Contains Python utility functions for the analysis of diffusion in molecular dynamics simulation trajectories.
The documentation for the project is available here: http://diffusion-analysis-md-simulations.readthedocs.org/en/latest/index.html
An IPython notebook containing an example diffusion calculation is available: https://github.com/tylerjereddy/diffusion_analysis_MD_simulations/blob/master/diffusion_analysis_sim126_extended.ipynb
Please cite:
And even better if you cite the original paper: Reddy et al. (2015) Structure 23: 584-97. [DOI]
For contributions:
- ensure all unit tests pass (run pytest)
- ensure all doctests pass (run doctesting.py)
- if you import new modules, you may need to mock them in the Sphinx conf.py documentation file so that the docs are properly compiled by readthedocs
- attempt to match the numpy documentation standard as closely as possible