w_eddist ======== usage:: w_eddist [-h] [-r RCFILE] [--quiet | --verbose | --debug] [--version] [--max-queue-length MAX_QUEUE_LENGTH] [-b BINEXPR] [-C] [--loose] --istate ISTATE --fstate FSTATE [--first-iter ITER_START] [--last-iter ITER_STOP] [-k KINETICS] [-o OUTPUT] [--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] Calculate time-resolved transition-event duration distribution from kinetics results Source data ----------- Source data is collected from the results of 'w_kinetics trace' (see w_kinetics trace --help for more information on generating this dataset). Histogram binning ----------------- By default, histograms are constructed with 100 bins in each dimension. This can be overridden by specifying -b/--bins, which accepts a number of different kinds of arguments:: a single integer N N uniformly spaced bins will be used in each dimension. a sequence of integers N1,N2,... (comma-separated) N1 uniformly spaced bins will be used for the first dimension, N2 for the second, and so on. a list of lists [[B11, B12, B13, ...], [B21, B22, B23, ...], ...] The bin boundaries B11, B12, B13, ... will be used for the first dimension, B21, B22, B23, ... for the second dimension, and so on. These bin boundaries need not be uniformly spaced. These expressions will be evaluated with Python's ``eval`` construct, with ``np`` available for use [e.g. to specify bins using np.arange()]. The first two forms (integer, list of integers) will trigger a scan of all data in each dimension in order to determine the minimum and maximum values, which may be very expensive for large datasets. This can be avoided by explicitly providing bin boundaries using the list-of-lists form. Note that these bins are *NOT* at all related to the bins used to drive WE sampling. Output format ------------- The output file produced (specified by -o/--output, defaulting to "pdist.h5") may be fed to plothist to generate plots (or appropriately processed text or HDF5 files) from this data. In short, the following datasets are created:: ``histograms`` Normalized histograms. The first axis corresponds to iteration, and remaining axes correspond to dimensions of the input dataset. ``/binbounds_0`` Vector of bin boundaries for the first (index 0) dimension. Additional datasets similarly named (/binbounds_1, /binbounds_2, ...) are created for additional dimensions. ``/midpoints_0`` Vector of bin midpoints for the first (index 0) dimension. Additional datasets similarly named are created for additional dimensions. ``n_iter`` Vector of iteration numbers corresponding to the stored histograms (i.e. the first axis of the ``histograms`` dataset). Subsequent processing --------------------- The output generated by this program (-o/--output, default "pdist.h5") may be plotted by the ``plothist`` program. See ``plothist --help`` for more information. Parallelization --------------- This tool supports parallelized binning, including reading of input data. Parallel processing is the default. For simple cases (reading pre-computed input data, modest numbers of segments), serial processing (--serial) may be more efficient. Command-line options -------------------- optional arguments:: -h, --help show this help message and exit -b BINEXPR, --bins BINEXPR Use BINEXPR for bins. This may be an integer, which will be used for each dimension of the progress coordinate; a list of integers (formatted as [n1,n2,...]) which will use n1 bins for the first dimension, n2 for the second dimension, and so on; or a list of lists of boundaries (formatted as [[a1, a2, ...], [b1, b2, ...], ... ]), which will use [a1, a2, ...] as bin boundaries for the first dimension, [b1, b2, ...] as bin boundaries for the second dimension, and so on. (Default: 100 bins in each dimension.) -C, --compress Compress histograms. May make storage of higher-dimensional histograms more tractable, at the (possible extreme) expense of increased analysis time. (Default: no compression.) --loose Ignore values that do not fall within bins. (Risky, as this can make buggy bin boundaries appear as reasonable data. Only use if you are sure of your bin boundary specification.) --istate ISTATE Initial state defining transition event --fstate FSTATE Final state defining transition event 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 --debug enable extra checks and emit copious 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. iteration range options:: --first-iter ITER_START Iteration to begin analysis (default: 1) --last-iter ITER_STOP Iteration to end analysis input/output options:: -k KINETICS, --kinetics KINETICS Populations and transition rates (including evolution) are stored in KINETICS (default: kintrace.h5). -o OUTPUT, --output OUTPUT Store results in OUTPUT (default: eddist.h5). 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\_eddist module --------------------------------- .. automodule:: westpa.cli.tools.w_eddist :members: :undoc-members: :show-inheritance: :imported-members: