Package schrodinger :: Package application :: Package jaguar :: Module output :: Class JaguarOutput
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Class JaguarOutput

Nested Classes [hide private]
  _results_class
A class for holding results for a specific geometry.
  _text_parser_class
A parser to create a JaguarOutput object from a Jaguar output file.
Instance Methods [hide private]
 
__init__(self, output=None)
Initialize from an output filename or output name.
 
__del__(self)
 
__getattr__(self, attr)
Fall back to the last_results object for attribute access.
 
buildDerivedAttributes(self)
 
_getRestart(self)
 
getDuration(self)
 
getScanStep(self)
 
getIrcStep(self)
 
__eq__(self, other)
 
__ne__(self, other)
 
diff(self, other, factor=1.0, short_circuit=False)
Return a list of all differing attributes.
 
_defaultStructureProperties(self)
Return a list of name, value tuples that are the default properties that should be added to all written mae structures for a given output file.
 
getStructures(self)
Get Structure objects for the geometries in the output file.
 
getStructure(self)
Return a structure object for the last geometry in the file.
 
write(self, filename=None, mimic_backend=False, add_title=False, add_entry=False)
Write a maestro file for the structure in the output file.
 
writeGrd(self, filename)
Write a .grd file for 1D or 2D visualization of scans in maestro to file 'filename'.
Class Variables [hide private]
  __doc__ = "\n".join(_tmp_description_list)
  _attributes = [_Attribute("method", "calculation type", "strin...
  mol_weight_precision = 1.0e-2
  restart = property(_getRestart, doc= ...
  duration = property(getDuration, doc= ...
  scan_step = property(getScanStep, doc= ...
  irc_step = property(getIrcStep, doc= ...
Method Details [hide private]

__init__(self, output=None)
(Constructor)

 

Initialize from an output filename or output name.

Exceptions:

IOError
    Raised if output file cannot be found.

JaguarParseError
    Raised if the output file can't be parsed. If this is raised,
    the state of the resulting object is not guaranteed to be
    useful.

__getattr__(self, attr)
(Qualification operator)

 

Fall back to the last_results object for attribute access.

If an attribute isn't present, try getting it from the last_results attribute.

diff(self, other, factor=1.0, short_circuit=False)

 

Return a list of all differing attributes.

Each item is a tuple of (property name, self value, other value).

Note that the property names are not necessarily usable in getattr;
some may be properties of atoms, such as "atom[1].forces".

Parameters

other (JaguarOutput)
    The JaguarOutput instance to compare against.

factor (float)
    A constant factor to multiply all float comparison tolerances
    by.

short_circuit (boolean)
    If true, will return immediately upon finding a difference. The
    values in the tuple will both be None in this case.

getStructures(self)

 

Get Structure objects for the geometries in the output file.

If this job is a geometry optimization, it will contain geometries for all steps. If it's a scan, it will contain the geometries for each scan point (but only the end geometries if it's a relaxed scan).

Return a list of Structure objects.

write(self, filename=None, mimic_backend=False, add_title=False, add_entry=False)

 

Write a maestro file for the structure in the output file.

Note that this method overwrites any file with the same pathname.

If this job is a geometry optimization, it will contain geometries
for all steps. If it's a scan, it will contain the geometries for
each scan point (but only the end geometries if it's a relaxed
scan).

filename (str)
    The filename to write to; if not specified, defaults to the
    restart name with the '.mae' suffix.

mimic_backend (bool)
    If false, all geometry optimization structures will be written.
    If true, the geometry optimization structures will be written as
    in regular jobs; by default, only the last geometry will be
    used, but if ip472 is greater than 1, all geometries will be
    included.

add_title (bool)
    If true, then an empty title will be replaced with the output
    file's jobname.

add_entry (bool)
    If the entry name is empty or starts with 'Scratch' it will be
    replaced with the output file's jobname.

writeGrd(self, filename)

 

Write a .grd file for 1D or 2D visualization of scans in maestro to file 'filename'.

If the job is not a scan job, this will raise a RuntimeError.


Class Variable Details [hide private]

_attributes

Value:
[_Attribute("method", "calculation type", "string", init= lambda: ctHF\
), _Attribute("functional", "DFT functional", "string"), _Attribute("c\
anonical_orbitals", "number of canonical orbitals", "int"), _Attribute\
("basis", "basis set", "string"), _Attribute("nbasis", "number of basi\
s functions", "int"), _Attribute("qm_atoms", "number of QM atoms", "in\
t"), _Attribute("stoichiometry", "stoichiometry", "string"), _Attribut\
e("point_group", "molecular point group of the input molecule", "strin\
g"), _Attribute("point_group_used", "point group used in the calculati\
...

restart

Value:
property(_getRestart, doc= """
        Return the restart name for this output object.

        """)

duration

Value:
property(getDuration, doc= """
        Return the duration of the job as a datetime.timedelta object.

        """)

scan_step

Value:
property(getScanStep, doc= """
        Return a list of final scan geometries for each scan step.

        """)

irc_step

Value:
property(getIrcStep, doc= """
        Return a list of final IRC geometries for each IRC step.

        """)