In this package, you can exchange atoms in crystal structures randomly with pymatgen.
In this package you should use python 3.5 or later.
We use pymatgen in order to handle crystal structures on your computer.
If you have pip, you can install pymatgen as follows:
> pip install --user pymatgen
First, you must read structure file from "cif", "poscar", "pymatgen.Structure" or many other structural format which can be handle in pymatgen package as follows:
> from REA import RandomExchangeAtoms as rea
> rea_object = rea("./sample_input/cif/Al2O3_hR30_R-3c_167.cif", format="cif")
If you want to exchange atoms randomly, you can use run_exchange(number) method where number is integer which means number of exchange.
rea_object.run_exchange(5)
If you also think to change cell shape, you can use modify_cell_size() method.
rea_object.modify_cell_size()
In order to export your newly structure, you should call export_dict(filename) method.
rea_object.export_dict(filename="new_structure")
In the default setting export data is the POSCAR (VASP) format.
Clone this package.
MIT License
Copyright (c) 2018 Taku MURAKAMI
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
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SOFTWARE.
Taku MURAKAMI@murakami17, master course student at Shizuoka university.
Please contant me via: e-mail or github issues.