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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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Unit conversion of q point (from iku to 1/a.u.) in yambo

Here are some necessary info about direct lattice and reciprocal lattice from yambo output file: ...
Muhammad Hasan's user avatar
1 vote
0 answers
23 views

Surface atoms concentration

I have a bulk crystal that contains 4 different elements. I want to cut the crystal in such a way that the atoms at the surface still obey the concentration of each atom in the bulk. At least close. ...
Nana Kofi Boakye's user avatar
3 votes
1 answer
74 views

How to fill in all atoms in unit cell starting from a CIF file?

I am trying to write code that builds a unit cell with all atoms explicitly specified, starting from a CIF file of a molecular crystal. The CIF files come from CSD. My first try was to use Gemmi to ...
Alex I's user avatar
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3 votes
1 answer
53 views

What are the specific differences between these two notations of supercell denoted by (√3×√3)R30∘ and (√3×√3)?

I am studying the super-cell structures in crystallography and came across two different notations: (√3×√3)R30∘ and (√3×√3). I would like to understand whether these two notations represent the same ...
Rubi Agrawal's user avatar
1 vote
1 answer
72 views

Why does my POSCAR file say I have 4 Pd atoms when I actually have 14 based on my structure from a crystal database?

I am having trouble getting my geometry optimization to run, and I think it may be my POSCAR. I downloaded a FCC Pd crystal structure from a crystal database. I downloaded the cif into materials ...
Raven's user avatar
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3 votes
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65 views

How to choose a proper rotation matrix and apply it to rotate unit cell about Cartesian axis to align I-Cr-I bonds parallel to Cartesian axis

I was surveying this paper Remarkably enhanced Curie temperature in monolayer CrI3 by hydrogen and oxygen adsorption: A first-principles calculations, where they have rotated the unit cell (without ...
Kratos1611's user avatar
4 votes
0 answers
39 views

Rich editing of ASE images

I want to produce some images related to graphene-like materials. I was able to draw them using ASE visualize module after constructing the atomistic model. However ...
Emu's user avatar
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2 votes
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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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6 votes
1 answer
108 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
134 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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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
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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
258 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
30 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
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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
36 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
156 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
1 answer
73 views

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
  • 103
3 votes
0 answers
24 views

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
271 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
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3 votes
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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
50 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
  • 989
4 votes
1 answer
177 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
185 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
  • 476
4 votes
1 answer
96 views

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
174 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
  • 451
5 votes
1 answer
114 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
45 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
  • 476
5 votes
1 answer
187 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
37 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
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5 votes
1 answer
117 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
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5 votes
0 answers
354 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
841 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
244 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
120 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
46 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
  • 1,970
2 votes
0 answers
29 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
50 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
739 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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3 votes
0 answers
31 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
  • 451
3 votes
1 answer
283 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
  • 451
4 votes
1 answer
255 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
  • 451
3 votes
0 answers
68 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
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3 votes
0 answers
35 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 ...
hendlim's user avatar
  • 131
9 votes
1 answer
219 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
57 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
133 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
  • 2,209
3 votes
1 answer
313 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
  • 451
5 votes
1 answer
587 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
  • 2,209
4 votes
1 answer
198 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
  • 989