w_states

usage:

w_states [-h] [-r RCFILE] [--quiet | --verbose | --debug] [--version]
               [--show | --append | --replace] [--bstate-file BSTATE_FILE] [--bstate BSTATES]
               [--tstate-file TSTATE_FILE] [--tstate TSTATES]
               [--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]

Display or manipulate basis (initial) or target (recycling) states for a WEST simulation. By default, states are displayed (or dumped to files). If --replace is specified, all basis/target states are replaced for the next iteration. If --append is specified, the given target state(s) are appended to the list for the next iteration. Appending basis states is not permitted, as this would require renormalizing basis state probabilities in ways that may be error-prone. Instead, use w_states --show --bstate-file=bstates.txt and then edit the resulting bstates.txt file to include the new desired basis states, then use w_states --replace --bstate-file=bstates.txt to update the WEST HDF5 file appropriately.

optional arguments:

-h, --help            show this help message and exit
--bstate-file BSTATE_FILE
                      Read (--append/--replace) or write (--show) basis state names, probabilities, and
                      data references from/to BSTATE_FILE.
--bstate BSTATES      Add the given basis state (specified as a string 'label,probability[,auxref]') to
                      the list of basis states (after those specified in --bstate-file, if any). This
                      argument may be specified more than once, in which case the given states are
                      appended in the order they are given on the command line.
--tstate-file TSTATE_FILE
                      Read (--append/--replace) or write (--show) target state names and representative
                      progress coordinates from/to TSTATE_FILE
--tstate TSTATES      Add the given target state (specified as a string 'label,pcoord0[,pcoord1[,...]]')
                      to the list of target states (after those specified in the file given by
                      --tstates-from, if any). This argument may be specified more than once, in which
                      case the given states are appended in the order they appear on the command line.

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

modes of operation:

--show                Display current basis/target states (or dump to files).
--append              Append the given basis/target states to those currently in use.
--replace             Replace current basis/target states with those specified.

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 'serial'
--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.core.w_states module

westpa.cli.core.w_states.make_work_manager(): Using cues from the environment, instantiate a pre-configured work manager.

class westpa.cli.core.w_states.Segment(n_iter=None, seg_id=None, weight=None, endpoint_type=None, parent_id=None, wtg_parent_ids=None, pcoord=None, status=None, walltime=None, cputime=None, data=None)

Bases: object

A class wrapping segment data that must be passed through the work manager or data manager. Most fields are self-explanatory. One item worth noting is that a negative parent ID means that the segment starts from the initial state with ID -(segment.parent_id+1)

SEG_STATUS_UNSET = 0

SEG_STATUS_PREPARED = 1

SEG_STATUS_COMPLETE = 2

SEG_STATUS_FAILED = 3

SEG_INITPOINT_UNSET = 0

SEG_INITPOINT_CONTINUES = 1

SEG_INITPOINT_NEWTRAJ = 2

SEG_ENDPOINT_UNSET = 0

SEG_ENDPOINT_CONTINUES = 1

SEG_ENDPOINT_MERGED = 2

SEG_ENDPOINT_RECYCLED = 3

statuses = {'SEG_STATUS_COMPLETE': 2, 'SEG_STATUS_FAILED': 3, 'SEG_STATUS_PREPARED': 1, 'SEG_STATUS_UNSET': 0}

initpoint_types = {'SEG_INITPOINT_CONTINUES': 1, 'SEG_INITPOINT_NEWTRAJ': 2, 'SEG_INITPOINT_UNSET': 0}

endpoint_types = {'SEG_ENDPOINT_CONTINUES': 1, 'SEG_ENDPOINT_MERGED': 2, 'SEG_ENDPOINT_RECYCLED': 3, 'SEG_ENDPOINT_UNSET': 0}

status_names = {0: 'SEG_STATUS_UNSET', 1: 'SEG_STATUS_PREPARED', 2: 'SEG_STATUS_COMPLETE', 3: 'SEG_STATUS_FAILED'}

initpoint_type_names = {0: 'SEG_INITPOINT_UNSET', 1: 'SEG_INITPOINT_CONTINUES', 2: 'SEG_INITPOINT_NEWTRAJ'}

endpoint_type_names = {0: 'SEG_ENDPOINT_UNSET', 1: 'SEG_ENDPOINT_CONTINUES', 2: 'SEG_ENDPOINT_MERGED', 3: 'SEG_ENDPOINT_RECYCLED'}

static initial_pcoord(segment): Return the initial progress coordinate point of this segment.

static final_pcoord(segment): Return the final progress coordinate point of this segment.

property initpoint_type

property initial_state_id

property status_text

property endpoint_type_text

class westpa.cli.core.w_states.BasisState(label, probability, pcoord=None, auxref=None, state_id=None)

Bases: object

Describes an basis (micro)state. These basis states are used to generate initial states for new trajectories, either at the beginning of the simulation (i.e. at w_init) or due to recycling.

Variables:

state_id – Integer identifier of this state, usually set by the data manager.
label – A descriptive label for this microstate (may be empty)
probability – Probability of this state to be selected when creating a new trajectory.
pcoord – The representative progress coordinate of this state.
auxref – A user-provided (string) reference for locating data associated with this state (usually a filesystem path).

classmethod states_to_file(states, fileobj): Write a file defining basis states, which may then be read by states_from_file().

classmethod states_from_file(statefile)

Read a file defining basis states. Each line defines a state, and contains a label, the probability, and optionally a data reference, separated by whitespace, as in:

unbound    1.0

or:

unbound_0    0.6        state0.pdb
unbound_1    0.4        state1.pdb

as_numpy_record(): Return the data for this state as a numpy record array.

class westpa.cli.core.w_states.TargetState(label, pcoord, state_id=None)

Bases: object

Describes a target state.

Variables:

state_id – Integer identifier of this state, usually set by the data manager.
label – A descriptive label for this microstate (may be empty)
pcoord – The representative progress coordinate of this state.

classmethod states_to_file(states, fileobj): Write a file defining basis states, which may then be read by states_from_file().

classmethod states_from_file(statefile, dtype)

Read a file defining target states. Each line defines a state, and contains a label followed by a representative progress coordinate value, separated by whitespace, as in:

bound     0.02

for a single target and one-dimensional progress coordinates or:

bound    2.7    0.0
drift    100    50.0

for two targets and a two-dimensional progress coordinate.

westpa.cli.core.w_states.entry_point()

westpa.cli.core.w_states.initialize(mode, bstates, _bstate_file, tstates, _tstate_file)