Class JaguarOutput

object --+
         |
        JaguarOutput

Known Subclasses:

• qsite.output.QSiteOutput

A class for accessing Jaguar output properties.

Stores a JaguarResults object for each geometry (multiple geometry
optimization steps in the geopt_step list, multiple scan steps in the
scan_step list). Each JaguarResults object holds all properties
specific     to a given geometry. (See the JaguarResults documentation
for more     detail.) Each JaguarResults object also holds a list of
JaguarAtomicResults objects for atomic specific properties.

General Attributes

job_id (string)
    job ID

opts (JaguarOptions)
    job calculation options

host (string)
    the job host

mae_out (string)
    Maestro output file

mae_in (string)
    Maestro input file

status (int)
    job status, set to one of the class variables UNKNOWN, OK, or
    SPLAT

fatal_error (string)
    error message in the event the job failed

fatal_errorno (string)
    error number in the event the job failed

glibc (string)
    reported glibc version

lastexe (string)
    last executable

start_time (datetime.datetime)
    the starting time of the calculation

end_time (datetime.datetime)
    the ending time of the calculation

sm_geopt_step (list of lists of JaguarResults)
    results for individual IRC geopt steps (see note below)

sm_n_steps (list of lists of JaguarResults)
    results for individual IRC geopt steps (see note below)

geopt_step (list of JaguarResults)
    results for each step in a geopt

gas_phase_geopt_step (list of JaguarResults)
    results for the gas phase geometry optimization in a solvated
    geopt

solution_phase_geopt_step (list of JaguarResults)
    results for the solution phase geometry optimization in a solvated
    geopt

scan_geopt_step (list of lists of JaguarResults)
    results for individual scan geopt steps (see note below)

irc_geopt_step (list of lists of JaguarResults)
    results for individual IRC geopt steps (see note below)

input_geometry (schrodinger.structure.Structure)
    the input geometry, unmodified by symmetrization

input_geometry2 (schrodinger.structure.Structure)
    the input geometry from zmat2, unmodified by symmetrization

input_geometry3 (schrodinger.structure.Structure)
    the input geometry from zmat3, unmodified by symmetrization

symmetrized (bool)
    whether the geometry has been symmetrized or not

geopt_stuck (bool)
    whether the geopt or tsopt got stuck

convergence_category (list of JaguarResults)
    results for the convergence category

The scan_geopt_step and irc_geopt_step attributes are both lists of
lists of JaguarResults. Each element of the list represents the geopt
steps taken within an individual scan or IRC step. In the case where
geometry optimization is not done with the scan or IRC calculation,
each     element is a list with a single JaguarResults element.

The properties scan_step     and irc_step are probably more useful.
They provide a list of the final     geometries for each scan/IRC
step.

Property Attributes

basis (string)
    basis set

canonical_orbitals (int)
    number of canonical orbitals

charge (int)
    total molecular charge

coords_frozen (int)
    number of frozen coordinates

coords_harmonic (int)
    number of harmonic constraints

coords_ind (int)
    number of independent coordinates

coords_nred (int)
    number of non-redundant coordinates

coords_opt (int)
    number of optimization coordinates

functional (string)
    DFT functional

method (string)
    calculation type

mol_weight (float, amu)
    molecular weight

multiplicity (int)
    total spin multiplicity

nbasis (int)
    number of basis functions

point_group (string)
    molecular point group of the input molecule

point_group_used (string)
    point group used in the calculation

qm_atoms (int)
    number of QM atoms

scan_coords (dictionary of Scan objects)
    scan coordinates

stoichiometry (string)
    stoichiometry

ts_component_descriptions (string)
    descriptions of the transition state vector components

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.

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.

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.