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
- 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()