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Command line tool for OpenPathSampling

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OpenPathSampling CLI

The command line interface to OpenPathSampling

OpenPathSampling is a powerful and flexible library for path sampling simulations. However, many users would prefer to interact with an executable on the command line, instead of writing everything in their own Python script. Here is that command line tool, including some useful scripts for dealing with OPS output files.

The CLI is used as a single executable, openpathsampling, with multiple subcommands. We recommend aliasing openpathsampling to something simpler (maybe ops?) to save typing!

Current categories of subcommands are for simulation running, and for miscellaneous operations on OPS output files.

Simulation Commands:

  • visit-all: Run MD to generate initial trajectories
  • equilibrate: Run equilibration for path sampling
  • pathsampling: Run any path sampling simulation, including TIS variants

Miscellaneous Commands:

  • contents: List named objects from an OPS .nc file
  • strip-snapshots: Remove coordinates/velocities from an OPS storage
  • append: add objects from INPUT_FILE to another file

Full documentation is at https://openpathsampling-cli.readthedocs.io/; a brief summary is below.

Installation

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

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

Note that installing the CLI will also install OpenPathSampling, if you don't already have it.

Workflow

Set up, then simulate! The overall idea is that you will first set up your simulation, and then use these scripts to run the resulting simulation setup files. Currently, writing a Python script (or better, using a Jupyter notebook to set things up interactively) is the best way to do that. Save the necessary simulation objects to a setup.nc file, and then use these scripts to run the simulation.

Creating your own commands

Creating your own commands is extremely easy. The OPS CLI uses a plug-in architecture so that installing your own commands is as easy as putting a Python file in your ~/.openpathsampling/cli-plugins/ directory. We provide a standard set of parameters as decorators, which can (and should) be re-used to load things from storage. The CLI is built on click, so additional arguments are easily added using functionality from click. See our developer documentation for details.

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