schrodinger.test.stu.outcomes.jaguar module

Provides the jaguarDiff workup method for use with jaguar and qsite jobs. It wraps the qsite/jaguar output class ‘diff’ function so that it produces results which are meaningful to STU. Can also be used from the command line.

$Revision 0.1 $

@copyright: (c) Schrodinger, LLC. All rights reserved

schrodinger.test.stu.outcomes.jaguar.jaguarDiff(testFile, refFile, *options)

Compare every property available in the Jaguar/QSite out file against a reference.

Usage:

# file.out         - Path of the file to be compared
# reference.out    - Path of the reference file
outcome_workup = jaguarDiff('file.out', 'reference.out', 'tol=1.0',
                            'log=workup.log', 'config=config.txt',
                            'value=1e-4')

Optional parameters:

• tol=value - A multipler to by which loosen ALL tolerances

• log=file - Path to an optional output log. If it is not provided, the output is written to the console.

• config=file - A configuration file format as follows: Any text after a ‘#’ character is a comment, and is ignored all other text is in key/value pairs, one per line. possible keys are: log, tol, and any value that appears in the output file i.e. value = 1e-4 overrides the tolerance for ‘value’ to 1e-4

• timing=boolean - if true, jobs can ‘fail’ based on timing alone. Default is false.

All other arguments are taken to be tolerance overrides for specific values

schrodinger.test.stu.outcomes.jaguar.get_tol_override(tolOverrides, prop)

search for override – allows for wildcards as *

schrodinger.test.stu.outcomes.jaguar.printline(prop, o_value, ref_value, logArray, tolOverrides)

Compares the difference between two properties to a tolerance. If the difference is greater than the tolerance, appends a string explaning this to an output array. This function recurses to examine differences within arrays and dictionaries.

Parameters

• prop – The name of the property

• o_value – The ‘output value’ to be compared

• ref_value – The reference value to be compared

• logArray – An array of strings, each of which describes a difference. Results are appended.

• tolOverrides (dict) – tolerance overrides for specific property names.

schrodinger.test.stu.outcomes.jaguar.getJagVersion(fileName)

Gets the jaguar version from a jaguar/qsite output file

schrodinger.test.stu.outcomes.jaguar.optionTest(aName, aValue, tolOverrides)

Parses input arguments. Can be used on either command line or config file. :param aName: Name of the parameter :type aName: str :param aValue: Parameter’s value :type aValue: str :param tolOverrides: Tolerances. Results are appended. :type tolOverrides: dict

schrodinger.test.stu.outcomes.jaguar.parseConfigFile(tolOverrides)

Parses a config file for use in this script. Config file follows this example format:

log = workup.log    #Everything following a pound is a comment
tol  2.0                    #equals signs are optional
energy_2_electron = 1e-2    #mostly, the config file is a place to
                            #put multiple tolerance overrides.

Parameters

tolOverrides – A dictionary containing any known options, mostly tolerance overrides

schrodinger.test.stu.outcomes.jaguar.n2s(number, precision=3)

some hackish formatting stuff

schrodinger.test.stu.outcomes.jaguar.getRMSD(test, ref)

finds the RMSD between the atoms in two structure objects

schrodinger.test.stu.outcomes.jaguar.get_mems_from_file(filename)

Scan a Jaguar outfile for memory used in each subprogram.

Parameters

filename (str) – file name

Returns

Memory used for each subprogram

Return type

dictionary

schrodinger.test.stu.outcomes.jaguar.getMemDiffs(test, ref, tolOverrides)

Finds the difference in memory usage (for each subprogram) between the two runs. This diff is skipped unless a tolerance is manually given.

Parameters

• test (str) – Name of the test output file

• ref (str) – Name of the reference output file

• tolOverrides (dict) – Tolerances for specific tests. This function is interested in Memory% which provides a minimum tolerance as a percent difference.

Returns

Memory differences of each executable type between the two files

Return type

list