OpenPathSampling CLI Commands¶
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 lineequilibrate
: run equilibration for path sampling (until first decorrelated trajectory); must provide move scheme and initial conditions on the command linepathsampling
: 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 useappend
: 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
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