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).