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A Basic Symmetry Module

Project description

PyPI version DOI status Build Status Test Coverage Documentation Status

bsym is a basic Python symmetry module. It consists of core classes that describe configuration vector spaces, their symmetry operations, and specific configurations of objects within these spaces. The module also contains an interface for working with pymatgen Structure objects, to allow simple generation of disordered symmetry-inequivalent structures from a symmetric parent crystal structure.

Examples are provided in a Jupyter notebook here.
API documentation is here.
Source code is available as a git repository at https://github.com/bjmorgan/bsym.

Installation

pip install bsym

Or download the latest release from GitHub, and install

cd bsym
python setup.py install

Or clone the latest development version

git clone git@github.com:bjmorgan/bsym.git

and install the same way.

cd bsym
python setup.py install 

Tests

Automated testing of the latest commit happens here.

Manual tests can be run using

python -m unittest discover

The code has been tested with Python versions 3.5 and above.

Documentation

An overview of the capabilities of bsym along with example code is contained in a Jupyter notebook in the repository examples directory examples/bsym_examples.ipynb.

API documentation is available here.

I want to generate a set of symmetry-inequivalent crystal structures

bsym can enumerate symmetry-inequivalent crystal structures generated by partial substitutions, starting from a parent structure described by a pymatgen Structure object.
Example code is in the example notebook.
Also refer to the bsym.interface.pymatgen.unique_structure_substitutions documentation.

Citing bsym

This code can be cited as:

Morgan, Benjamin J. (2017). bsym - a Basic Symmetry Module. The Journal of Open Source Software. http://doi.org/10.21105/joss.00370

BibTeX

@article{Morgan_JOSS2017b,
  doi = {10.21105/joss.00370},
  url = {https://doi.org/10.21105/joss.00370},
  year  = {2017},
  month = {aug},
  publisher = {The Open Journal},
  volume = {2},
  number = {16},
  author = {Benjamin J. Morgan},
  title = {bsym: A basic symmetry module},
  journal = {The Journal of Open Source Software}
}

Project details


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