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}\...
- 1,426
8
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 ...
- 2,027
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 ...
- 6,647
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 ...
- 808
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 ...
- 348
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}...
- 10.9k
6
votes
Accepted
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 ...
- 7,281
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 ...
- 1,124
5
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 ...
- 913
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 ...
- 6,647
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 ...
- 1,491
5
votes
Accepted
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 ...
- 505
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 ...
- 10.9k
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 $1\times1\times1$...
- 10.9k
5
votes
Accepted
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 ...
- 141
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 ...
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 ...
- 22.3k
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 ...
- 14.9k
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 ...
- 2,895
4
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 ...
- 2,895
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 ...
- 608
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 ...
- 490
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 -&...
- 1,901
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 ...
- 113
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 ...
- 139
1
vote
Number of k-points for unit and super cell
I will explicit my comment, the use of plane waves (PWs) for 1s and 2s is completely absurd when a linear combination of atomic orbitals gives a fast convergence. Even if they lack of significant ...
- 896
1
vote
Accepted
How to calculate the lattice parameter of a supercell using Phonopy? (For Quantum ESPRESSO)
The process you described for obtaining a supercell can be found here.
If the 1*1*1 unit cell has a lattice parameter of a, then a 2*2*2 supercell will have a lattice parameter of 2a, a 3*3*3 ...
- 2,101
1
vote
What happens to the position coordinates of the nearest neighbors in supercell studies?
In solid-state calculations, DFT code does not know whether you give it a crystalline unit cell or a supercell. Instead, it treats every input structure as a "unit cell".
So my answer is &...
- 353
1
vote
Accepted
How to sort a supercell for a molecular crystal?
ASE can be used to achieve what you require. Basically we need to:
Read the structure.
Determine the molecules using neighborlist class in ASE.
Sort each of the molecules in the required manner using ...
- 1,124
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