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9 votes

Using LAMMPS for a small system

There are a couple of potential problems. First, the assumption of periodic simulations is that your box size is large enough that there is no effect on an atom from its nearest periodic replica. I ...
dwhswenson's user avatar
  • 2,057
9 votes
Accepted

Help understanding square root notation of supercell

The main idea here is to preserve the periodic boundary conditions when creating a fractional supercell. Therefore, not all combinations are possible, such as $\sqrt{2}\times\sqrt{2}$ or$\sqrt{5}\...
Shahid Sattar's user avatar
8 votes
Accepted

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

There are two major computational resources we should consider: the computational time, and the computational storage (RAM). Computational time In conventional DFT, the computational time scales ...
Phil Hasnip's user avatar
  • 7,897
7 votes

Number of k-points for unit and super cell

Why is plane wave basis set is good for 1s and 2s orbitals, but for higher convergence is poor? I guess by "higher" you mean higher principle quantum number $n$ (i.e., 3s, 4s-orbitals). For ...
Chengcheng Xiao's user avatar
7 votes

Different band gap observed in unitcell and in the supercell

First off, those values are pretty close, probably within the accuracy of your method (I assume DFT). Notice that you state all input parameters stay the same except that cell size. However, some ...
che_kid's user avatar
  • 358
6 votes
Accepted

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

Setup. Consider a primitive cell with lattice vectors $\mathbf{a}_{p_1}$, $\mathbf{a}_{p_2}$, and $\mathbf{a}_{p_3}$. You can construct a supercell with lattice vectors $\mathbf{a}_{s_1}$, $\mathbf{a}...
ProfM's user avatar
  • 11.1k
6 votes
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Extracting the coordinates of a super cell in Vesta or Avogadro

One option is to use the Atomic Simulation Environment's sort function. The function ase.build.sort() takes a required Atoms ...
Andrew Rosen's user avatar
  • 7,391
6 votes
Accepted

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

As far as I understand, this warning can be safely ignored. While parsing a cif structure, the get_spacegroup() function in the cif parser of ASE, checks whether ...
Rashid Rafeek's user avatar
6 votes
Accepted

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

In a single unit cell calculation, the inclusion of vacuum space depends on the specific requirements and characteristics of your system. Here are a few situations that you should consider about ...
Jaafar Mehrez's user avatar
5 votes

Indirect to direct band gap transition in SUPERCELLS?

This is allowed, in fact you can almost always construct a supercell where this has to happen. Consider the band eigenvalue at k-point $\vec{k}=(0,0,\frac{1}{p})$ in a given unit cell; if I now make a ...
Phil Hasnip's user avatar
  • 7,897
5 votes
Accepted

How to get rotation matrix elements from root integer notation?

$\sqrt{3}$ Case $ \left( \sqrt{3} \times \sqrt{3}\right)R30$ is a short way of representing a supercell in Woods notation (1, 2), which essentially means that each of the basis vectors of the ...
Vandan Revanur's user avatar
5 votes

How to sort a supercell for a molecular crystal?

I don't know if this is exactly what you want to do, but pymatgen may be able to help (disclosure, I am a developer of this package). See this example code below ...
Matt Horton's user avatar
  • 1,531
5 votes
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Energy per unit cell in NWChem differs for different supercells despite the same k-points density

It turns out, that NWchem do not support K-points with Gaussian basis. The nwpw section in my input files, that contains the K-point grid specification, actually ...
user36313's user avatar
  • 730
5 votes

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

I have never used VASPKIT, so my answer is of a general nature. If you have a $4\times4\times1$ supercell of a perfect crystal, you have redundant information ...
ProfM's user avatar
  • 11.1k
5 votes

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

If you have a system without periodicity like your disordered solid solution, then you should use a $1\times1\times1$ $\mathbf{q}$-point grid for a phonon calculation (equivalent to a $1\times1\times1$...
ProfM's user avatar
  • 11.1k
5 votes
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Different band structure in supercell, but not due to band folding

Answer: band folding is a little more subtle than I originally thought. I'd only really come across band folding in the textbook example of 1D and rather naively assumed that in higher dimensions if ...
MSteg's user avatar
  • 311
5 votes
Accepted

Density of states does not scale properly with supercell

When the size of the supercell increases, you can reduce the number of k-points in an inverse manner to get the same accuracy as the one with the smaller cell. This is because the relation between ...
Abdul Muhaymin -Free Palestine's user avatar
4 votes

Help understanding square root notation of supercell

If you want to achieve this using VESTA you can follow what Shahid said in his answer but you have to keep in mind how lattice vectors are defined in VESTA which in turn will change the rotation ...
Khondker Shihabul Hoque's user avatar
4 votes

How to make left and right handed material interface using python

CIF2Cell (only about generating supercells) CIF2Cell is a tool to generate the geometrical setup for various electronic structure codes from a CIF (Crystallographic Information Framework) file. The ...
Camps's user avatar
  • 23.4k
4 votes

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

I assume that you are considering 2D materials. In short, you can use the undoped primitive cell to generate a k-path to plot the band structure of your $4\times4\times1$ supercell with doping. Why ...
Jack's user avatar
  • 15.2k
4 votes
Accepted

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

You can't construct the thin film itself with Quantum Espresso, but only calculate it's properties. You first have to create the unit cell of the thin film with some other software. As an example here ...
Amir K's user avatar
  • 628
4 votes

Transform Supercell to Unitcell

ASE You could use ASE (Atomic Simulation Environment) to achieve this. Here is a sample code. I have tried the below code on three CIF files which can be found on the Crystallography Open Database ...
Vandan Revanur's user avatar
4 votes
Accepted

Errors in CASTEP supercell geometry optimization

The error message says that the computer did not have enough memory to perform the calculation (line 2 of the log you photographed). You don't give any details about your calculation, but in general ...
Phil Hasnip's user avatar
  • 7,897
3 votes
Accepted

Kpt boundaries for cubic supercell

Ciao Marco! Once you make the supercell the reciprocal lattice vectors are divided by 2 (or whatever factor) automatically. The kptbounds are in reduced coordinates so no need to change the bound. ...
matthieu verstraete's user avatar
3 votes

VESTA using command line

In line with the comments, I'm not sure if you can achieve this in VESTA, but a simple ASE or Pymatgen based script can easily do it. This is the Pymatgen script I use. ...
CW Tan's user avatar
  • 1,316
3 votes

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

DFT calculations based on a supercell method utilize the periodicity of a perfect, infinite lattice by imposing periodic boundary conditions onto the wavefunction of the system (Bloch's theorem). In ...
Sha's user avatar
  • 500
3 votes

Extracting the coordinates of a super cell in Vesta or Avogadro

This is in Avogadro 1.2.0. I will check behavior on Avogadro 2 later: File -> Open -> Choose your cif file Build -> Super Cell Builder -> Choose the number of repeats File -> Save As -&...
WaterMolecule's user avatar
2 votes

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

You can directly create a supercell using your input file of the optimized unit cell without optimizing the supercell. The optimized structure of the unit cell represents the most stable configuration ...
Marko_B's user avatar
  • 123
2 votes

Program to classify structures of different composition?

You may want to look into cluster expansion codes because they generally have a robust structure generation/mapping system. The general idea with this type of code is that you start with a particular ...
kpoint's user avatar
  • 139

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