cifkit 0.1.1

A description of cifkit

cifkit

• preprocess .cif files for high-throuhgput processing
• move, copy, filter files based on a comprehensive set of attributes such as coordination number, elements, tags
• determine nearest neighbor and coordination environments at each site
• facilitate the plotting of polyhedrons and

Overview

cifkit provides two primary objects: Cif and CifEnsemble.

• Cif: Initializes with a .cif file path. It parses the .cif file, preprocesses ill-formatted files, generates supercells, and computes nearest neighbors. It also determines coordination numbers using four different methods and generates polyhedrons for each site.

• CifEnsemble: Initializes with a folder path containing .cif files. It identifies unique attributes, such as space groups and elements, across the .cif files, moves and copies files based on these attributes. It generates histograms for all attribute.

Motivation

• High throughput analysis tools using .cif files for research. The tools analyze bonding distances, site analysis, and coordination numbers.
• Each tool requires preprocesing, formatting, copying, moving, and sorting .cif files.
• To streamline the above tasks, I developed cifkit that can be easily imported for the above tasks.

Documentation

Please see the tutorial provided here (TBA).

Installation

To run locally:

pip install -e .

Developer

Sangjoon Bob Lee (@bobleesj)

MkDocs

pip install mkdocstrings
pip install mkdocstrings-python
pip install mkdocs
pip install mkdocs-material
pip install mkdocs-jupyter
mkdocs serve