8 votes
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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}\...
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7 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 ...
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  • 6,852
7 votes
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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 ...
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7 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 ...
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  • 1,877
6 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 ...
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  • 1,411
6 votes
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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}...
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  • 10.2k
6 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 ...
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  • 338
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 $1\times1\times1$...
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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 ...
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  • 430
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 ...
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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 ...
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  • 13.6k
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 ...
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  • 18.7k
3 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 ...
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3 votes
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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 ...
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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 -&...
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