w_dumpsegs

westpa.cli.tools.w_dumpsegs module

westpa.cli.tools.w_dumpsegs.warn()

Issue a warning, or maybe ignore it or raise an exception.

message: Text of the warning message.
category: The Warning category subclass. Defaults to UserWarning.
stacklevel: How far up the call stack to make this warning appear. A value of 2 for example attributes the warning to the caller of the code calling warn().
source: If supplied, the destroyed object which emitted a ResourceWarning
skip_file_prefixes: An optional tuple of module filename prefixes indicating frames to skip during stacklevel computations for stack frame attribution.

class westpa.cli.tools.w_dumpsegs.WESTTool

Bases: WESTToolComponent

Base class for WEST command line tools

prog = None

usage = None

description = None

epilog = None

add_args(parser): Add arguments specific to this tool to the given argparse parser.

process_args(args): Take argparse-processed arguments associated with this tool and deal with them appropriately (setting instance variables, etc)

make_parser(prog=None, usage=None, description=None, epilog=None, args=None)

make_parser_and_process(prog=None, usage=None, description=None, epilog=None, args=None): A convenience function to create a parser, call add_all_args(), and then call process_all_args(). The argument namespace is returned.

go(): Perform the analysis associated with this tool.

main(): A convenience function to make a parser, parse and process arguments, then call self.go()

class westpa.cli.tools.w_dumpsegs.WESTDataReader

Bases: WESTToolComponent

Tool for reading data from WEST-related HDF5 files. Coordinates finding the main HDF5 file from west.cfg or command line arguments, caching of certain kinds of data (eventually), and retrieving auxiliary data sets from various places.

add_args(parser): Add arguments specific to this component to the given argparse parser.

process_args(args): Take argparse-processed arguments associated with this component and deal with them appropriately (setting instance variables, etc)

open(mode='r')

close()

property weight_dsspec

property parent_id_dsspec

class westpa.cli.tools.w_dumpsegs.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.tools.w_dumpsegs.WDumpSegs

Bases: WESTTool

prog = 'w_dumpsegs'

description = 'Dump segment data as text. This is very inefficient, so this tool should be used\nas a last resort (use hdfview/h5ls to look at data, and access HDF5 directly for\nsignificant analysis tasks).\n'

add_args(parser): Add arguments specific to this tool to the given argparse parser.

process_args(args): Take argparse-processed arguments associated with this tool and deal with them appropriately (setting instance variables, etc)

go(): Perform the analysis associated with this tool.

westpa.cli.tools.w_dumpsegs.entry_point()