w_kinetics

WARNING: w_kinetics is being deprecated. Please use w_direct instead.

usage:

w_kinetics trace [-h] [-W WEST_H5FILE] [--first-iter N_ITER] [--last-iter N_ITER]
                       [--step-iter STEP] [-a ASSIGNMENTS] [-o OUTPUT]

Calculate state-to-state rates and transition event durations by tracing trajectories.

A bin assignment file (usually “assign.h5”) including trajectory labeling is required (see “w_assign –help” for information on generating this file).

This subcommand for w_direct is used as input for all other w_direct subcommands, which will convert the flux data in the output file into average rates/fluxes/populations with confidence intervals.

Output format

The output file (-o/–output, by default “direct.h5”) contains the following datasets:

``/conditional_fluxes`` [iteration][state][state]
  *(Floating-point)* Macrostate-to-macrostate fluxes. These are **not**
  normalized by the population of the initial macrostate.

``/conditional_arrivals`` [iteration][stateA][stateB]
  *(Integer)* Number of trajectories arriving at state *stateB* in a given
  iteration, given that they departed from *stateA*.

``/total_fluxes`` [iteration][state]
  *(Floating-point)* Total flux into a given macrostate.

``/arrivals`` [iteration][state]
  *(Integer)* Number of trajectories arriving at a given state in a given
  iteration, regardless of where they originated.

``/duration_count`` [iteration]
  *(Integer)* The number of event durations recorded in each iteration.

``/durations`` [iteration][event duration]
  *(Structured -- see below)*  Event durations for transition events ending
  during a given iteration. These are stored as follows:

    istate
      *(Integer)* Initial state of transition event.
    fstate
      *(Integer)* Final state of transition event.
    duration
      *(Floating-point)* Duration of transition, in units of tau.
    weight
      *(Floating-point)* Weight of trajectory at end of transition, **not**
      normalized by initial state population.

Because state-to-state fluxes stored in this file are not normalized by initial macrostate population, they cannot be used as rates without further processing. The w_direct kinetics command is used to perform this normalization while taking statistical fluctuation and correlation into account. See w_direct kinetics --help for more information. Target fluxes (total flux into a given state) require no such normalization.

Command-line options

optional arguments:

-h, --help            show this help message and exit

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).

iteration range:

--first-iter N_ITER   Begin analysis at iteration N_ITER (default: 1).
--last-iter N_ITER    Conclude analysis with N_ITER, inclusive (default: last completed iteration).
--step-iter STEP      Analyze/report in blocks of STEP iterations.

input/output options:

-a ASSIGNMENTS, --assignments ASSIGNMENTS
                      Bin assignments and macrostate definitions are in ASSIGNMENTS (default:
                      assign.h5).
-o OUTPUT, --output OUTPUT
                      Store results in OUTPUT (default: kintrace.h5).