man:w_bins - westpa/westpa GitHub Wiki

By Ali Sinan Saglam

w_bins deals with binning modification and statistics

Table of Contents Overview Command-Line Options Options Under 'info' Options Under 'rebin' Binning options for 'rebin' Input Options Examples

Usage:

 w_bins [-h] [-r RCFILE] [--quiet | --verbose | --debug] [--version]
              [-W WEST_H5FILE]
              {info,rebin} ...

Display information and statistics about binning in a WEST simulation, or modify the binning for the current iteration of a WEST simulation.

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

Usage:

 w_bins info [-h] [-n N_ITER] [--detail]
                   [--bins-from-system | --bins-from-expr BINS_FROM_EXPR | --bins-from-function BINS_FROM_FUNCTION | --bins-from-file]

Positional option;

'''info'''

Display information about binning.

Options for 'info';

'''-n ''N_ITER,''''' '''--n-iter ''N_ITER'''''

Consider initial points of segment N_ITER (default: current iteration).

'''--detail'''

Display detailed per-bin information in addition to summary information.

Binning options for 'info';

'''--bins-from-system'''

Bins are constructed by the system driver specified in the WEST configuration file (default where stored bin definitions not available).

'''--bins-from-expr ''BINS_FROM_EXPR,''''' '''--binbounds ''BINS_FROM_EXPR'''''

Construct bins on a rectilinear grid according to the given BINEXPR. This must be a list of lists of bin boundaries (one list of bin boundaries for each dimension of the progress coordinate), formatted as a Python expression. E.g. "[[0,1,2,4,inf],[-inf,0,inf]]". The numpy module and the special symbol "inf" (for floating-point infinity) are available for use within BINEXPR.

'''-n ''N_ITER,''''' '''--n-iter ''N_ITER'''''

Consider initial points of segment N_ITER (default: current iteration).

'''--bins-from-function ''BINS_FROM_FUNCTION,''''' '''--binfunc ''BINS_FROM_FUNCTION'''''

Supply an external function which, when called, returns a properly constructed bin mapper which will then be used for bin assignments. This should be formatted as "[PATH:]MODULE.FUNC", where the function FUNC in module MODULE will be used; the optional PATH will be prepended to the module search path when loading MODULE.

'''--bins-from-file'''

Load bin specification from the data file being examined (default where stored bin definitions available).

Usage:

 w_bins rebin [-h] [--confirm] [--detail]
                    [--bins-from-system | --bins-from-expr BINS_FROM_EXPR | --bins-from-function BINS_FROM_FUNCTION]
                    [--target-counts TARGET_COUNTS | --target-counts-from FILENAME]

Positional option;

'''rebin'''

Rebuild current iteration with new binning.

Options for 'rebin';

'''--confirm'''

Commit the revised iteration to HDF5; without this option, the effects of the new binning are only calculated and printed.

'''--detail'''

Display detailed per-bin information in addition to summary information.

'''-n ''N_ITER,''''' '''--n-iter ''N_ITER'''''

Consider initial points of segment N_ITER (default: current iteration).

Same as the binning options for 'info'.

Bin target count options for 'rebin';

'''--target-counts ''TARGET_COUNTS'''''

Use TARGET_COUNTS instead of stored or system driver target counts. TARGET_COUNTS is a comma-separated list of integers. As a special case, a single integer is acceptable, in which case the same target count is used for all bins.

'''--target-counts-from ''FILENAME'''''

Read target counts from the text file FILENAME instead of using stored or system driver target counts. FILENAME must contain a list of integers, separated by arbitrary whitespace (including newlines).

'''-W ''WEST_H5FILE,''''' '''--west_data''WEST_H5FILE'''''

Take WEST data from WEST_H5FILE (default: read from the HDF5 file specified in west.cfg).

(TODO: Write up an example)