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Questions tagged [supercell]

Questions about or related to supercells.

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Unit cell size for phonon modes

Based on this and some other literature I realize that the number of phonon modes is contingent upon the size of the unit cell. I also understand that in using Quantum ESPRESSO, the study of defects ...
R Walser's user avatar
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5 votes
0 answers
40 views

How to determine the unit cell in heterostructure?

I’ve to create a heterostructure from two monolayers, for example, two graphene sheets or two metal layers. And then I want to rotate the first layer relative to another one by some angle. The ...
Victor's user avatar
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4 votes
1 answer
176 views

Density of states does not scale properly with supercell

I am performing some DFT calculations of monolayer hexagonal boron nitride in Quantum ESPRESSO. I have been trying to calculate the density of states of a 7 x 7 supercell of h-BN, but the resulting ...
TheSimulator's user avatar
4 votes
0 answers
73 views

Automatic construction of supercell VESTA

Good afternoon, everyone.Please help me understand my question. When I upload some of my cif structure files, VESTA automatically creates huge supercells. I want to remove this function by standard ...
Agrail616's user avatar
2 votes
1 answer
111 views

Errors in CASTEP supercell geometry optimization

These are the errors when I run my supercell on material studio using CASTEP module. I have tried decreasing k points and also increased the cutoff energy. Furthermore I deleted all the files related ...
Noor's user avatar
  • 55
4 votes
1 answer
67 views

Supercell Elastic Constant

Suppose, that one wants to study a bulk structure which is doped by several impurities. More precisely, I want to calculate the elastic constants using a DFT code (VASP) by fitting stress to strain (...
Lukas's user avatar
  • 303
2 votes
1 answer
117 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
7 votes
1 answer
319 views

For a single unit cell calculation, is it necessary to add a vacuum?

Much of the information I find is about super-cells. What about for a single unit cell? Is it necessary to add a vacuum space?
Gabriel Elyas's user avatar
4 votes
0 answers
44 views

supercell nscf kpoints for optical properties

I am calculating the optical properties of 200 atoms supercell with quantum espresso. What is the approximate number of the nscf kpoints (nk nk nk)should I start with, to avoid lengthy kpoints ...
hakou elhaj's user avatar
5 votes
1 answer
57 views

Kpt boundaries for cubic supercell

I have a question on how to make a supercell in abinit. I am trying to calculate the EBS of a cubic perovskite supercell (2x2x2 cubic STO). The geometry information can be found on the MP here. I need ...
Marco Di Gennaro's user avatar
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
5 votes
1 answer
104 views

Indirect to direct band gap transition in SUPERCELLS?

My compound under investigation are cubic and construct corresponding 2x2x2 supercell. Properties like optical and mechanical seem to be correct as expected. However a problem arises in their ...
Bernard's user avatar
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3 votes
1 answer
223 views

Transform Supercell to Unitcell

I’ve supercells of around 10,000 Metal–organic frameworks (MOF) structures in CIF format. I’m looking to convert them to unit cells. But I’m not able to find packages (or any other libraries like ...
hari's user avatar
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2 votes
0 answers
49 views

How can I correctly create the input files for DOS and Optical Properties of a supercell using Quantum ESPRESSO? [closed]

I have a unit cell, and I want to create a 3x3x3 supercell. Please, I need guidance on how to create properly the input files for Density of States (DOS) calculation (SCF and NSCF) and the input files ...
Camilla's user avatar
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6 votes
2 answers
258 views

Number of k-points for unit and super cell

I am just new with solid state calculation and would like to know one thing. Why is plane wave basis set is good for 1s and 2s orbitals, but for higher convergence is poor? Why is it better to use ...
Alexander Teryahskin's user avatar
5 votes
1 answer
232 views

How to get rotation matrix elements from root integer notation?

For example, I am reading a paper, where they put one layer on top of another, and in order to minimize the lattice mismatch, they transform unit cells of both layers. They report it in a root integer ...
Vladislav Gladkikh's user avatar
3 votes
0 answers
114 views

How to calculate the formation energy of a defect using the unit cell? [duplicate]

I want to dope CuI conventional unit cell using Quantum ESPRESSO. In previous papers they used different formulas of defect formation energies,and they use supercell. So I'm confused. What's the ...
Camilla's user avatar
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4 votes
1 answer
223 views

How to calculate the lattice parameter of a supercell using Phonopy? (For Quantum ESPRESSO)

I found in the internet a method to generate a supercell from the input file using Phonopy code. And I have a question if someone can clarify my doubts please. The method is as following: We make an ...
Camilla's user avatar
  • 2,169
4 votes
1 answer
612 views

What's the appropriate method to create a supercell for Quantum ESPRESSO?

I created a CIF file using the experimental parameters of my material, then I used it to create my input file for the unit cell using Cif2Cell. After that, I ...
Camilla's user avatar
  • 2,169
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
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4 votes
0 answers
111 views

An issue of running Phonopy for graphene using Siesta [closed]

I have used Siesta in the example attached with phonopy to run phonon for graphene, and when I typed the command to create force ...
Omar Alrawi's user avatar
2 votes
0 answers
258 views

Confusion in primitive, conventional and supercell crystal structure [closed]

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
  • 2,611
3 votes
2 answers
71 views

What happens to the position coordinates of the nearest neighbors in supercell studies?

Can anyone tell what happens to the position coordinates of the nearest neighbors when we choose to study supercell of the same material. That remains intact or any changes will be there? For example ...
Alpha_Roy's user avatar
  • 123
6 votes
1 answer
400 views

Number of k-points vs number of electrons: which is more significant in terms of computational cost for plane-wave calculations?

When using plane-wave codes for solid-state calculations, which computational parameter is more significant in increasing the computational cost: number of electrons or number of k-points? I ask this ...
Memories's user avatar
  • 353
6 votes
1 answer
583 views

How to construct thin film structure of desired thickness in quantum espresso?

I want to study the properties of thin films using DFT calculation. I have done the bulk crystal calculations in Quantum ESPRESSO but have no idea how can I construct the thin film of desired ...
UJM's user avatar
  • 2,611
9 votes
1 answer
512 views

Different band structure in supercell, but not due to band folding

This is my first time asking a question - if I mess something up please let me know and I'll amend. I believe this goes beyond questions on how to use QE so here seems appropriate over the QE forums. ...
MSteg's user avatar
  • 311
8 votes
1 answer
495 views

How could I fold a specific high symmetry point to the Gamma point?

How could I get the Brillouin Zone of 2*2 supercell? I tried to use see k-path website, but when I upload a supercell, it still generates the Brillouin Zone of the unit cell. What I want to do is to ...
Jack's user avatar
  • 2,057
7 votes
1 answer
225 views

Different band gap observed in unitcell and in the supercell

I calculated the bandgap for one system in the unit cell and in the supercell of 2x2x1 and 3x1x1. Although 3x1x1 gives the same bandgap as I got from the unit cell (1.79 eV) but 2x2x1 is giving 1.75 ...
poonam sharma's user avatar
10 votes
0 answers
529 views

Difference of high-frequency and static dielectric constants? [closed]

I found in an article [1] the following definition of FNV (Freysoldt, Neugebauer and Van de Walle) energy correction term for a charged defect in a cubic supercell: $$E_{\text{corr}}=\frac{\alpha_Mq^2}...
Rogério Gouvêa's user avatar
10 votes
2 answers
2k views

Help understanding square root notation of supercell

I often see supercells and slabs explained like this: $2\sqrt{2} \times 6$ slab of $\ce{MoS2}$ (001) $\sqrt{2} \times \sqrt{2} \times 2$ supercell of $\ce{Y Ba(1−x)Sr(x)CuFeO5}$ (see here). Take $\...
user1029384756's user avatar
8 votes
0 answers
86 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, ...
breadcrumbs's user avatar
3 votes
1 answer
94 views

How to make left and right handed material interface using python

I have a crystal structure, a B20 compound. I want to make an interface of that bulk compound with left and right-hand material. Is there any python code for writing such interfaces. or for writing ...
ashice's user avatar
  • 47
5 votes
1 answer
202 views

Supercell model for a disordered system in phonon calculations using the harmonic approximation

I studied a disordered state (FCC solid solution) and used a special quasirandom structure supercell with 32 atoms to represent the system. After relaxing it thoroughly with ...
Hitanshu Sachania's user avatar
12 votes
2 answers
516 views

How to sort a supercell for a molecular crystal?

I am trying to build a supercell of the following (below) molecular crystal from its .cif file. How do I sort a supercell here according to each molecule in the supercell? I'm not tethered to a ...
user avatar
5 votes
1 answer
811 views

ASE: why do I get warnings about "monoclinic" and "orthorhombic" not being interpreted?

I am trying to use ASE (Atomic Simulation Environment) to build a supercell of some molecular crystals and then output the result to a file with the atoms given in a specified order for each molecule, ...
user avatar
11 votes
1 answer
438 views

Using LAMMPS for a small system

I want to run a classical molecular dynamics simulation on silicane using LAMMPS. Since I don't have access to any HPC nor do I have a powerful desktop PC, I'm planning on making the system small. By ...
jboy's user avatar
  • 1,151
8 votes
2 answers
886 views

Extracting the coordinates of a super cell in Vesta or Avogadro

I am trying to use a program such as Vesta or Avogadro to build a super cell from a .cif file for a molecular crystal. In neither program can I seem to figure out how to order the output of the ...
user avatar
4 votes
2 answers
198 views

Energy per unit cell in NWChem differs for different supercells despite the same k-points density

I try to compute the unit cell energy of the $\ce{Ti2CO2}$ MXene with NWchem. Computing the 1x1 supercell with 4x4x1 K-points grid I got -1875 Ha. Computing the 2x2 supercell with 2x2x1 K-points grid ...
user36313's user avatar
  • 730
7 votes
2 answers
334 views

What is the meaning of the "PRIMCELL.vasp" file generated by VASPKIT tool during bandstructure inputs generation?

When I use VASPKIT tool to generate K-path KPOINTS file for Bandstructure calcualtion of a 4x4x1 supercell of a pure material, ...
Chi Kou's user avatar
  • 5,833