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 further information, please see 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).

To help us fund development, please cite the article listed above 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.

Installation

After obtaining a copy of the code (see https://chong.chem.pitt.edu/wewiki/Obtaining_the_WESTPA_code for details), run setup.sh in the westpa directory. If the version of Python you will be using to run the code is not first on your $PATH, then set the environment variable WEST_PYTHON to the Python interpreter you want to use. For example:

cd westpa
export WEST_PYTHON=/opt/anaconda/bin/python2.7
./setup.sh

Getting started

High-level tutorials of how to use the WESTPA software are available from https://chong.chem.pitt.edu/wewiki/WESTPA_tutorials. Further, all WESTPA command-line tools (located in westpa/bin) provide detailed help when given the -h/--help option.

Getting help

Documentation is available from the WESTPA wiki, located at https://chong.chem.pitt.edu/wewiki.

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.

Copyright and license information 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.