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One option is to use the Atomic Simulation Environment's sort function. The function ase.build.sort() takes a required Atoms object (e.g. the supercell of the original CIF) and an optional tags argument that allows you to sort however you wish. It's then just up to you to find out how to flag each individual molecule in the order that you'd like.

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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 the space group evaluated by ASE is consistent with the cell symmetry mentioned in the cif file. The relevant part of the function is shown below: if setting_name: no = Spacegroup(...

6

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 for your example input file: from pymatgen.core.structure import Structure, Molecule from pymatgen.analysis.graphs import StructureGraph from pymatgen.analysis.local_env import JmolNN # load the ...

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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 come from the world of biomolecular simulations, where we typically "pad" our proteins with at least 1 nm of water. I would guess that your entire ...

5

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 $1\times1\times1$ supercell). Using a larger supercell will introduce an artificial periodicity in the system. Having said this, it is still really important to converge with ...

5

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 configures another calculation (with plane-wave basis) that is never launched by the task directive. Summing up, with NWchem you can use either K-points with plane-waves, or a supercell with ...

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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 because you could always rebuild the supercell starting from the primitive cell by applying a supercell matrix. My guess is that the PRIMCELL.vasp file simply contains this primitive cell as a computer ...

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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$\sqrt{5}\times\sqrt{5}$ for the case of MoS$_2$. Basically, you need to define a rotation matrix for creating such supercells. e.g., B=RA (in matrix form), where A is the ...

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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 program currently supports output for a number of popular electronic structure programs, including ABINIT, ASE, CASTEP, CP2K, CPMD, CRYSTAL09, Elk, EMTO, ...

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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 can you do this?

3

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 ase.build.sort. The following code does this: import numpy as np from ase.io import read, write from ase import Atoms, neighborlist from ase.build import sort ...

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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 -> Choose desired file type (XYZ and PDB work. Avogadro 1.2.0 seems to lock up on my system when I try to write mol2 files by this procedure. I would guess ...

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