tesliper.extraction.gaussian_parser

Paser for Gaussian output files.

Classes

GaussianParser()

Parser for extracting data from human-readable output files from Gaussian computational chemistry software (.log and .out files).

class tesliper.extraction.gaussian_parser.GaussianParser

Parser for extracting data from human-readable output files from Gaussian computational chemistry software (.log and .out files).

This class implements methods for reading information about conducted calculations’ parameters, molecule energy, structure optimization, and calculation of spectral properties. It’s use is as straightforward as:

>>> parser = GaussianParser()
>>> with open('path/to/file.out') as file:
>>>     data = parser.parse(file)

Dictionary with data extracted is also stored as data attribute of instance used for parsing. Each key in said dictionary is a name of its value data type, called from now on a ‘data genre’ (to avoid confusion with Python’s data type). Below is a full list of data genres recognized by this parser, with their description:

freqlist of floats, available from freq job

harmonic vibrational frequencies (cm^-1)

masslist of floats, available from freq job

reduced masses (AMU)

frclist of floats, available from freq job

force constants (mDyne/A)

irilist of floats, available from freq job

IR intensities (KM/mole)

diplist of floats, available from freq=VCD job

dipole strengths (10**-40 esu**2-cm**2)

rotlist of floats, available from freq=VCD job

rotational strengths (10**-44 esu**2-cm**2)

emanglist of floats, available from freq=VCD job

E-M angle = Angle between electric and magnetic dipole transition moments (deg)

depolarplist of floats, available from freq=Raman job

depolarization ratios for plane incident light

depolarulist of floats, available from freq=Raman job

depolarization ratios for unpolarized incident light

ramanactivlist of floats, available from freq=Raman job

Raman scattering activities (A**4/AMU)

ramactlist of floats, available from freq=ROA job

Raman scattering activities (A**4/AMU)

depplist of floats, available from freq=ROA job

depolarization ratios for plane incident light

depulist of floats, available from freq=ROA job

depolarization ratios for unpolarized incident light

alpha2list of floats, available from freq=ROA job

Raman invariants Alpha2 = alpha**2 (A**4/AMU)

beta2list of floats, available from freq=ROA job

Raman invariants Beta2 = beta(alpha)**2 (A**4/AMU)

alphaglist of floats, available from freq=ROA job

ROA invariants AlphaG = alphaG’(10**4 A**5/AMU)

gamma2list of floats, available from freq=ROA job

ROA invariants Gamma2 = beta(G’)**2 (10**4 A**5/AMU)

delta2list of floats, available from freq=ROA job

ROA invariants Delta2 = beta(A)**2, (10**4 A**5/AMU)

raman1list of floats, available from freq=ROA job

Far-From-Resonance Raman intensities =ICPu/SCPu(180) (K)

roa1list of floats, available from freq=ROA job

ROA intensities =ICPu/SCPu(180) (10**4 K)

cid1list of floats, available from freq=ROA job

CID=(ROA/Raman)*10**4 =ICPu/SCPu(180)

raman2list of floats, available from freq=ROA job

Far-From-Resonance Raman intensities =ICPd/SCPd(90) (K)

roa2list of floats, available from freq=ROA job

ROA intensities =ICPd/SCPd(90) (10**4 K)

cid2list of floats, available from freq=ROA job

CID=(ROA/Raman)*10**4 =ICPd/SCPd(90)

raman3list of floats, available from freq=ROA job

Far-From-Resonance Raman intensities =DCPI(180) (K)

roa3list of floats, available from freq=ROA job

ROA intensities =DCPI(180) (10**4 K)

cid3list of floats, available from freq=ROA job

CID=(ROA/Raman)*10**4 =DCPI(180)

rc180list of floats, available from freq=ROA job

RC180 = degree of circularity

wavelenlist of floats, available from td job

excitation energies (nm)

ex_enlist of floats, available from td job

excitation energies (eV)

eemanglist of floats, available from td job

E-M angle = Angle between electric and magnetic dipole transition moments (deg)

vdiplist of floats, available from td job

dipole strengths (velocity)

ldiplist of floats, available from td job

dipole strengths (length)

vrotlist of floats, available from td job

rotatory strengths (velocity) in cgs (10**-40 erg-esu-cm/Gauss)

lrotlist of floats, available from td job

rotatory strengths (length) in cgs (10**-40 erg-esu-cm/Gauss)

vosclist of floats, available from td job

oscillator strengths

losclist of floats, available from td job

oscillator strengths

transitionslist of lists of lists of (int, int, float), available from td job

transitions (first to second) and their coefficients (third)

scffloat, always available

SCF energy

zpefloat, available from freq job

Sum of electronic and zero-point Energies (Hartree/Particle)

tenfloat, available from freq job

Sum of electronic and thermal Energies (Hartree/Particle)

entfloat, available from freq job

Sum of electronic and thermal Enthalpies (Hartree/Particle)

gibfloat, available from freq job

Sum of electronic and thermal Free Energies (Hartree/Particle)

zpecorrfloat, available from freq job

Zero-point correction (Hartree/Particle)

tencorrfloat, available from freq job

Thermal correction to Energy (Hartree/Particle)

entcorrfloat, available from freq job

Thermal correction to Enthalpy (Hartree/Particle)

gibcorrfloat, available from freq job

Thermal correction to Gibbs Free Energy (Hartree/Particle)

commandstr, always available

command used for calculations

normal_terminationbool, always available

true if Gaussian job seem to exit normally, false otherwise

optimization_completedbool, available from opt job

true if structure optimization was performed successfully

versionstr, always available

version of Gaussian software used

chargeint, always available

molecule’s charge

multiplicityint, always available

molecule’s spin multiplicity

input_atomslist of str, always available

input atoms as a list of atoms’ symbols

input_geomlist of lists of floats, always available

input geometry as X, Y, Z coordinates of atoms

stoichiometrystr, always available

molecule’s stoichiometry

last_read_atomslist of ints, always available

molecule’s atoms as atomic numbers

last_read_geomlist of lists of floats, always available

molecule’s geometry (last one found in file) as X, Y, Z coordinates of atoms

optimized_atomslist of ints, available from successful opt job

molecule’s atoms read from optimized geometry as atomic numbers

optimized_geomlist of lists of floats, available from successful opt job

optimized geometry as X, Y, Z coordinates of atoms

data

Data extracted during last parsing.

Type

dict

parse(lines) → dict

Parses content of Gaussian output file and returns dictionary of found data.

Parameters

lines (iterator) – Gaussian output file in a form iterable by lines of text. It may be a file handle, a list of strings, an io.StringIO instance, or similar. Please note that it should not be just a string instance, as it is normally iterated by a character, not by a line.

Returns

Dictionary of extracted data.

Return type

dict

initial(line: str) → None

First step of parsing Gaussian output file. It populates parser.data dictionary with these data genes: ‘normal_termination’, ‘version’, ‘command’, ‘charge’, ‘multiplicity’, ‘input_geom’. Optionally, ‘optimization_completed’ genre is added if optimization was requested in calculation job.

Parameters

line (str) – Line of text to parse.

wait(line: str) → None

This function searches for lines of text triggering other parsing states. It also updates a parser.data dictionary with ‘normal_termination’, ‘scf’, ‘stoichiometry’ data genres.

Parameters

line (str) – Line of text to parse.

geometry(line: str) → None

Function for extracting information about molecule standard orientation geometry from Gaussian output files. It updates parser.data dictionary with ‘last_read_atoms’ and ‘last_read_geom’ data genres.

Parameters

line (str) – Line of text to parse.

optimization(line: str) → None

This method scans optimization data in Gaussian output file, updating parser.data dictionary with ‘stoichiometry’, ‘scf’, ‘optimization_completed’, ‘optimized_atoms’, and ‘optimized_geom’ data genres (last two via geometry() method).

Parameters

line (str) – Line of text to parse.

frequencies(line: str) → None

Responsible for extracting harmonic vibrations-related data and information about molecule’s energy.

Parameters

line (str) – Line of text to parse.

excited(line: str) → None

Responsible for extracting electronic transitions-related data from Gaussian output file. Updates parser.data dictionary with ‘ldip’, ‘losc’, ‘vdip’, ‘vosc’, ‘vrot’, ‘eemang’, ‘lrot’, ‘wavelen’, ‘ex_en’, and ‘transitions’ data genres.

Parameters

line (str) – Line of text to parse.

add_state(state: Callable, name: str = '', trigger: str = '')

Register callable as parser’s state.

This method registers a callable under name key in states dictionary. If trigger parameter is given, it is registered under the same key in triggers dictionary.

Parameters

• state (Callable) – callable, that is to be registered as parser’s state

• name (str, optional) – name under which the callable should be registered; defaults to callable.__name__

• trigger (str, optional) – string with regular expression, that will be compiled with re module

Returns

callable object registered as state

Return type

Callable

remove_state(name: str)

Removes the state from parser’s registered states.

Parameters

name (str) – name of state, that should be unregistered

Raises

InvalidStateError – if no callable was registered under the name ‘name’

static state(state=None, trigger=None)

Convenience decorator for registering a method as parser’s state. It can be with or without ‘trigger’ parameter, like this:

>>> @ParserBase.state
... def method(self, arg): pass

or

>>> @ParserBase.state(trigger='triggering regex')
... def method(self, arg): pass

This function marks a method state as parser’s state by defining is_state attribute on said method and setting its values to True. If trigger is given, it is stored in method’s attribute trigger. During instantiation of ParserBase’s subclass, methods marked as states are registered under method.__name__ key in its states (and possibly triggers) attribute. It is meaningless if used outside of ParserBase’s subclass definition.

Parameters

• state (Callable) – callable, that is to be registered as parser’s state

• trigger (str, optional) – string with regular expression, that will be compiled with re module

Returns

callable object registered as state if ‘state’ was given or decorator if only ‘trigger’ was given

Return type

Callable

Raises

• TypeError – if no arguments given

• InvalidStateError – if state argument is not callable

property workhorse: Callable

Callable marked as a current state used by parser object.

Setter can take a callable or a string as a parameter. If name as string is passed to setter, it will be translated to a method registered as state. If no method was registered under this name, InvalidStateError will be raised. No other checks are performed when argument is callable.