OpenPathSampling CLI Commands

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 (3.6+)

Documentation Tool

Sphinx, numpydoc format (ReST)

Application Documentation

http://openpathsampling-cli.readthedocs.io/

Relevant Training Material

http://openpathsampling.org/

Licence

MIT

Software module developed by

David W.H. Swenson

This module provides the commands available to the OpenPathSampling command line interface as of version 0.1.

Purpose of Module

As discussed in the OpenPathSampling CLI Core module, a command line interface will make path sampling easier for a broader range of users. The OPS CLI is initially designed to support a few functions that will be most useful to users. More commands will be added over time, but the initial commands are outlined below.

Simulation commands

• visit-all: create initial trajectories by running MD until all states have been visited (works for MSTIS or any 2-state system); must provide states, engine, and initial snapshot on command line
• equilibrate: run equilibration for path sampling (until first decorrelated trajectory); must provide move scheme and initial conditions on the command line
• pathsampling: run path sampling with a given move scheme (suitable for custom TPS schemes as well as TIS/RETIS); must provide move scheme, iniital conditions, and number of MC steps on command line

Commands for dealing with files

• contents: list all the named objects in an OPS storage, organized by store (type); this is extremely useful to get the name of an object to use
• append : add an object from once OPS storage into another one; this is useful for getting everything into a single file before running a simulation

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:

• OPS documentation: http://openpathsampling.org
• OPS source code: http://github.com/openpathsampling/openpathsampling

Detailed documentation on the CLI can be found at https://openpathsampling-cli.readthedocs.io/

Testing

The OPS CLI can be installed with either pip or conda:

pip install openpathsampling-cli
# or
conda install openpathsampling-cli

Tests in the OpenPathSampling CLI use pytest. The requirements for testing are pytest and nose, both of which can also be installed with either pip or conda.

With the package and its testing tools installed, tests can be run with:

py.test --pyargs paths_cli

Examples

Basic examples of how to use the OPS CLI can be found in:

• http://openpathsampling.org/latest/cli.html
• https://gitlab.e-cam2020.eu:10443/dwhswenson/ops_tutorial/-/blob/master/5_advanced_customize_shooting.ipynb

Source Code

The source code for the OpenPathSampling CLI can be found in the its GitHub repository: http://github.com/openpathsampling/openpathsampling-cli.

This module covers the code for commands included in the OpenPathSampling CLI as of release version 0.1.

Specifically, it includes the following files, and their associated test suites:

• commands/append.py
• commands/contents.py
• commands/equilibrate.py
• commands/pathsampling.py
• commands/visit_all.py