* Weighted Ensemble Python (wepy)

[[./info/logo/wepy.svg]]

[[https://adicksonlab.github.io/wepy/index.html][Sphinx Documentation]]

[[https://github.com/ADicksonLab/wepy/blob/master/info/README.org][Plaintext Org-Mode Docs]]

Modular implementation and framework for running weighted ensemble (WE)
simulations in pure python, where the aim is to have simple things
simple and complicated things possible. The latter being the priority.

The goal of the architecture is that it should be highly modular to
allow extension, but provide a "killer app" for most uses that just
works, no questions asked.

Comes equipped with support for [[https://github.com/pandegroup/openmm][OpenMM]] molecular dynamics,
parallelization using multiprocessing, the [[http://pubs.acs.org/doi/abs/10.1021/jp411479c][WExplore]] 
and REVO (Resampling Ensembles by Variance Optimization) resampling
algorithms, and an HDF5 file format and library for storing and
querying your WE datasets that can be used from the command line.

The deeper architecture of ~wepy~ is intended to be loosely coupled,
so that unforeseen use cases can be accomodated, but tightly
integrated for the most common of use cases, i.e. molecular dynamics.

This allows freedom for fast development of new methods.

Full [[https://github.com/ADicksonLab/wepy/blob/master/info/introduction.org][introduction]].

** Installation

Also see: [[info/installation.org][Installation Instructions]]

To install from pip:

#+BEGIN_SRC bash
  pip install wepy[all]
#+END_SRC

Which will install most dependencies.

To install the optional, but likely desired feature, OpenMM you should
probably just use the omnia channel on conda, otherwise you will need
to compile it yourself.

#+BEGIN_SRC bash
  conda install -c omnia openmm
#+END_SRC

Check its installed by running the command line interface:

#+begin_src bash :tangle check_installation.bash
wepy --help
#+end_src

** Citations

Current [[https://zenodo.org/badge/latestdoi/101077926][Zenodo DOI]]

Lotz and Dickson. 2020. in preparation.



