w_succ

usage:

w_succ [-h] [-r RCFILE] [--quiet | --verbose | --debug] [--version] [-A H5FILE] [-W WEST_H5FILE]
             [-o OUTPUT_FILE]

List segments which successfully reach a target state.

optional arguments:

-h, --help            show this help message and exit
-o OUTPUT_FILE, --output OUTPUT_FILE
                      Store output in OUTPUT_FILE (default: write to standard output).

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

general analysis options:

-A H5FILE, --analysis-file H5FILE
                      Store intermediate and final results in H5FILE (default: analysis.h5).

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).

westpa.cli.core.w_succ module

class westpa.cli.core.w_succ.Segment(n_iter=None, seg_id=None, weight=None, endpoint_type=None, parent_id=None, wtg_parent_ids=None, pcoord=None, status=None, walltime=None, cputime=None, data=None)

Bases: object

A class wrapping segment data that must be passed through the work manager or data manager. Most fields are self-explanatory. One item worth noting is that a negative parent ID means that the segment starts from the initial state with ID -(segment.parent_id+1)

SEG_STATUS_UNSET = 0

SEG_STATUS_PREPARED = 1

SEG_STATUS_COMPLETE = 2

SEG_STATUS_FAILED = 3

SEG_INITPOINT_UNSET = 0

SEG_INITPOINT_CONTINUES = 1

SEG_INITPOINT_NEWTRAJ = 2

SEG_ENDPOINT_UNSET = 0

SEG_ENDPOINT_CONTINUES = 1

SEG_ENDPOINT_MERGED = 2

SEG_ENDPOINT_RECYCLED = 3

statuses = {'SEG_STATUS_COMPLETE': 2, 'SEG_STATUS_FAILED': 3, 'SEG_STATUS_PREPARED': 1, 'SEG_STATUS_UNSET': 0}

initpoint_types = {'SEG_INITPOINT_CONTINUES': 1, 'SEG_INITPOINT_NEWTRAJ': 2, 'SEG_INITPOINT_UNSET': 0}

endpoint_types = {'SEG_ENDPOINT_CONTINUES': 1, 'SEG_ENDPOINT_MERGED': 2, 'SEG_ENDPOINT_RECYCLED': 3, 'SEG_ENDPOINT_UNSET': 0}

status_names = {0: 'SEG_STATUS_UNSET', 1: 'SEG_STATUS_PREPARED', 2: 'SEG_STATUS_COMPLETE', 3: 'SEG_STATUS_FAILED'}

initpoint_type_names = {0: 'SEG_INITPOINT_UNSET', 1: 'SEG_INITPOINT_CONTINUES', 2: 'SEG_INITPOINT_NEWTRAJ'}

endpoint_type_names = {0: 'SEG_ENDPOINT_UNSET', 1: 'SEG_ENDPOINT_CONTINUES', 2: 'SEG_ENDPOINT_MERGED', 3: 'SEG_ENDPOINT_RECYCLED'}

static initial_pcoord(segment): Return the initial progress coordinate point of this segment.

static final_pcoord(segment): Return the final progress coordinate point of this segment.

property initpoint_type

property initial_state_id

property status_text

property endpoint_type_text

class westpa.cli.core.w_succ.WESTAnalysisTool

Bases: object

add_args(parser, upcall=True): Add arguments to a parser common to all analyses of this type.

process_args(args, upcall=True)

open_analysis_backing()

close_analysis_backing()

require_analysis_group(groupname, replace=False)

class westpa.cli.core.w_succ.WESTDataReaderMixin

Bases: AnalysisMixin

A mixin for analysis requiring access to the HDF5 files generated during a WEST run.

add_args(parser, upcall=True)

process_args(args, upcall=True)

clear_run_cache()

property cache_pcoords

Whether or not to cache progress coordinate data. While caching this data can significantly speed up some analysis operations, this requires copious RAM.

Setting this to False when it was formerly True will release any cached data.

get_summary_table()

get_iter_group(n_iter): Return the HDF5 group corresponding to n_iter

get_segments(n_iter, include_pcoords=True): Return all segments present in iteration n_iter

get_segments_by_id(n_iter, seg_ids, include_pcoords=True): Get segments from the data manager, employing caching where possible

get_children(segment, include_pcoords=True)

get_seg_index(n_iter)

get_wtg_parent_array(n_iter)

get_parent_array(n_iter)

get_pcoord_array(n_iter)

get_pcoord_dataset(n_iter)

get_pcoords(n_iter, seg_ids)

get_seg_ids(n_iter, bool_array=None)

get_created_seg_ids(n_iter): Return a list of seg_ids corresponding to segments which were created for the given iteration (are not continuations).

max_iter_segs_in_range(first_iter, last_iter): Return the maximum number of segments present in any iteration in the range selected

total_segs_in_range(first_iter, last_iter): Return the total number of segments present in all iterations in the range selected

get_pcoord_len(n_iter): Get the length of the progress coordinate array for the given iteration.

get_total_time(first_iter=None, last_iter=None, dt=None): Return the total amount of simulation time spanned between first_iter and last_iter (inclusive).

class westpa.cli.core.w_succ.CommonOutputMixin

Bases: AnalysisMixin

add_common_output_args(parser_or_group)

process_common_output_args(args)

class westpa.cli.core.w_succ.WSucc

Bases: CommonOutputMixin, WESTDataReaderMixin, WESTAnalysisTool

find_successful_trajs()

westpa.cli.core.w_succ.entry_point()