OPS Visit All States Ensemble

Software Technical Information

The information in this section describes OpenPathSampling as a whole. Information specific to the additions in this module are in subsequent sections.

Language
Python (2.7, 3.6, 3.7)
Documentation Tool
Sphinx, numpydoc format (ReST)
Application Documentation
http://openpathsampling.org
Relevant Training Material
http://openpathsampling.org/latest/examples/
Licence
LGPL, v. 2.1 or later
Software module developed by
David W.H. Swenson

This module adds a convenient new OpenPathSampling ensemble that allows trajectories to continue until they have visited all the states in the system. In addition, it provides real-time reporting about the progress.

Purpose of Module

One of the ways to get initial trajectories for path sampling is to use dynamics that aren’t physical for the ensemble of interest, such as using an increased temperature. If a trajectory has a frame in every state, then it must have subtrajectories that connect from each state to another one, and therefore it has all the information to start a MSTIS simulation. The ensemble definition tools in OPS make it easy to create such custom sequential ensembles [1].

However, users often want to do simulation setup in an interactive mode, such as in a Jupyter notebook, or at a minimum want to have a sense of the progress made on a long trajectory such as this. The default OPS ensemble gives no output and therefore no sense of how much progress has been made.

This module provides a custom OPS ensemble that gives such output during its simulation. It outputs the length of the trajectory so far, as well as the states that have and have not already been visited. This gives a much better sense of how long the simulation will take to run.

This module includes:

  • default_state_progress_report: A function to create the progress report string. This can be replaced by another function to customize the output.
  • VisitAllStatesEnsemble: A class that wraps an OPS SequentialEnsemble. The can_append method, called while generating the dynamics, can output information about the progress. The behavior of this output can be set with the initialization variable progress, which can take the values of default for the default output, silent for no output, or can take a 2-tuple of callables where the first determines what to write, and the second determined how to emit the information.
[1]D.W.H. Swenson, J.-H. Prinz, F. Noe, J.D. Chodera, and P.G. Bolhuis. J. Chem. Theory Comput. 15, 837 (2019); http://doi.org/10.1021/acs.jctc.8b00627

Background Information

This module builds on OpenPathSampling, a Python package for path sampling simulations. To learn more about OpenPathSampling, you might be interested in reading:

Testing

Tests in OpenPathSampling use pytest.

This module has been included in the OpenPathSampling core. Its tests can be run by installing pytest and OPS (with commit 8e767872, which will be part of release 1.0 and later), and running the command py.test --pyargs openpathsampling.

Examples

This module is used in the OPS alanine dipeptide MSTIS example, during the creation of initial trajectories.

Source Code

This module has been merged into OpenPathSampling. It is composed of the following pull requests: