schrodinger.application.jaguar.output module

Classes for parsing Jaguar output files and accessing output properties programmatically.

Copyright Schrodinger, LLC. All rights reserved.

schrodinger.application.jaguar.output.join_structure_files(name, files)[source]

Pull the CTs out of each .mae file in the ‘files’ list and put them into a new .mae file called ‘name’, which is expected to already contain the .mae extension. If a file called ‘name’ already exists, it will be overwritten.

schrodinger.application.jaguar.output.restart_name(name)[source]

Generate a restart name from a job name. If there is no number suffix for the job this will be jobname.01; otherwise the suffix will be incremented.

schrodinger.application.jaguar.output.get_section(fname, sect_start, sect_end=None)[source]

Generator of lines for a section of a (jaguar) file.

The section is defined by a start and optionally by an end.

Note that if sect_end is not specified the remainder of the file after a sect_start will be returned by the generator.

Note that, if multiple sections defined by sect_start and sect_end are present in the file, all will appear in the order they appear

Parameters

  • fname (string) – Name of file to parse for section

  • sect_start (string) – Indicator of where section begins, i.e. the first line of desired section

  • sect_end (string (or None)) – If specified, indicator of the end of a section, i.e. the last line in the desired section

schrodinger.application.jaguar.output.get_overlap_dim(fname)[source]

Get size of overlap matrix from output file.

Unfortunately, this does not necessarily match the nbasis of JaguarOutput (possibly the overlap matrix is always in caretesians, i.e. numd=6, but since we aren’t 100% sure, we will just check how many rows are in the printed overlap matrix.

Parameters

fname (string) – name of output file

Return type

int

Returns

dimension of overlap matrix

schrodinger.application.jaguar.output.parse_overlap_mat(fname)[source]

Parse overlap matrix from output file

Parameters

fname (string) – name of output file

Returns

nbas x nbas overlap matrix as numpy array

class schrodinger.application.jaguar.output.JaguarOutput(output=None, partial_ok=False)[source]

Bases: object

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)

Job Host

mae_out (string)

Maestro output file

mae_in (string)

Maestro input file

status (int)

Job status - set to 0, 1, or 2 corresponding to UNKNOWN, OK, or SPLAT respectively

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 Jaguar Executable Used

start_time (datetime.datetime)

Starting time of the calculation - NOT CURRENTLY SUPPORTED

end_time (datetime.datetime)

Ending time of the calculation - NOT CURRENTLY SUPPORTED

symmetrized (bool)

Whether the geometry has been symmetrized or not

geopt_stuck (bool)

Whether the geopt or tsopt got stuck

sm_geopt_step (list of lists of JaguarResults)

results for individual SM geopt steps (see note below) - NOT CURRENTLY SUPPORTED

sm_n_steps (list of lists of JaguarResults)

results for individual string method steps (see note below) - NOT CURRENTLY SUPPORTED

geopt_step (list of JaguarResults)

results for each step in a geopt - NOT CURRENTLY SUPPORTED

gas_phase_geopt_step (list of JaguarResults)

results for the gas phase geometry optimization in a solvated geopt - NOT CURRENTLY SUPPORTED

solution_phase_geopt_step (list of JaguarResults)

results for the solution phase geometry optimization in a solvated geopt - NOT CURRENTLY SUPPORTED

scan_geopt_step (list of lists of JaguarResults)

results for individual scan geopt steps (see note below) - NOT CURRENTLY SUPPORTED

irc_geopt_step (list of lists of JaguarResults)

results for individual IRC geopt steps (see note below) - NOT CURRENTLY SUPPORTED

input_geometry (schrodinger.structure.Structure)

the input geometry, unmodified by symmetrization - NOT CURRENTLY SUPPORTED

input_geometry2 (schrodinger.structure.Structure)

the input geometry from zmat2, unmodified by symmetrization - NOT CURRENTLY SUPPORTED

input_geometry3 (schrodinger.structure.Structure)

the input geometry from zmat3, unmodified by symmetrization - NOT CURRENTLY SUPPORTED

convergence_category (list of JaguarResults)

Results for the convergence category - NOT CURRENTLY SUPPORTED

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

_sm_n_points (int)

number of string method points

basis (string)

Basis Set

charge (int)

Molecular charge of Input Structure

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 of input geometry

multiplicity (int)

Spin Multiplicity of Input Structure

nbasis (int)

Number of Basis Functions

nelectron (int)

Number of Electrons

path_structures (list of Structure instances)

path structures for IRC/RSM jobs - NOT CURRENTLY SUPPORTED

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 (list of Scan objects)

scan coordinates - NOT CURRENTLY SUPPORTED

stoichiometry (string)

Stoichiometry of input geometry

ts_component_descriptions (string)

Descriptions of the transition state vector components

UNKNOWN = 0
OK = 1
SPLAT = 2
mol_weight_precision = 0.01
rmsd_precision = 0.0001
__init__(output=None, partial_ok=False)[source]

Initialize from an output filename or output name.

Parameters

  • output (str) – The name of the Jaguar output file to read. Can be the .out or .out.gz name or a file with the same basename as the desired .out/.out.gz file.

  • partial_ok (bool) – Do not raise an exception if parsing fails partway through the file. Instead, process what has been read and store the parsing error in the parsing_error attribute. The resulting JaguarOutput object may be in an incomplete state.

Exceptions:

Raises

  • 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.

  • StopIteration – Raised in some cases if the file ends unexpectedly If this is raised, the state of the resulting object is not guaranteed to be useful.

property restart

Return the restart name for this output object.

getDuration()[source]
property duration

Return the duration of the job as a datetime.timedelta object.

getScanStep()[source]
property scan_step

Return a list of final scan geometries for each scan step.

getIrcStep()[source]
property irc_step

Return a list of final IRC geometries for each IRC step.

diff(other, factor=1.0, short_circuit=False)[source]

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.

property path_structures

List of structures along path for IRC or RSM jobs, empty list otherwise

getStructures()[source]

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.

getStructure()[source]

Return a structure object for the last geometry in the file.

write(filename=None, mimic_backend=False, add_title=False, add_entry=False)[source]

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(filename)[source]

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.