w_kinavg
WARNING: w_kinavg is being deprecated. Please use w_direct instead.
usage:
w_kinavg trace [-h] [-W WEST_H5FILE] [--first-iter N_ITER] [--last-iter N_ITER] [--step-iter STEP]
[-a ASSIGNMENTS] [-o OUTPUT] [-k KINETICS] [--disable-bootstrap] [--disable-correl]
[--alpha ALPHA] [--autocorrel-alpha ACALPHA] [--nsets NSETS]
[-e {cumulative,blocked,none}] [--window-frac WINDOW_FRAC] [--disable-averages]
Calculate average rates/fluxes and associated errors from weighted ensemble data. Bin assignments (usually “assign.h5”) and kinetics data (usually “direct.h5”) data files must have been previously generated (see “w_assign –help” and “w_direct init –help” for information on generating these files).
The evolution of all datasets may be calculated, with or without confidence intervals.
Output format
The output file (-o/–output, usually “direct.h5”) contains the following dataset:
/avg_rates [state,state]
(Structured -- see below) State-to-state rates based on entire window of
iterations selected.
/avg_total_fluxes [state]
(Structured -- see below) Total fluxes into each state based on entire
window of iterations selected.
/avg_conditional_fluxes [state,state]
(Structured -- see below) State-to-state fluxes based on entire window of
iterations selected.
If –evolution-mode is specified, then the following additional datasets are available:
/rate_evolution [window][state][state]
(Structured -- see below). State-to-state rates based on windows of
iterations of varying width. If --evolution-mode=cumulative, then
these windows all begin at the iteration specified with
--start-iter and grow in length by --step-iter for each successive
element. If --evolution-mode=blocked, then these windows are all of
width --step-iter (excluding the last, which may be shorter), the first
of which begins at iteration --start-iter.
/target_flux_evolution [window,state]
(Structured -- see below). Total flux into a given macro state based on
windows of iterations of varying width, as in /rate_evolution.
/conditional_flux_evolution [window,state,state]
(Structured -- see below). State-to-state fluxes based on windows of
varying width, as in /rate_evolution.
The structure of these datasets is as follows:
iter_start
(Integer) Iteration at which the averaging window begins (inclusive).
iter_stop
(Integer) Iteration at which the averaging window ends (exclusive).
expected
(Floating-point) Expected (mean) value of the observable as evaluated within
this window, in units of inverse tau.
ci_lbound
(Floating-point) Lower bound of the confidence interval of the observable
within this window, in units of inverse tau.
ci_ubound
(Floating-point) Upper bound of the confidence interval of the observable
within this window, in units of inverse tau.
stderr
(Floating-point) The standard error of the mean of the observable
within this window, in units of inverse tau.
corr_len
(Integer) Correlation length of the observable within this window, in units
of tau.
Each of these datasets is also stamped with a number of attributes:
mcbs_alpha
(Floating-point) Alpha value of confidence intervals. (For example,
*alpha=0.05* corresponds to a 95% confidence interval.)
mcbs_nsets
(Integer) Number of bootstrap data sets used in generating confidence
intervals.
mcbs_acalpha
(Floating-point) Alpha value for determining correlation lengths.
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: kinavg.h5).
input/output options:
-k KINETICS, --kinetics KINETICS
Populations and transition rates are stored in KINETICS (default: kintrace.h5).
confidence interval calculation options:
--disable-bootstrap, -db
Enable the use of Monte Carlo Block Bootstrapping.
--disable-correl, -dc
Disable the correlation analysis.
--alpha ALPHA Calculate a (1-ALPHA) confidence interval' (default: 0.05)
--autocorrel-alpha ACALPHA
Evaluate autocorrelation to (1-ACALPHA) significance. Note that too small an
ACALPHA will result in failure to detect autocorrelation in a noisy flux signal.
(Default: same as ALPHA.)
--nsets NSETS Use NSETS samples for bootstrapping (default: chosen based on ALPHA)
calculation options:
-e {cumulative,blocked,none}, --evolution-mode {cumulative,blocked,none}
How to calculate time evolution of rate estimates. ``cumulative`` evaluates rates
over windows starting with --start-iter and getting progressively wider to --stop-
iter by steps of --step-iter. ``blocked`` evaluates rates over windows of width
--step-iter, the first of which begins at --start-iter. ``none`` (the default)
disables calculation of the time evolution of rate estimates.
--window-frac WINDOW_FRAC
Fraction of iterations to use in each window when running in ``cumulative`` mode.
The (1 - frac) fraction of iterations will be discarded from the start of each
window.
misc options:
--disable-averages, -da
Whether or not the averages should be printed to the console (set to FALSE if flag
is used).