Machine learning fingerprints for particle environments
Project description
Pythia is a library to generate numerical descriptions of particle systems. Most methods rely heavily on freud for efficient neighbor search and other accelerated calculations.
Installation
Pythia is available on PyPI as pythia-learn:
$ pip install pythia-learn freud-analysis
You can install pythia from source like this:
$ git clone https://github.com/glotzerlab/pythia.git $ # now install $ cd pythia && python setup.py install --user
Citation
In addition to the citations referenced in the docstring of each function, we encourage users to cite the pythia project itself.
Documentation
The documentation is available as standard sphinx documentation:
$ cd doc $ make html
Automatically-built documentation is available at https://pythia-learn.readthedocs.io .
Usage
In general, data types follow the hoomd-blue schema:
Positions are an Nx3 array of particle coordinates, with (0, 0, 0) being the center of the box
Boxes are specified as an object with Lx, Ly, Lz, xy, xz, and yz elements
Orientations are specified as orientation quaternions: an Nx4 array of (r, i, j, k) elements
Examples
Example notebooks are available in the examples directory:
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