Package schrodinger :: Package test :: Package stu :: Package outcomes :: Module jaguar

Module jaguar

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 $

Functions

[hide private]

jaguarDiff(testFile, refFile, *options)
Compare every property available in the Jaguar/QSite out file against a reference.

get_tol_override(tolOverrides, prop)
search for override -- allows for wildcards as *

printline(prop, o_value, ref_value, logArray, tolOverrides)
Compares the difference between two properties to a tolerance.

getJagVersion(fileName)
Gets the jaguar version from a jaguar/qsite output file

optionTest(aName, aValue, tolOverrides)
Parses input arguments.

parseConfigFile(tolOverrides)
Parses a config file for use in this script.

n2s(number, precision=3)
some hackish formatting stuff

getRMSD(test, ref)
finds the RMSD between the atoms in two structure objects

dictionary

get_mems_from_file(filename)
Scan a Jaguar outfile for memory used in each subprogram.

list

getMemDiffs(test, ref, tolOverrides)
Finds the difference in memory usage (for each subprogram) between the two runs.

Variables

[hide private]

_version = '$Revision 0.1 $'

minPrecision = 2e-06

minPrecisionPercent = 5.0

__package__ = 'schrodinger.test.stu.outcomes'

Function Details

[hide private]

jaguarDiff(testFile, refFile, *options)

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

Usage:

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

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.

optionTest(aName, aValue, tolOverrides)

Parses input arguments. Can be used on either command line or config file.

Parameters:

aName (str) - Name of the parameter
aValue (str) - Parameter's value
tolOverrides (dict) - Tolerances. Results are appended.

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

get_mems_from_file(filename)

Scan a Jaguar outfile for memory used in each subprogram.

Parameters:

filename (str) - file name

Returns: dictionary

Memory used for each subprogram

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: list

Memory differences of each executable type between the two files