w_ipa ===== The ``w_ipa`` is a (beta) WESTPA tool that automates analysis using analysis schemes and enables interactive analysis of WESTPA simulation data. The tool can do a variety of different types of analysis, including the following: * Calculate fluxes and rate constants * Adjust and use alternate state definitions * Trace trajectory segments, including statistical weights, position along the progress coordinate, and other auxiliary data * Plot all of the above in the terminal! If you are using ``w_ipa`` for kinetics automated kinetics analysis, keep in mind that ``w_ipa`` is running ``w_assign`` and ``w_direct`` using the scheme designated in your ``west.cfg`` file. For more diverse kinetics analysis options, consider using ``w_assign`` and ``w_direct`` manually. This can be useful if you'd like to use auxiliary coordinates that aren't your progress coordinate, in one or two dimension options. usage:: w_ipa [-h] [-r RCFILE] [--quiet] [--verbose] [--version] [--max-queue-length MAX_QUEUE_LENGTH] [-W WEST_H5FILE] [--analysis-only] [--reanalyze] [--ignore-hash] [--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. WEST input data options: -W WEST_H5FILE, --west-data WEST_H5FILE Take WEST data from WEST_H5FILE (default: read from the HDF5 file specified in west.cfg). runtime options:: --analysis-only, -ao Use this flag to run the analysis and return to the terminal. --reanalyze, -ra Use this flag to delete the existing files and reanalyze. --ignore-hash, -ih Ignore hash and don't regenerate files. --debug, -d Debug output largely intended for development. --terminal, -t Plot output in terminal. parallelization options:: --serial run in serial mode --parallel run in parallel mode (using processes) --work-manager WORK_MANAGER use the given work manager for parallel task distribution. Available work managers are ('serial', 'threads', 'processes', 'zmq'); default is 'processes' --n-workers N_WORKERS Use up to N_WORKERS on this host, for work managers which support this option. Use 0 for a dedicated server. (Ignored by work managers which do not support this option.) options for ZeroMQ ("zmq") work manager (master or node):: --zmq-mode MODE Operate as a master (server) or a node (workers/client). "server" is a deprecated synonym for "master" and "client" is a deprecated synonym for "node". --zmq-comm-mode COMM_MODE Use the given communication mode -- TCP or IPC (Unix-domain) -- sockets for communication within a node. IPC (the default) may be more efficient but is not available on (exceptionally rare) systems without node-local storage (e.g. /tmp); on such systems, TCP may be used instead. --zmq-write-host-info INFO_FILE Store hostname and port information needed to connect to this instance in INFO_FILE. This allows the master and nodes assisting in coordinating the communication of other nodes to choose ports randomly. Downstream nodes read this file with --zmq-read-host-info and know where how to connect. --zmq-read-host-info INFO_FILE Read hostname and port information needed to connect to the master (or other coordinating node) from INFO_FILE. This allows the master and nodes assisting in coordinating the communication of other nodes to choose ports randomly, writing that information with --zmq-write-host-info for this instance to read. --zmq-upstream-rr-endpoint ENDPOINT ZeroMQ endpoint to which to send request/response (task and result) traffic toward the master. --zmq-upstream-ann-endpoint ENDPOINT ZeroMQ endpoint on which to receive announcement (heartbeat and shutdown notification) traffic from the master. --zmq-downstream-rr-endpoint ENDPOINT ZeroMQ endpoint on which to listen for request/response (task and result) traffic from subsidiary workers. --zmq-downstream-ann-endpoint ENDPOINT ZeroMQ endpoint on which to send announcement (heartbeat and shutdown notification) traffic toward workers. --zmq-master-heartbeat MASTER_HEARTBEAT Every MASTER_HEARTBEAT seconds, the master announces its presence to workers. --zmq-worker-heartbeat WORKER_HEARTBEAT Every WORKER_HEARTBEAT seconds, workers announce their presence to the master. --zmq-timeout-factor FACTOR Scaling factor for heartbeat timeouts. If the master doesn't hear from a worker in WORKER_HEARTBEAT*FACTOR, the worker is assumed to have crashed. If a worker doesn't hear from the master in MASTER_HEARTBEAT*FACTOR seconds, the master is assumed to have crashed. Both cases result in shutdown. --zmq-startup-timeout STARTUP_TIMEOUT Amount of time (in seconds) to wait for communication between the master and at least one worker. This may need to be changed on very large, heavily-loaded computer systems that start all processes simultaneously. --zmq-shutdown-timeout SHUTDOWN_TIMEOUT Amount of time (in seconds) to wait for workers to shut down. westpa.cli.tools.w\_ipa module -------------------------------- .. automodule:: westpa.cli.tools.w_ipa :members: :undoc-members: :show-inheritance: :imported-members: