w_red

usage:

w_red [-h] [-r RCFILE] [--quiet] [--verbose] [--version] [--max-queue-length MAX_QUEUE_LENGTH]
            [--debug] [--terminal]
            [--serial | --parallel | --work-manager WORK_MANAGER] [--n-workers N_WORKERS]
            [--zmq-mode MODE] [--zmq-comm-mode COMM_MODE] [--zmq-write-host-info INFO_FILE]
            [--zmq-read-host-info INFO_FILE] [--zmq-upstream-rr-endpoint ENDPOINT]
            [--zmq-upstream-ann-endpoint ENDPOINT] [--zmq-downstream-rr-endpoint ENDPOINT]
            [--zmq-downstream-ann-endpoint ENDPOINT] [--zmq-master-heartbeat MASTER_HEARTBEAT]
            [--zmq-worker-heartbeat WORKER_HEARTBEAT] [--zmq-timeout-factor FACTOR]
            [--zmq-startup-timeout STARTUP_TIMEOUT] [--zmq-shutdown-timeout SHUTDOWN_TIMEOUT]

optional arguments:

-h, --help            show this help message and exit

general options:

-r RCFILE, --rcfile RCFILE: use RCFILE as the WEST run-time configuration file (default: west.cfg)
--quiet: emit only essential information
--verbose: emit extra information
--version: show program’s version number and exit

parallelization options:

--max-queue-length MAX_QUEUE_LENGTH
                      Maximum number of tasks that can be queued. Useful to limit RAM use for tasks that
                      have very large requests/response. Default: no limit.

parallelization options:

--serial              run in serial mode
--parallel            run in parallel mode (using processes)
--work-manager WORK_MANAGER

westpa.cli.tools.w_red module

westpa.cli.tools.w_red.H5File: alias of File

class westpa.cli.tools.w_red.WESTParallelTool(wm_env=None)

Bases: WESTTool

Base class for command-line tools parallelized with wwmgr. This automatically adds and processes wwmgr command-line arguments and creates a work manager at self.work_manager.

make_parser_and_process(prog=None, usage=None, description=None, epilog=None, args=None): A convenience function to create a parser, call add_all_args(), and then call process_all_args(). The argument namespace is returned.

add_args(parser): Add arguments specific to this tool to the given argparse parser.

process_args(args): Take argparse-processed arguments associated with this tool and deal with them appropriately (setting instance variables, etc)

go(): Perform the analysis associated with this tool.

main(): A convenience function to make a parser, parse and process arguments, then run self.go() in the master process.

class westpa.cli.tools.w_red.DurationCorrector(durations, weights, dtau, maxduration=None)

Bases: object

static from_kinetics_file(directh5, istate, fstate, dtau, n_iters=None)

property event_duration_histogram

property cumulative_event_duration_histogram

correction(iters, freqs=None)

Return the correction factor

t=theta tau=t |

|     |                 |
|       | ~                 |
|       | f(tau) dtau dt    |      * maxduration

| | |

t=0 tau=0 |

|_ _|

where: ~` ^ f(tau) is proportional to f(tau)/(theta-tau), and is normalized to

^

integrate to 1, and f(tau) is sum of the weights of walkers with duration time tau.

westpa.cli.tools.w_red.get_raw_rates(directh5, istate, fstate, n_iters=None)

westpa.cli.tools.w_red.calc_avg_rate(directh5_path, istate, fstate, **kwargs)

Return the raw or RED-corrected rate constant with the confidence interval.

Parameters:

nstiter (duration of each iteration (number of steps))
ntpr (report inteval (number of steps))

westpa.cli.tools.w_red.calc_rates(directh5_path, istate, fstate, **kwargs)

Return the raw and RED-corrected rate constants vs. iterations. This code is faster than calling calc_rate() iteratively

Parameters:

nstiter (duration of each iteration (number of steps))
ntpr (report inteval (number of steps))

class westpa.cli.tools.w_red.RateCalculator(directh5, istate, fstate, assignh5=None, **kwargs)

Bases: object

property conditional_fluxes

property populations

property tau

property dtau

property istate

property fstate

property n_iters

calc_rate(i_iter=None, red=False, **kwargs)

calc_rates(n_iters=None, **kwargs)

class westpa.cli.tools.w_red.WRed

Bases: WESTParallelTool

prog = 'w_red'

description = 'Apply the RED scheme to estimate steady-state WE fluxes from\nshorter trajectories.\n\n-----------------------------------------------------------------------------\nSource data\n-----------------------------------------------------------------------------\n\nSource data is provided as a w_ipa "scheme" which is typically defined\nin the west.cfg file. For instance, if a user wishes to estimate RED\nfluxes for a scheme named "DEFAULT" that argument would be provided\nto w_red and WRed would estimate RED fluxes based off of the data\ncontained in the assign.h5 and direct.h5 files in ANALYSIS/DEFAULT.\n\n'

go(): Perform the analysis associated with this tool.

westpa.cli.tools.w_red.entry_point()