w_multi_west

The w_multi_west tool combines multiple WESTPA simulations into a single aggregate simulation to facilitate the analysis of the set of simulations. In particular, the tool creates a single west.h5 file that contains all of the data from the west.h5 files of the individual simulations. Each iteration x in the new file contains all of the segments from iteration x from each of the set of simulation, all normalized to the total weight.

Overview

usage:

w_multi_west [-h] [-m master] [-n sims] [--quiet | --verbose | --debug] [--version]
             [-W WEST_H5FILE] [-a aux] [--auxall] [--ibstates]
             [--serial | --parallel | --work-manager WORK_MANAGER] [--n-workers N_WORKERS]
             [--zmq-mode MODE] [--zmq-comm-mode COMM_MODE] [--zmq-write-host-info INFO_FILE]
             [--zmq-read-host-info INFO_FILE] [--zmq-upstream-rr-endpoint ENDPOINT]
             [--zmq-upstream-ann-endpoint ENDPOINT] [--zmq-downstream-rr-endpoint ENDPOINT]
             [--zmq-downstream-ann-endpoint ENDPOINT] [--zmq-master-heartbeat MASTER_HEARTBEAT]
             [--zmq-worker-heartbeat WORKER_HEARTBEAT] [--zmq-timeout-factor FACTOR]
             [--zmq-startup-timeout STARTUP_TIMEOUT] [--zmq-shutdown-timeout SHUTDOWN_TIMEOUT]

optional arguments:

-h, --help           show this help message and exit

General options::

-m, --master directory: Master path of simulations where all the smaller simulations are stored (default: Current Directory)
-n, --sims n: Number of simulation directories. Assumes leading zeros. (default: 0)
--quiet: emit only essential information
--verbose: emit extra information
--version: show program’s version number and exit

Command-Line Options

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

Input/output options

These arguments allow the user to specify where to read input simulation result data and where to output calculated progress coordinate probability distribution data.

Both input and output files are hdf5 format:

-W, --west, --WEST_H5FILE file
  The name of the main .h5 file inside each simulation directory. (Default: west.h5)

-o, --output file
  Store this tool's output in file. (Default: multi.h5)

-a, --aux auxdata
  Name of additional auxiliary dataset to be combined. Can be called multiple times.
  (Default: None)

-aa, --auxall
  Combine all auxiliary datsets as labeled in ``west.h5`` in folder 01. (Default: False)

-nr, --no-reweight
  Do not perform reweighting. (Default: False)

-ib, --ibstates
  Attempt to combine ``ibstates`` dataset if the basis states are identical across
  all simulations. Needed when tracing with ``westpa.analysis``. (Default: False)

Examples

If you have five simulations, set up your directory such that you have five directories are named numerically with leading zeroes, and each directory contains a west.h5 file. For this example, each west.h5 also contains an auxiliary dataset called RMSD. If you run ls, you will see the following output:

01 02 03 04 05

To run the w_multi_west tool, do the following:

w_multi_west.py -m . -n 5 --aux=RMSD

If you used any custom WESTSystem, include that in the directory where you run the code.

To proceed in analyzing the aggregated simulation data as a single simulation, rename the output file multi.h5 to west.h5.

westpa.cli.tools.w_multi_west module

class westpa.cli.tools.w_multi_west.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()

westpa.cli.tools.w_multi_west.n_iter_dtype: alias of uint32

class westpa.cli.tools.w_multi_west.ProgressIndicatorComponent

Bases: WESTToolComponent

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)

class westpa.cli.tools.w_multi_west.WESTMultiTool(wm_env=None)

Bases: WESTParallelTool

Base class for command-line tools which work with multiple simulations. Automatically parses for and gives commands to load multiple files.

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.

parse_from_yaml(yamlfilepath): Parse options from YAML input file. Command line arguments take precedence over options specified in the YAML hierarchy. TODO: add description on how YAML files should be constructed.

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

exception NoSimulationsException: Bases: Exception

generate_file_list(key_list): A convenience function which takes in a list of keys that are filenames, and returns a dictionary which contains all the individual files loaded inside of a dictionary keyed to the filename.

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.

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

westpa.cli.tools.w_multi_west.get_bin_mapper(we_h5file, hashval): Look up the given hash value in the binning table, unpickling and returning the corresponding bin mapper if available, or raising KeyError if not.

westpa.cli.tools.w_multi_west.create_idtype_array(input_array): Return a new array with the new istate_dtype while preserving old data.

class westpa.cli.tools.w_multi_west.WMultiWest

Bases: WESTMultiTool

prog = 'w_multi_west'

description = 'Tool designed to combine multiple WESTPA simulations while accounting for\nreweighting.\n-----------------------------------------------------------------------------\nCommand-line options\n-----------------------------------------------------------------------------\n'

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

open_files()

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

total_number_of_walkers()

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

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