chic

Important

This project is under active development. Until version 1.0.0 is released, breaking changes to the API may occur.

chic is a Python package for coarse-graining hybrid and inorganic crystals.

Quickstart

Install using pip install chic-lib, and then use Structure to begin processing your structure…

>>> from chic import Structure
>>> struct = Structure.from_cif("ZIF-4-cag.cif")
>>> struct.remove_sites_by_symbol("O")

… find the nodes, linkers, and underlying net…

>>> struct.get_neighbours_crystalnn()
>>> struct.find_atomic_clusters()
>>> struct.get_coarse_grained_net()
>>> struct.net_to_cif("cag-net.cif")

… and redecorate with a different chemistry…

>>> cag_net = struct.to_net()
>>> cag_net.add_zif_atoms(template="CH3") # methyl-substituted imidazolate

chic is built upon the pymatgen.core.Structure class:

>>> struct
Structure Summary
Lattice
   abc : 16.8509 16.8509 16.8509
angles : 90.0 90.0 90.0
volume : 4784.860756696228
      A : 16.8509 0.0 1.0318200373876067e-15
      B : -1.0318200373876067e-15 16.8509 1.0318200373876067e-15
      C : 0.0 0.0 16.8509
   pbc : True True True
PeriodicSite: H (7.669, 7.093, 15.44) [0.4551, 0.4209, 0.9161]
PeriodicSite: H (7.093, 7.669, 15.44) [0.4209, 0.4551, 0.9161]
[...]

for which all of the usual functionality is available.

Contributing

chic was developed by me, Thomas Nicholas, as part of my PhD research at the University of Oxford within the Goodwin Group and the Deringer Group. During this time, it has been adapted several times over, with new directions defined by collaborations too (see publications)!

Please do open an issue or pull request on the GitHub repository if you are interested in suggesting new functionality, identifying and/or fixing a bug, or simply want to start a dicussion.