chic-lib 0.1.8

A set of tools for coarse-graining and back-mapping frameworks.

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