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).