Command line tool for OpenPathSampling
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.
visit-all: Run MD to generate initial trajectories
equilibrate: Run equilibration for path sampling
pathsampling: Run any path sampling simulation, including TIS variants
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.
The OPS CLI can be installed with either
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.
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
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
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
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
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