Package schrodinger :: Package application :: Package mopac

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Package mopac

Functions for running MOPAC calculations and parsing results.

Classes

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MopacCalculationError

MopacCalculation
A class for running MOPAC calculations.

MopacResults
A class to store MOPAC results.

Functions

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_make_scratch_dir(tmpdir, basename)
Make a separate directory for the job to enable easy cleanup.

_open_file(basename, suffix)
Open a file with a unique name based on basename and suffix in the form "basename-<index>.suffix", where "<index>" is an integer that is incremented until the file can be created.

_run_locally(inputfile, method=None, structure=None)
Run a MOPAC calculation in the local directory.

is_mopac_file(filename)
Determine if the file provided is a MOPAC input file or not.

get_mopac_jobname(pathname)
Get the MOPAC jobname that will be used.

run(inputfile, jobname=None, tmpdir='', save_output_file=False, scratch_cleanup='remove')
Run a MOPAC job from an existing MOPAC input file in a scratch directory and clean up afterwards.

_cleanup_external(inputfile, start_dir)
If the input file has a relative path specification for an EXTERNAL file, rewrite it to the local dir, then copy the original file to the current directory.

_run_cleanup(results, start_dir, scr_dir, jobname, save_output_file, scratch_cleanup)
Cleanup from a subdirectory run.

calculate(structure, jobname=None, method='RM1', minimize=True, kwdict=None, keywords='', tmpdir='', input_file=False, save_output_file=False, scratch_cleanup='remove')
Run a MOPAC calculation without explicitly setting up a MopacCalculation object.

get_error_text()
Get the error text set during the main MOPAC calculation.

Variables

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_logger = log.get_logger("schrodinger.application.mopac")

_method_keywords = ['AM1', 'MNDO', 'MNDOD', 'PM3', 'RM1']

_methods = set(['AM1', 'MNDO', 'MNDOD', 'PM3', 'RM1'])

_external_re = re.compile(r'(?i)EXTERNAL *= *(\S+)')

AM1 = 'AM1'

MNDO = 'MNDO'

MNDOd = 'MNDOD'

PM3 = 'PM3'

REMOVE = 'remove'

RM1 = 'RM1'

SAVE = 'save'

ZIP = 'zip'

__package__ = 'schrodinger.application.mopac'

Function Details

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_make_scratch_dir(tmpdir, basename)

Make a separate directory for the job to enable easy cleanup.

Parameters:

basename (str) - A name that will be used to generate a scratch dir name. The name used will either be basename or basename.1, basename.2, etc.
tmpdir (str) - A directory that will hold the scratch directory.

Returns:

The name of the directory that was created.

_open_file(basename, suffix)

Open a file with a unique name based on basename and suffix in the form "basename-<index>.suffix", where "<index>" is an integer that is incremented until the file can be created. Return the opened file object.

is_mopac_file(filename)

Determine if the file provided is a MOPAC input file or not. Returns True or False.

run(inputfile, jobname=None, tmpdir=`''`, save_output_file=False, scratch_cleanup=`'remove'`)

Run a MOPAC job from an existing MOPAC input file in a scratch directory and clean up afterwards.

Parameters:

jobname (str) - An alternate jobname. If None, the jobname will be determined by the function get_mopac_jobname().
inputfile (str) - A MOPAC input file.
tmpdir (str) - A directory in which a scratch directory based on the inputfile name will be created.
save_output_file (bool) - If True, copy the output file from the scratch dir back to the starting directory.
scratch_cleanup (enum) - If REMOVE, simply remove the scratch dir at the end of the job; if ZIP, create a zip file of the scratch directory contents; if SAVE, do no cleanup.

Returns:

A MopacResults object.

_run_cleanup(results, start_dir, scr_dir, jobname, save_output_file, scratch_cleanup)

Cleanup from a subdirectory run.

This will completely nuke the scratch dir and cd to the start_dir.

Parameters:

results (MopacResults) - A MopacResults object, in which output filename and zipped_output filenames are stored if available.
start_dir (str) - The launch directory for the job.
scr_dir (str) - The scratch directory for the job as an absolute path.
jobname (str) - The base job name.
save_output_file (bool) - If True, copy the output file from the scratch dir back to the starting directory.
scratch_cleanup (enum) - If REMOVE, simply remove the scratch dir at the end of the job; if ZIP, create a zip file of the scratch directory contents; if SAVE, do no cleanup.

calculate(structure, jobname=None, method=`'RM1'`, minimize=True, kwdict=None, keywords=`''`, tmpdir=`''`, input_file=False, save_output_file=False, scratch_cleanup=`'remove'`)

Run a MOPAC calculation without explicitly setting up a MopacCalculation object.

All keyword arguments are passed on to the MopacCalculation constructor.

get_error_text()

Get the error text set during the main MOPAC calculation.

If there is no error text, returns the empty string.

Package mopac

_make_scratch_dir(tmpdir, basename)

_open_file(basename, suffix)

is_mopac_file(filename)

run(inputfile, jobname=None, tmpdir='', save_output_file=False, scratch_cleanup='remove')

_run_cleanup(results, start_dir, scr_dir, jobname, save_output_file, scratch_cleanup)

calculate(structure, jobname=None, method='RM1', minimize=True, kwdict=None, keywords='', tmpdir='', input_file=False, save_output_file=False, scratch_cleanup='remove')

get_error_text()

run(inputfile, jobname=None, tmpdir=`''`, save_output_file=False, scratch_cleanup=`'remove'`)

calculate(structure, jobname=None, method=`'RM1'`, minimize=True, kwdict=None, keywords=`''`, tmpdir=`''`, input_file=False, save_output_file=False, scratch_cleanup=`'remove'`)