Python utility functions for the analysis of diffusion in molecular dynamics simulation trajectories.
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README.md

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Analysis of particle diffusion in molecular dynamics simulations

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: DOI

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 nosetests)
  • 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