A set of tools for coarse-graining and back-mapping frameworks.
Project description
CHIC
Coarse-graining Hybrid Iorganic Crystals.
Getting started
Install with pip install chic-lib
, and you're ready to go!
By way of a quick example, ZIF-8 (CSD RefCode: FAWCEN) can be coarse-grained by running:
from chic import Structure
# read in structure and delete oxygen from the pores.
zif8 = Structure.from_cif('FAWCEN.cif')
zif8.remove_species('O')
# compute neighbour list, find atomic clusters, and coarse-grain.
zif8.get_neighbours_crystalnn()
zif8.find_atomic_clusters()
zif8.get_coarse_grained_net()
# export structure as TopoCIF.
zif8.net_to_cif('ZIF-8-sod-cg.cif', write_bonds=True, name='ZIF-8-cg')
Head over to the chic docs to see examples and more details!
ToDo list
- Add docs.
- Add simple distance cut-off algorithm for neighbour list building.
- Add custom implementation of optimised CrystalNN algorithm.
- Integrate back-mapping code.
- Integrate extraction of local energies from LAMMPS dump format.
- Add registry to Net class for easier future development beyond ZIFs.
Authors
Thomas C. Nicholas
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