Full CLI

This is a full description of the commands available in the CLI, automatically generated from the help for each command. Note that this currently gives all commands alphabetically, without regard to section. In general, this is not yet well-organized; contributions to improve that would be appreciated.

openpathsampling

OpenPathSampling is a Python library for path sampling simulations. This command line tool facilitates common tasks when working with OpenPathSampling. To use it, use one of the subcommands below. For example, you can get more information about the pathsampling tool with:

openpathsampling pathsampling –help

openpathsampling [OPTIONS] COMMAND [ARGS]...

Options

--log <log>

logging configuration file

append

Append objects from INPUT_FILE to another file.

openpathsampling append [OPTIONS] INPUT_FILE

Options

-a, --append-file <append_file>

Required file to append to

--engine <engine>

name or index of engine; may be used more than once

--cv <cv>

name of CV; may be used more than once

--volume <volume>

name or index of volume; may be used more than once

--network <network>

name or index of network; may be used more than once

--scheme <scheme>

name or index of move scheme; may be used more than once

--tag <tag>

tag for object; may be used more than once

--save-tag <save_tag>

save object to a tag; requires that only one object be specfied. Can also be used to rename tagged objects. To append a tagged object without a tag, use –save-tag “”

Arguments

INPUT_FILE

Required argument

contents

List the names of named objects in an OPS .nc file.

This is particularly useful when getting ready to use one of simulation scripts (i.e., to identify exactly how a state or engine is named.)

openpathsampling contents [OPTIONS] INPUT_FILE

Options

--table <table>

table to show results from

Arguments

INPUT_FILE

Required argument

equilibrate

Run path sampling equilibration, based on INPUT_FILE.

This just runs the normal path sampling simulation, but the number of steps depends on how long it takes to create a fully decorrelated sample set (no frames from the initial trajectories are still active).

If N_DECORR is the number of steps to fully decorrelate, the total number of steps run is: N_DECORR * MULTIPLIER + EXTRA_STEPS

openpathsampling equilibrate [OPTIONS] INPUT_FILE

Options

-o, --output-file <output_file>

Required output ncfile

-m, --scheme <scheme>

identifier for the move scheme

-t, --init-conds <init_conds>

identifier for initial conditions (sample set or trajectory); may be used more than once

--multiplier <multiplier>

run number of steps equal to MULTIPLIER times the number of stepss to decorrelate

--extra-steps <extra_steps>

run EXTRA-STEPS additional steps

Arguments

INPUT_FILE

Required argument

md

Run MD for for time of steps or until ensembles are satisfied.

This can either take a –nsteps or –ensemble, but not both. If the –ensemble option is specfied more than once, then this will attempt to run until all ensembles are satisfied by a subtrajectory.

This still respects the maximum number of frames as set in the engine, and will terminate if the trajectory gets longer than that.

openpathsampling md [OPTIONS] INPUT_FILE

Options

-o, --output-file <output_file>

Required output ncfile

-e, --engine <engine>

identifer for the engine

--ensemble <ensemble>

name of index of ensemble; may be used more than once

-n, --nsteps <nsteps>

number of MD steps to run

-f, --init-frame <init_frame>

identifier for initial snapshot

Arguments

INPUT_FILE

Required argument

pathsampling

General path sampling, using setup in INPUT_FILE

openpathsampling pathsampling [OPTIONS] INPUT_FILE

Options

-o, --output-file <output_file>

Required output ncfile

-m, --scheme <scheme>

identifier for the move scheme

-t, --init-conds <init_conds>

identifier for initial conditions (sample set or trajectory); may be used more than once

-n, --nsteps <nsteps>

number of Monte Carlo trials to run

Arguments

INPUT_FILE

Required argument

visit-all

Run until initial trajectory for TPS/MSTPS/MSTIS achieved.

This runs until all given states have been visited. That creates a long trajectory, subtrajectories of which will work for the initial trajectories in TPS, MSTPS, or MSTIS. Typically, you’ll use a different engine from the TPS production engine (often high temperature).

openpathsampling visit-all [OPTIONS] INPUT_FILE

Options

-o, --output-file <output_file>

Required output ncfile

-s, --state <state>

Required name of state; may be used more than once

-e, --engine <engine>

identifer for the engine

-f, --init-frame <init_frame>

identifier for initial snapshot

Arguments

INPUT_FILE

Required argument