w_ntop

usage:

w_ntop [-h] [-r RCFILE] [--quiet | --verbose | --debug] [--version] [-W WEST_H5FILE]
             [--first-iter N_ITER] [--last-iter N_ITER] [-a ASSIGNMENTS] [-n COUNT] [-t TIMEPOINT]
             [--highweight | --lowweight | --random] [-o OUTPUT]

Select walkers from bins . An assignment file mapping walkers to bins at each timepoint is required (see``w_assign –help`` for further information on generating this file). By default, high-weight walkers are selected (hence the name w_ntop: select the N top-weighted walkers from each bin); however, minimum weight walkers and randomly-selected walkers may be selected instead.

Output format

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

``/n_iter`` [iteration]
  *(Integer)* Iteration numbers for each entry in other datasets.

``/n_segs`` [iteration][bin]
  *(Integer)* Number of segments in each bin/state in the given iteration.
  This will generally be the same as the number requested with
  ``--n/--count`` but may be smaller if the requested number of walkers
  does not exist.

``/seg_ids`` [iteration][bin][segment]
  *(Integer)* Matching segments in each iteration for each bin.
  For an iteration ``n_iter``, only the first ``n_iter`` entries are
  valid. For example, the full list of matching seg_ids in bin 0 in the
  first stored iteration is ``seg_ids[0][0][:n_segs[0]]``.

``/weights`` [iteration][bin][segment]
  *(Floating-point)* Weights for each matching segment in ``/seg_ids``.

Command-line arguments

optional arguments:

-h, --help            show this help message and exit
--highweight          Select COUNT highest-weight walkers from each bin.
--lowweight           Select COUNT lowest-weight walkers from each bin.
--random              Select COUNT walkers randomly from each bin.

general options:

-r RCFILE, --rcfile RCFILE
                      use RCFILE as the WEST run-time configuration file (default: west.cfg)
--quiet               emit only essential information
--verbose             emit extra information
--debug               enable extra checks and emit copious information
--version             show program's version number 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).

input options:

-a ASSIGNMENTS, --assignments ASSIGNMENTS
                      Use assignments from the given ASSIGNMENTS file (default: assign.h5).

selection options:

-n COUNT, --count COUNT
                      Select COUNT walkers from each iteration for each bin (default: 1).
-t TIMEPOINT, --timepoint TIMEPOINT
                      Base selection on the given TIMEPOINT within each iteration. Default (-1)
                      corresponds to the last timepoint.

output options:

-o OUTPUT, --output OUTPUT
                      Write output to OUTPUT (default: ntop.h5).