WESTPA: The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis
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README.rst

WESTPA 1.0 beta

Overview

WESTPA is a package for constructing and running stochastic simulations using the "weighted ensemble" approach of Huber and Kim (1996). For use of WESTPA please cite the following:

Zwier, M.C., Adelman, J.L., Kaus, J.W., Pratt, A.J., Wong, K.F., Rego, N.B., Suarez, E., Lettieri, S., Wang, D. W., Grabe, M., Zuckerman, D. M., and Chong, L. T. "WESTPA: An Interoperable, Highly Scalable Software Package For Weighted Ensemble Simulation and Analysis," J. Chem. Theory Comput., 11: 800−809 (2015).

See this page for an overview of weighted ensemble simulation.

To help us fund development and improve WESTPA please fill out a one-minute survey and consider contributing documentation or code to the WESTPA community.

WESTPA is free software, licensed under the terms of the GNU General Public License, Version 3. See the file COPYING for more information.

Requirements

WESTPA is written in Python and requires version 2.7. WESTPA further requires a large number of scientific software libraries for Python and other languages. The simplest way to meet these requirements is to download the Anaconda Python distribution from www.continuum.io (free for all users).

WESTPA currently runs on Unix-like operating systems, including Linux and Mac OS X. It is developed and tested on x86_64 machines running Linux.

Obtaining and Installing WESTPA

WESTPA is developed and tested on Unix-like operating systems, including Linux and Mac OS X.

Before installing WESTPA, you will need to first install the Python 2.7 version provided by the latest free Anaconda Python distribution. After installing the Anaconda Python distribution, either add the Python executable to your $PATH or set the environment variable WEST_PYTHON:

export WEST_PYTHON=/opt/anaconda/bin/python2.7

We recommend obtaining the latest release of WESTPA by downloading the corresponding tar.gz file from the releases page. After downloading the file, unpack the file and install WESTPA by executing the following:

tar xvzf westpa-master.tar.gz
cd westpa
./setup.sh

A westpa.sh script is created during installation, and will set the following environment variables:

WEST_ROOT
WEST_BIN
WEST_PYTHON

These environment variables must be set in order to run WESTPA on your computing cluster.

Getting started

WESTPA simulation checklist

To define environment variables post-installation, simply source the westpa.sh script in the westpa directory from the command line or your setup scripts.

High-level tutorials of how to use the WESTPA software can be found here. Further, all WESTPA command-line tools (located in westpa/bin) provide detailed help when given the -h/--help option.

Finally, while WESTPA is a powerful tool that enables expert simulators to access much longer timescales than is practical with standard simulations, there can be a steep learning curve to figuring out how to effectively run the simulations on your computing resource of choice. For serious users who have completed the online tutorials and are ready for production simulations of their system, we invite you to contact Lillian Chong (ltchong AT pitt DOT edu) about spending a few days with her lab and/or setting up video conferencing sessions to help you get your simulations off the ground.

Getting help

WESTPA FAQ

A mailing list for WESTPA is available, at which one can ask questions (or see if a question one has was previously addressed). This is the preferred means for obtaining help and support. See http://groups.google.com/group/westpa-users to sign up or search archived messages.

Copyright, license, and warranty information

For WESTPA

The WESTPA package is copyright (c) 2013, Matthew C. Zwier and Lillian T. Chong. (Individual contributions noted in each source file.)

WESTPA is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

WESTPA is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program (see the included file COPYING). If not, see <http://www.gnu.org/licenses/>.

Unless otherwise noted, source files included in this distribution and lacking a more specific attribution are subject to the above copyright, terms, and conditions.

For included software

Distributions of WESTPA include a number of components without modification, each of which is subject to its own individual terms and conditions. Please see each package's documentation for the most up-to-date possible information on authorship and licensing. Such packages include:

h5py
See lib/h5py/docs/source/licenses.rst
blessings
See lib/blessings/LICENSE

In addition, the wwmgr work manager is derived from the concurrent.futures module (as included in Python 3.2) by Brian Quinlan and copyright 2011 the Python Software Foundation. See http://docs.python.org/3/license.html for more information.