w_init

w_init initializes the weighted ensemble simulation, creates the main HDF5 file and prepares the first iteration.

Overview

Usage:

w_init [-h] [-r RCFILE] [--quiet | --verbose | --debug] [--version]
             [--force] [--bstate-file BSTATE_FILE] [--bstate BSTATES]
             [--tstate-file TSTATE_FILE] [--tstate TSTATES]
             [--segs-per-state N] [--no-we] [--wm-work-manager WORK_MANAGER]
             [--wm-n-workers N_WORKERS] [--wm-zmq-mode MODE]
             [--wm-zmq-info INFO_FILE] [--wm-zmq-task-endpoint TASK_ENDPOINT]
             [--wm-zmq-result-endpoint RESULT_ENDPOINT]
             [--wm-zmq-announce-endpoint ANNOUNCE_ENDPOINT]
             [--wm-zmq-heartbeat-interval INTERVAL]
             [--wm-zmq-task-timeout TIMEOUT] [--wm-zmq-client-comm-mode MODE]

Initialize a new WEST simulation, creating the WEST HDF5 file and preparing the first iteration’s segments. Initial states are generated from one or more “basis states” which are specified either in a file specified with --bstates-from, or by one or more --bstate arguments. If neither --bstates-from nor at least one --bstate argument is provided, then a default basis state of probability one identified by the state ID zero and label “basis” will be created (a warning will be printed in this case, to remind you of this behavior, in case it is not what you wanted). Target states for (non- equilibrium) steady-state simulations are specified either in a file specified with --tstates-from, or by one or more --tstate arguments. If neither --tstates-from nor at least one --tstate argument is provided, then an equilibrium simulation (without any sinks) will be performed.

Command-Line Options

See the general command-line tool reference for more information on the general options.

State Options

--force
  Overwrites any existing simulation data

--bstate BSTATES
  Add the given basis state (specified as a string
  'label,probability[,auxref]') to the list of basis states (after
  those specified in --bstates-from, 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.

--bstate-file BSTATE_FILE, --bstates-from BSTATE_FILE
  Read basis state names, probabilities, and (optionally) data
  references from BSTATE_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.

--tstate-file TSTATE_FILE, --tstates-from TSTATE_FILE
  Read target state names and representative progress coordinates from
  TSTATE_FILE. WESTPA uses the representative progress coordinate of a target state and
  converts the **entire** bin containing that progress coordinate into a
  recycling sink.

--segs-per-state N
  Initialize N segments from each basis state (default: 1).

--no-we, --shotgun
  Do not run the weighted ensemble bin/split/merge algorithm on
  newly-created segments.

Examples

(TODO: write 3 examples; Setting up the basis states, explanation of bstates and istates. Setting up an equilibrium simulation, w/o target(s) for recycling. Setting up a simulation with one/multiple target states.)

westpa.cli.core.w_init module

class westpa.cli.core.w_init.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).

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

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

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

class westpa.cli.core.w_init.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_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.

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

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

westpa.cli.core.w_init.entry_point()

westpa.cli.core.w_init.initialize(tstates, tstate_file, bstates, bstate_file, sstates=None, sstate_file=None, segs_per_state=1, shotgun=False)

Initialize a WESTPA simulation.

tstates : list of str

tstate_file : str

bstates : list of str

bstate_file : str

sstates : list of str

sstate_file : str

segs_per_state : int

shotgun : bool