tesliper.glassware.arrays

Implements DataArray-like objects for handling arrayed data.

DataArray-like objects are concrete implementations of ArrayBase base class that collect specific data for multiple conformers and provide an easy access to genre-specific functionality. Instances of DataArray subclasses are produced by the Conformers.arrayed() method and Tesliper’s subscription mechanism.

Classes

`Averagable`()	Mix-in for DataArray subclasses, that may be averaged based on populations of conformers.
`Bands`(genre, filenames, values[, ...])	Special kind of data array for band values, to which spectral data or activities corespond.
`BooleanArray`(genre, filenames, values[, ...])	For handling data of `bool` type.
`DataArray`(genre, filenames, values[, ...])	Base class for data holding objects.
`ElectronicActivities`(genre, filenames, ...)	For handling electronic spectral activity data.
`ElectronicData`(genre, filenames, values, wavelen)	For handling electronic data that is not a spectral activity.
`Energies`(genre, filenames, values[, t, ...])	For handling data about the energy of conformers.
`FilenamesArray`([genre, filenames, values, ...])	Special case of `DataArray`, holds only filenames.
`FloatArray`(genre, filenames, values[, ...])	For handling data of `float` type.
`Geometry`(genre, filenames, values, atoms[, ...])	For handling information about geometry of conformers.
`InfoArray`(genre, filenames, values[, ...])	For handling data of `str` type.
`IntegerArray`(genre, filenames, values[, ...])	For handling data of `int` type.
`ScatteringActivities`(genre, filenames, ...)	For handling scattering spectral activity data.
`ScatteringData`(genre, filenames, values, freq)	For handling scattering data that is not a spectral activity.
`SpectralActivities`(genre, filenames, values)	Base class for spectral activities genres.
`SpectralData`(genre, filenames, values[, ...])	Base class for spectral data genres, that are not spectral activities.
`Transitions`(genre, filenames, values[, ...])	For handling information about electronic transitions from ground to excited state contributing to each band.
`VibrationalActivities`(genre, filenames, ...)	For handling electronic spectral activity data.
`VibrationalData`(genre, filenames, values, freq)	For handling vibrational data that is not a spectral activity.

class tesliper.glassware.arrays.DataArray(genre: str, filenames: Sequence[str], values: Sequence, allow_data_inconsistency: bool = False)[source]

Base class for data holding objects.

Parameters

genre – Name of the data genre that values represent.
filenames – Sequence of conformers’ identifiers.
values – Sequence of values for genre for each conformer in filenames.
allow_data_inconsistency – Flag signalizing if instance should allow data inconsistency (see ArrayProperty for details).

classmethod get_init_params() → Dict[str, Union[str, inspect.Parameter]]: Returns parameters used to instantiate this class. genre is a genre of data array that is to be instantiated.

get_repr_args() → Dict[str, Any]: Returns dictionary that can be used as keword-value pairs to instantiate identical object.

class tesliper.glassware.arrays.IntegerArray(genre: str, filenames: Sequence[str], values: Sequence, allow_data_inconsistency: bool = False)[source]

For handling data of int type.

Genres associated with this class:
charge	multiplicity

Parameters

genre – Name of the data genre that values represent.
filenames – Sequence of conformers’ identifiers.
values – Sequence of values for genre for each conformer in filenames.
allow_data_inconsistency – Flag signalizing if instance should allow data inconsistency (see ArrayProperty for details).

classmethod get_init_params() → Dict[str, Union[str, inspect.Parameter]]: Returns parameters used to instantiate this class. genre is a genre of data array that is to be instantiated.

get_repr_args() → Dict[str, Any]: Returns dictionary that can be used as keword-value pairs to instantiate identical object.

class tesliper.glassware.arrays.FloatArray(genre: str, filenames: Sequence[str], values: Sequence, allow_data_inconsistency: bool = False)[source]

For handling data of float type.

Genres associated with this class:
zpecorr	tencorr	entcorr	gibcorr

Parameters

genre – Name of the data genre that values represent.
filenames – Sequence of conformers’ identifiers.
values – Sequence of values for genre for each conformer in filenames.
allow_data_inconsistency – Flag signalizing if instance should allow data inconsistency (see ArrayProperty for details).

classmethod get_init_params() → Dict[str, Union[str, inspect.Parameter]]: Returns parameters used to instantiate this class. genre is a genre of data array that is to be instantiated.

get_repr_args() → Dict[str, Any]: Returns dictionary that can be used as keword-value pairs to instantiate identical object.

class tesliper.glassware.arrays.InfoArray(genre: str, filenames: Sequence[str], values: Sequence, allow_data_inconsistency: bool = False)[source]

For handling data of str type.

Genres associated with this class:
command	stoichiometry

Parameters

genre – Name of the data genre that values represent.
filenames – Sequence of conformers’ identifiers.
values – Sequence of values for genre for each conformer in filenames.
allow_data_inconsistency – Flag signalizing if instance should allow data inconsistency (see ArrayProperty for details).

classmethod get_init_params() → Dict[str, Union[str, inspect.Parameter]]: Returns parameters used to instantiate this class. genre is a genre of data array that is to be instantiated.

get_repr_args() → Dict[str, Any]: Returns dictionary that can be used as keword-value pairs to instantiate identical object.

class tesliper.glassware.arrays.FilenamesArray(genre: str = 'filenames', filenames: Union[Sequence, numpy.ndarray] = (), values: Optional[Any] = None, allow_data_inconsistency: bool = False)[source]

Special case of DataArray, holds only filenames. values property returns same as filenames and ignores any value given to its setter. Only genre associated with this class is filenames pseudo-genre.

Parameters

genre (str) – Name of genre, should be ‘filenames’.
filenames (numpy.ndarray(dtype=str)) – List of filenames of gaussian output files, from which data were extracted.
values (numpy.ndarray(dtype=str)) – Always returns same as filenames.

property values

Property, that validates array-like value given to its setter and stores it as numpy.ndarray.

Value given to property setter is:

(optionally) sanitized with user-provided sanitizer function;
(optionally) compared with another array-like attribute of the owner regarding their shape;
transformed to numpy.ndarray of desired data type;
stored in owner’s __dict__.

Setting, getting and deletition of the value may be customized using standard setter, getter and deleter decorators. Additionally, ArrayProperty provides an ArrayProperty.sanitizer decorator. If sanitizer function is provided, it is called as a first step of data validation and should return sanitized array-like value (given original value as a positional parameter).

Validation regarding shape of the value is triggered if check_against parameter is provided. It should be a name of owner’s other array-like attribute as a string. Shape of the value is than compared to the shape of this reference attribute. If shapes are not identical up to the first check_depth dimensions, InconsistentDataError is raised.

Value is always transformed to numpy.ndarray of specified dtype (float by default.) If such conversion cannot be done because value is a jagged array, InconsistentDataError will be raised. However, if owner allows for data inconsistency by defining owner.allow_data_inconsistency = True, non-matching shapes will be ignored and jugged arrays will be padded with fill_value and stored as numpy.ma.masked_array.

classmethod get_init_params() → Dict[str, Union[str, inspect.Parameter]]: Returns parameters used to instantiate this class. genre is a genre of data array that is to be instantiated.

get_repr_args() → Dict[str, Any]: Returns dictionary that can be used as keword-value pairs to instantiate identical object.

class tesliper.glassware.arrays.BooleanArray(genre: str, filenames: Sequence[str], values: Sequence, allow_data_inconsistency: bool = False)[source]

For handling data of bool type.

Genres associated with this class:
normal_termination	optimization_completed

Parameters

genre – Name of the data genre that values represent.
filenames – Sequence of conformers’ identifiers.
values – Sequence of values for genre for each conformer in filenames.
allow_data_inconsistency – Flag signalizing if instance should allow data inconsistency (see ArrayProperty for details).

classmethod get_init_params() → Dict[str, Union[str, inspect.Parameter]]: Returns parameters used to instantiate this class. genre is a genre of data array that is to be instantiated.

get_repr_args() → Dict[str, Any]: Returns dictionary that can be used as keword-value pairs to instantiate identical object.

class tesliper.glassware.arrays.Energies(genre, filenames, values, t=298.15, allow_data_inconsistency=False)[source]

For handling data about the energy of conformers.

Genres associated with this class:
scf	zpe	ten	ent	gib

Parameters

genre (str) – genre of energy.
filenames (numpy.ndarray(dtype=str)) – List of filenames of gaussian output files, from which data were extracted.
values (numpy.ndarray(dtype=float)) – Energy value for each conformer.
t (int or float) – Temperature of calculated state in K.

property as_kcal_per_mol: Energy values converted to kcal/mol.

property deltas

Calculates energy difference between each conformer and lowest energy conformer. Converts energy to kcal/mol.

Returns: List of energy differences from lowest energy in kcal/mol.
Return type: numpy.ndarray

property min_factors

Calculates list of conformers’ Boltzmann factors respective to lowest energy conformer in system.

Notes

Boltzmann factor of two states is defined as: F(state_1)/F(state_2) = exp((E_1 - E_2)/kt) where E_1 and E_2 are energies of states 1 and 2, k is Boltzmann constant, k = 0.0019872041 kcal/(mol*K), and t is temperature of the system.

Returns: List of conformers’ Boltzmann factors respective to lowest energy conformer.
Return type: numpy.ndarary

property populations

Calculates Boltzmann distribution of conformers.

Returns: List of conformers populations calculated as Boltzmann distribution.
Return type: numpy.ndarary

calculate_populations(t)[source]

Calculates conformers’ Boltzmann distribution in given temperature.

Parameters: t (int or float) – Temperature of calculated state in K.

classmethod get_init_params() → Dict[str, Union[str, inspect.Parameter]]: Returns parameters used to instantiate this class. genre is a genre of data array that is to be instantiated.

get_repr_args() → Dict[str, Any]: Returns dictionary that can be used as keword-value pairs to instantiate identical object.

class tesliper.glassware.arrays.Averagable[source]

Mix-in for DataArray subclasses, that may be averaged based on populations of conformers.

average_conformers(energies) → tesliper.glassware.arrays.DataArray[source]

A method for averaging values by population of conformers.

Parameters: energies (Energies or iterable) – Object with populations and genre attributes, containing respectively: list of populations values as numpy.ndarray and string specifying energy type. Alternatively, list of weights for each conformer.
Returns: New instance of DataArray’s subclass, on which average method was called, containing averaged values.
Return type: DataArray
Raises: TypeError – If creation of an instance based on its __init__ signature is impossible.

class tesliper.glassware.arrays.Bands(genre: str, filenames: Sequence[str], values: Sequence, allow_data_inconsistency: bool = False)[source]

Special kind of data array for band values, to which spectral data or activities corespond. Provides an easy way to convert values between their different representations: frequency, wavelength, and excitation energy.

Genres associated with this class:
freq	wavelen	ex_en

Parameters

genre – Name of the data genre that values represent.
filenames – Sequence of conformers’ identifiers.
values – Sequence of values for genre for each conformer in filenames.
allow_data_inconsistency – Flag signalizing if instance should allow data inconsistency (see ArrayProperty for details).

property freq: Values converted to frequencies in \(\mathrm{cm}^{-1}\).

property frequencies: Values converted to frequencies in \(\mathrm{cm}^{-1}\). A convenience alias for Bands.frequencies.

property wavelen: Values converted to wavelengths in nm.

property wavelengths: Values converted to wavelengths in nm. A convenience alias for Bands.wavelen.

property ex_en: Values converted to excitation energy in eV.

property excitation_energy: Values converted to excitation energy in eV. A convenience alias for Bands.ex_en.

property imaginary

Finds number of imaginary frequencies of each conformer.

Returns: Number of imaginary frequencies of each conformer.
Return type: numpy.ndarray

find_imaginary()[source]

Reports number of imaginary frequencies of each conformer that has any.

Returns: Dictionary of {filename: number-of-imaginary-frequencies} for each conformer with at least one imaginary frequency.
Return type: dict

classmethod get_init_params() → Dict[str, Union[str, inspect.Parameter]]: Returns parameters used to instantiate this class. genre is a genre of data array that is to be instantiated.

get_repr_args() → Dict[str, Any]: Returns dictionary that can be used as keword-value pairs to instantiate identical object.

class tesliper.glassware.arrays.SpectralData(genre: str, filenames: Sequence[str], values: Sequence, allow_data_inconsistency: bool = False)[source]

Base class for spectral data genres, that are not spectral activities.

When subclassed, one of the attributes: freq or wavelen should be overridden with a concrete setter and getter - use of ArrayProperty is recommended. The other one may use implementation from this base class by call to super().freq or super().wavelen to get converted values.

Parameters

genre – Name of the data genre that values represent.
filenames – Sequence of conformers’ identifiers.
values – Sequence of values for genre for each conformer in filenames.
allow_data_inconsistency – Flag signalizing if instance should allow data inconsistency (see ArrayProperty for details).

abstract property spectra_type: Type of spectra, that genres associated with SpectralData’s subclass relate to. Should be a class-level attribute with value of either “vibrational”, “electronic”, or “scattering”.

abstract property freq

Bands values converted to frequencies in \(\mathrm{cm}^{-1}\). If wavelen is provided, this may be overridden with a simple call to super():

@property
def freq(self):
    return super().freq()  # values converted to cm^(-1)

property frequencies: Bands values converted to frequencies in \(\mathrm{cm}^{-1}\). A convenience alias for freq.

abstract property wavelen

Bands values converted to wavelengths in nm. If freq is provided, this may be overridden with a simple call to super():

@property
def wavelen(self):
    return super().wavelen()  # values converted to nm

property wavelengths: Bands values converted to wavelengths in nm. A convenience alias for wavelen.

classmethod get_init_params() → Dict[str, Union[str, inspect.Parameter]]: Returns parameters used to instantiate this class. genre is a genre of data array that is to be instantiated.

get_repr_args() → Dict[str, Any]: Returns dictionary that can be used as keword-value pairs to instantiate identical object.

class tesliper.glassware.arrays.VibrationalData(genre, filenames, values, freq, allow_data_inconsistency=False)[source]

For handling vibrational data that is not a spectral activity.

Genres associated with this class:
mass	frc	emang

Parameters

genre – Name of the data genre that values represent.
filenames – Sequence of conformers’ identifiers.
values – Sequence of values for genre for each conformer in filenames.
freq – Frequency for each value in each conformer in \(\mathrm{cm}^{-1}\) units.
allow_data_inconsistency – Flag signalizing if instance should allow data inconsistency (see ArrayPropety for details).

property spectra_type: Type of spectra, that genres associated with SpectralData’s subclass relate to. Should be a class-level attribute with value of either “vibrational”, “electronic”, or “scattering”.

property frequencies: Bands values converted to frequencies in \(\mathrm{cm}^{-1}\). A convenience alias for freq.

classmethod get_init_params() → Dict[str, Union[str, inspect.Parameter]]: Returns parameters used to instantiate this class. genre is a genre of data array that is to be instantiated.

get_repr_args() → Dict[str, Any]: Returns dictionary that can be used as keword-value pairs to instantiate identical object.

property wavelen: Bands values converted to wavelengths in nm.

property wavelengths: Bands values converted to wavelengths in nm. A convenience alias for wavelen.

class tesliper.glassware.arrays.ScatteringData(genre, filenames, values, freq, t=298.15, laser=532, allow_data_inconsistency=False)[source]

For handling scattering data that is not a spectral activity.

Genres associated with this class:
depolarp	depolaru	depp	depu	alpha2
beta2	alphag	gamma2	delta2	cid1
cid2	cid3	rc180

Parameters

genre – Name of the data genre that values represent.
filenames – Sequence of conformers’ identifiers.
values – Sequence of values for genre for each conformer in filenames.
freq – Frequency for each value in each conformer in \(\mathrm{cm}^{-1}\) units.
allow_data_inconsistency – Flag signalizing if instance should allow data inconsistency (see ArrayPropety for details).

property spectra_type: Type of spectra, that genres associated with SpectralData’s subclass relate to. Should be a class-level attribute with value of either “vibrational”, “electronic”, or “scattering”.

property frequencies: Bands values converted to frequencies in \(\mathrm{cm}^{-1}\). A convenience alias for freq.

classmethod get_init_params() → Dict[str, Union[str, inspect.Parameter]]: Returns parameters used to instantiate this class. genre is a genre of data array that is to be instantiated.

get_repr_args() → Dict[str, Any]: Returns dictionary that can be used as keword-value pairs to instantiate identical object.

property wavelen: Bands values converted to wavelengths in nm.

property wavelengths: Bands values converted to wavelengths in nm. A convenience alias for wavelen.

class tesliper.glassware.arrays.ElectronicData(genre, filenames, values, wavelen, allow_data_inconsistency=False)[source]

For handling electronic data that is not a spectral activity.

Genres associated with this class:
eemang

Parameters

genre – Name of the data genre that values represent.
filenames – Sequence of conformers’ identifiers.
values – Sequence of values for genre for each conformer in filenames.
allow_data_inconsistency – Flag signalizing if instance should allow data inconsistency (see ArrayProperty for details).

property spectra_type: Type of spectra, that genres associated with SpectralData’s subclass relate to. Should be a class-level attribute with value of either “vibrational”, “electronic”, or “scattering”.

property freq

Bands values converted to frequencies in \(\mathrm{cm}^{-1}\). If wavelen is provided, this may be overridden with a simple call to super():

@property
def freq(self):
    return super().freq()  # values converted to cm^(-1)

property frequencies: Bands values converted to frequencies in \(\mathrm{cm}^{-1}\). A convenience alias for freq.

classmethod get_init_params() → Dict[str, Union[str, inspect.Parameter]]: Returns parameters used to instantiate this class. genre is a genre of data array that is to be instantiated.

get_repr_args() → Dict[str, Any]: Returns dictionary that can be used as keword-value pairs to instantiate identical object.

property wavelengths: Bands values converted to wavelengths in nm. A convenience alias for wavelen.

class tesliper.glassware.arrays.SpectralActivities(genre: str, filenames: Sequence[str], values: Sequence, allow_data_inconsistency: bool = False)[source]

Base class for spectral activities genres.

Parameters

genre – Name of the data genre that values represent.
filenames – Sequence of conformers’ identifiers.
values – Sequence of values for genre for each conformer in filenames.
allow_data_inconsistency – Flag signalizing if instance should allow data inconsistency (see ArrayProperty for details).

property intensities

Converts spectral activity calculated by quantum chemistry software to signal intensity.

Returns: Signal intensities for each conformer.
Return type: numpy.ndarray
Raises: NotImplementedError – if genre does not provide values conversion to intensities.

average_conformers(energies) → tesliper.glassware.arrays.DataArray

A method for averaging values by population of conformers.

Parameters: energies (Energies or iterable) – Object with populations and genre attributes, containing respectively: list of populations values as numpy.ndarray and string specifying energy type. Alternatively, list of weights for each conformer.
Returns: New instance of DataArray’s subclass, on which average method was called, containing averaged values.
Return type: DataArray
Raises: TypeError – If creation of an instance based on its __init__ signature is impossible.

abstract property freq

Bands values converted to frequencies in \(\mathrm{cm}^{-1}\). If wavelen is provided, this may be overridden with a simple call to super():

@property
def freq(self):
    return super().freq()  # values converted to cm^(-1)

property frequencies: Bands values converted to frequencies in \(\mathrm{cm}^{-1}\). A convenience alias for freq.

classmethod get_init_params() → Dict[str, Union[str, inspect.Parameter]]: Returns parameters used to instantiate this class. genre is a genre of data array that is to be instantiated.

get_repr_args() → Dict[str, Any]: Returns dictionary that can be used as keword-value pairs to instantiate identical object.

abstract property spectra_type: Type of spectra, that genres associated with SpectralData’s subclass relate to. Should be a class-level attribute with value of either “vibrational”, “electronic”, or “scattering”.

abstract property wavelen

Bands values converted to wavelengths in nm. If freq is provided, this may be overridden with a simple call to super():

@property
def wavelen(self):
    return super().wavelen()  # values converted to nm

property wavelengths: Bands values converted to wavelengths in nm. A convenience alias for wavelen.

class tesliper.glassware.arrays.VibrationalActivities(genre, filenames, values, freq, allow_data_inconsistency=False)[source]

For handling electronic spectral activity data.

Genres associated with this class:
iri	dip	rot

Parameters

genre – Name of the data genre that values represent.
filenames – Sequence of conformers’ identifiers.
values – Sequence of values for genre for each conformer in filenames.
freq – Frequency for each value in each conformer in \(\mathrm{cm}^{-1}\) units.
allow_data_inconsistency – Flag signalizing if instance should allow data inconsistency (see ArrayPropety for details).

average_conformers(energies) → tesliper.glassware.arrays.DataArray

A method for averaging values by population of conformers.

Parameters: energies (Energies or iterable) – Object with populations and genre attributes, containing respectively: list of populations values as numpy.ndarray and string specifying energy type. Alternatively, list of weights for each conformer.
Returns: New instance of DataArray’s subclass, on which average method was called, containing averaged values.
Return type: DataArray
Raises: TypeError – If creation of an instance based on its __init__ signature is impossible.

calculate_spectra(start, stop, step, width, fitting)

Calculates spectrum for each individual conformer.

Parameters

start (int or float) – Number representing start of spectral range in relevant units.
stop (int or float) – Number representing end of spectral range in relevant units.
step (int or float) – Number representing step of spectral range in relevant units.
width (int or float) – Number representing half width of maximum peak height.
fitting (function) – Function, which takes spectral data, freqs, abscissa, width as parameters and returns numpy.array of calculated, non-corrected spectrum points.

Returns

Calculated spectrum.

Return type

SingleSpectrum

Raises

ValueError – If given start, stop, and step values would produce an empty or one-element sequence; i.e. if start is grater than stop or if start - stop < step, assuming step is a positive value.

property frequencies: Bands values converted to frequencies in \(\mathrm{cm}^{-1}\). A convenience alias for freq.

classmethod get_init_params() → Dict[str, Union[str, inspect.Parameter]]: Returns parameters used to instantiate this class. genre is a genre of data array that is to be instantiated.

get_repr_args() → Dict[str, Any]: Returns dictionary that can be used as keword-value pairs to instantiate identical object.

property intensities

Converts spectral activity calculated by quantum chemistry software to signal intensity.

Returns: Signal intensities for each conformer.
Return type: numpy.ndarray
Raises: NotImplementedError – if genre does not provide values conversion to intensities.

property spectra_type: Type of spectra, that genres associated with SpectralData’s subclass relate to. Should be a class-level attribute with value of either “vibrational”, “electronic”, or “scattering”.

property wavelen: Bands values converted to wavelengths in nm.

property wavelengths: Bands values converted to wavelengths in nm. A convenience alias for wavelen.

class tesliper.glassware.arrays.ScatteringActivities(genre, filenames, values, freq, t=298.15, laser=532, allow_data_inconsistency=False)[source]

For handling scattering spectral activity data.

Genres associated with this class:
ramanactiv	ramact	raman1	roa1
raman2	roa2	raman3	roa3

Parameters

genre – Name of the data genre that values represent.
filenames – Sequence of conformers’ identifiers.
values – Sequence of values for genre for each conformer in filenames.
freq – Frequency for each value in each conformer in \(\mathrm{cm}^{-1}\) units.
allow_data_inconsistency – Flag signalizing if instance should allow data inconsistency (see ArrayPropety for details).

property intensities

Converts spectral activity calculated by quantum chemistry software to signal intensity.

Returns: Signal intensities for each conformer.
Return type: numpy.ndarray
Raises: NotImplementedError – if genre does not provide values conversion to intensities.

average_conformers(energies) → tesliper.glassware.arrays.DataArray

A method for averaging values by population of conformers.

Parameters: energies (Energies or iterable) – Object with populations and genre attributes, containing respectively: list of populations values as numpy.ndarray and string specifying energy type. Alternatively, list of weights for each conformer.
Returns: New instance of DataArray’s subclass, on which average method was called, containing averaged values.
Return type: DataArray
Raises: TypeError – If creation of an instance based on its __init__ signature is impossible.

calculate_spectra(start, stop, step, width, fitting)

Calculates spectrum for each individual conformer.

Parameters

start (int or float) – Number representing start of spectral range in relevant units.
stop (int or float) – Number representing end of spectral range in relevant units.
step (int or float) – Number representing step of spectral range in relevant units.
width (int or float) – Number representing half width of maximum peak height.
fitting (function) – Function, which takes spectral data, freqs, abscissa, width as parameters and returns numpy.array of calculated, non-corrected spectrum points.

Returns

Calculated spectrum.

Return type

SingleSpectrum

Raises

ValueError – If given start, stop, and step values would produce an empty or one-element sequence; i.e. if start is grater than stop or if start - stop < step, assuming step is a positive value.

property frequencies: Bands values converted to frequencies in \(\mathrm{cm}^{-1}\). A convenience alias for freq.

classmethod get_init_params() → Dict[str, Union[str, inspect.Parameter]]: Returns parameters used to instantiate this class. genre is a genre of data array that is to be instantiated.

get_repr_args() → Dict[str, Any]: Returns dictionary that can be used as keword-value pairs to instantiate identical object.

property spectra_type: Type of spectra, that genres associated with SpectralData’s subclass relate to. Should be a class-level attribute with value of either “vibrational”, “electronic”, or “scattering”.

property wavelen: Bands values converted to wavelengths in nm.

property wavelengths: Bands values converted to wavelengths in nm. A convenience alias for wavelen.

class tesliper.glassware.arrays.ElectronicActivities(genre, filenames, values, wavelen, allow_data_inconsistency=False)[source]

For handling electronic spectral activity data.

Genres associated with this class:
vdip	ldip	vrot	lrot	vosc	losc

Parameters

genre – Name of the data genre that values represent.
filenames – Sequence of conformers’ identifiers.
values – Sequence of values for genre for each conformer in filenames.
allow_data_inconsistency – Flag signalizing if instance should allow data inconsistency (see ArrayProperty for details).

property intensities

Converts spectral activity calculated by quantum chemistry software to signal intensity.

Returns: Signal intensities for each conformer.
Return type: numpy.ndarray
Raises: NotImplementedError – if genre does not provide values conversion to intensities.

calculate_spectra(start, stop, step, width, fitting)[source]

Calculates spectrum for each individual conformer.

Parameters

start (int or float) – Number representing start of spectral range in relevant units.
stop (int or float) – Number representing end of spectral range in relevant units.
step (int or float) – Number representing step of spectral range in relevant units.
width (int or float) – Number representing half width of maximum peak height.
fitting (function) – Function, which takes spectral data, freqs, abscissa, width as parameters and returns numpy.array of calculated, non-corrected spectrum points.

Returns

Calculated spectrum.

Return type

SingleSpectrum

Raises

ValueError – If given start, stop, and step values would produce an empty or one-element sequence; i.e. if start is grater than stop or if start - stop < step, assuming step is a positive value.

average_conformers(energies) → tesliper.glassware.arrays.DataArray

A method for averaging values by population of conformers.

Parameters: energies (Energies or iterable) – Object with populations and genre attributes, containing respectively: list of populations values as numpy.ndarray and string specifying energy type. Alternatively, list of weights for each conformer.
Returns: New instance of DataArray’s subclass, on which average method was called, containing averaged values.
Return type: DataArray
Raises: TypeError – If creation of an instance based on its __init__ signature is impossible.

property freq

Bands values converted to frequencies in \(\mathrm{cm}^{-1}\). If wavelen is provided, this may be overridden with a simple call to super():

@property
def freq(self):
    return super().freq()  # values converted to cm^(-1)

property frequencies: Bands values converted to frequencies in \(\mathrm{cm}^{-1}\). A convenience alias for freq.

classmethod get_init_params() → Dict[str, Union[str, inspect.Parameter]]: Returns parameters used to instantiate this class. genre is a genre of data array that is to be instantiated.

get_repr_args() → Dict[str, Any]: Returns dictionary that can be used as keword-value pairs to instantiate identical object.

property spectra_type: Type of spectra, that genres associated with SpectralData’s subclass relate to. Should be a class-level attribute with value of either “vibrational”, “electronic”, or “scattering”.

property wavelengths: Bands values converted to wavelengths in nm. A convenience alias for wavelen.

class tesliper.glassware.arrays.Transitions(genre: str, filenames: Sequence[str], values: Sequence[Sequence[Sequence[Tuple[int, int, float]]]], allow_data_inconsistency: bool = False)[source]

For handling information about electronic transitions from ground to excited state contributing to each band.

Data is stored in three attributes: ground, excited, and values, which are respectively: list of ground state electronic subshells, list of excited state electronic subshells, and list of coefficients of transitions from corresponding ground to excited subshell. Each of these arrays is of shape (conformers, bands, max_transitions), where ‘max_transitions’ is a highest number of transitions contributing to single band across all bands of all conformers.

Genres associated with this class:
transitions

values

List of coefficients of each transition. It is a 3-dimensional of shape (conformers, bands, max_transitions).

Type: numpy.ndarray(dtype=float)

ground

List of ground state electronic subshells, stored as integers assigned to them by used quantum computations program. It is a 3-dimensional array of shape (conformers, bands, max_transitions).

Type: numpy.ndarray(dtype=int)

excited

List of excited state electronic subshells, stored as integers assigned to them by used quantum computations program. It is a 3-dimensional array of shape (conformers, bands, max_transitions).

Type: numpy.ndarray(dtype=int)

Parameters

genre – Name of the data genre that values represent.
filenames – Sequence of conformers’ identifiers.
values (list of lists of lists of tuples of (int, int, float)) – Transitions data (ground and excited state electronic subshell and coefficient of transition from former to latter) for each transition of each band of each conformer.
allow_data_inconsistency – Flag signalizing if instance should allow data inconsistency (see ArrayPropety for details).

static unpack_values(values: Sequence[Sequence[Sequence[Tuple[int, int, float]]]])[source]

Unpack transitions data stored as list of tuples of (ground, excited, coefficient) to separate lists for each information pice, keeping original dimensionality (conformers, bands, transitions).

Parameters

values (list of lists of lists of tuples of (int, int, float)) – Transitions data (ground and excited state electronic subshell and coefficient of transition from former to latter) for each transition of each band of each conformer.

Returns

list of lists of lists of int,
list of lists of lists of int,
list of lists of lists of float – Transitions data separated to lists of ground, excited, and coefficients, for each transition of each band of each conformer.

property coefficients: numpy.ndarray: Coefficients of each transition, alias for values.

property contribution: numpy.ndarray: Contribution of each transition to given band, calculated as 2 * coef^2. To get values in percent, multiply by 100.

property indices_highest: Tuple[numpy.ndarray, numpy.ndarray, numpy.ndarray]: Indices of coefficients of highest contribution to band in form that can be used in numpy’s advanced indexing mechanism.

property highest_contribution: Tuple[numpy.ndarray, numpy.ndarray, numpy.ndarray, numpy.ndarray]: Electronic transitions data limited to transition of highest contribution to each band. Returns tuple with 4 arrays: ground and excited state electronic subshell, coefficient of transition from former to latter, and its contribution, for each band of each conformer.

classmethod get_init_params() → Dict[str, Union[str, inspect.Parameter]]: Returns parameters used to instantiate this class. genre is a genre of data array that is to be instantiated.

get_repr_args() → Dict[str, Any]: Returns dictionary that can be used as keword-value pairs to instantiate identical object.

class tesliper.glassware.arrays.Geometry(genre: str, filenames: Sequence[str], values: Sequence[Sequence[Sequence[float]]], atoms: Union[Sequence[Union[int, str]], Sequence[Sequence[Union[int, str]]]], allow_data_inconsistency: bool = False)[source]

For handling information about geometry of conformers.

Genres associated with this class:
last_read_geom	input_geom	optimized_geom

Parameters

genre – Name of the data genre that values represent.
filenames – Sequence of conformers’ identifiers.
values – List of x, y, z coordinated for each conformer, for each atom.
allow_data_inconsistency – Flag signalizing if instance should allow data inconsistency (see ArrayPropety for details). False by default.
atoms – List of atomic numbers representing atoms in conformer, one for each coordinate. Should be a list of integers or list of strings, that can be interpreted as integers or symbols of atoms. May also be a list of such lists - one list of atoms for each conformer. All those lists should be identical in such case, otherwise InconsistentDataError is raised. Only one list of atoms is stored in either case.

get_repr_args() → Dict[str, Any]: Returns dictionary that can be used as keword-value pairs to instantiate identical object.

classmethod get_init_params() → Dict[str, Union[str, inspect.Parameter, tesliper.glassware.array_base.DependentParameter]][source]: Returns parameters used to instantiate this class. genre is a genre of data array that is to be instantiated.