w_fluxanl¶

w_fluxanl calculates the probability flux of a weighted ensemble simulation based on a pre-defined target state. Also calculates confidence interval of average flux. Monte Carlo bootstrapping techniques are used to account for autocorrelation between fluxes and/or errors that are not normally distributed.

Overview¶

usage:

$WEST_ROOT/bin/w_fluxanl [-h] [-r RCFILE] [--quiet | --verbose | --debug] [--version]
                         [-W WEST_H5FILE] [-o OUTPUT]
                         [--first-iter N_ITER] [--last-iter N_ITER]
                         [-a ALPHA] [--autocorrel-alpha ACALPHA] [-N NSETS] [--evol] [--evol-step ESTEP]

Note: All command line arguments are optional for w_fluxanl.

Command-Line Options¶

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

Input/output options¶

These arguments allow the user to specify where to read input simulation result data and where to output calculated progress coordinate probability distribution data.

Both input and output files are hdf5 format.:

-W, --west-data file
  Read simulation result data from file *file*. (**Default:** The
  *hdf5* file specified in the configuration file)

-o, --output file
  Store this tool's output in *file*. (**Default:** The *hdf5* file
  **pcpdist.h5**)

Iteration range options¶

Specify the range of iterations over which to construct the progress coordinate probability distribution.:

--first-iter n_iter
  Construct probability distribution starting with iteration *n_iter*
  (**Default:** 1)

--last-iter n_iter
  Construct probability distribution's time evolution up to (and
  including) iteration *n_iter* (**Default:** Last completed
  iteration)

Confidence interval and bootstrapping options¶

Specify alpha values of constructed confidence intervals.:

-a alpha
  Calculate a (1 - *alpha*) confidence interval for the mean flux
  (**Default:** 0.05)

--autocorrel-alpha ACalpha
  Identify autocorrelation of fluxes at *ACalpha* significance level.
  Note: Specifying an *ACalpha* level that is too small may result in
  failure to find autocorrelation in noisy flux signals (**Default:**
  Same level as *alpha*)

-N n_sets, --nsets n_sets
  Use *n_sets* samples for bootstrapping (**Default:** Chosen based
  on *alpha*)

--evol
  Calculate the time evolution of flux confidence intervals
  (**Warning:** computationally expensive calculation)

--evol-step estep
  (if ``'--evol'`` specified) Calculate the time evolution of flux
  confidence intervals for every *estep* iterations (**Default:** 1)

Examples¶

Calculate the time evolution flux every 5 iterations:

$WEST_ROOT/bin/w_fluxanl --evol --evol-step 5

Calculate mean flux confidence intervals at 0.01 signicance level and calculate autocorrelations at 0.05 significance:

$WEST_ROOT/bin/w_fluxanl --alpha 0.01 --autocorrel-alpha 0.05

Calculate the mean flux confidence intervals using a custom bootstrap sample size of 500:

$WEST_ROOT/bin/w_fluxanl --n-sets 500