS method or MCSQS and ...
Mou Arceus Tao's user avatar
2 votes
1 answer
47 views

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
  • 969
4 votes
1 answer
153 views

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
170 views

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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4 votes
1 answer
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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
0 answers
124 views

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
  • 441
5 votes
1 answer
100 views

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
0 answers
41 views

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
  • 406
5 votes
1 answer
134 views

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
3 votes
0 answers
36 views

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
  • 223
5 votes
1 answer
107 views

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
  • 1,038
5 votes
0 answers
244 views

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
  • 133
2 votes
1 answer
471 views

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
  • 21
3 votes
1 answer
158 views

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
3 votes
1 answer
104 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
5 votes
0 answers
45 views

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
  • 1,885
2 votes
0 answers
28 views

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
  • 211
3 votes
0 answers
48 views

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
  • 211
3 votes
1 answer
576 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
  • 2,159
2 votes
0 answers
30 views

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
  • 441
3 votes
1 answer
227 views

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
  • 441
4 votes
1 answer
250 views

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
  • 441
2 votes
0 answers
46 views

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
  • 2,034
3 votes
0 answers
34 views

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
  • 31
9 votes
1 answer
184 views

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
55 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
  • 141
5 votes
0 answers
108 views

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
  • 2,159
3 votes
1 answer
253 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
  • 441
5 votes
1 answer
586 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 ...
Camilla's user avatar
  • 2,159
4 votes
1 answer
184 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 ...
Saha_1994's user avatar
  • 969
8 votes
2 answers
411 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
  • 83
5 votes
0 answers
127 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
  • 2,159
2 votes
1 answer
45 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 ...
artist_and_not_EE_by_training'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
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 ...
leire's user avatar
  • 183
4 votes
1 answer
252 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
  • 936
2 votes
0 answers
34 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