pmutt.empirical.references.References

class pmutt.empirical.references.References(offset=None, references=None, descriptor='elements', T_ref=298.15)

Bases: _ModelBase

Holds reference species to adjust DFT energies to experimental data.

offset

Dimensionless enthalpy offset for each descriptor

Type:: dict

references

Reference species. Each member of the list should have the attributes T_ref and HoRT_ref

Type:: list of Reference, optional

descriptor

Descriptor to use to calculate offset. Default is ‘elements’

Type:: str, optional

T_ref

Reference temperature in K. Default is 298.15 K

Type:: float, optional

__init__(offset=None, references=None, descriptor='elements', T_ref=298.15)

Methods

`__init__`([offset, references, descriptor, T_ref])
`append`(obj)
`clear_offset`()	Removes all entries from descriptor offset dictionary.
`extend`(seq)
`fit_HoRT_offset`()	Calculate the descriptoral offset between DFT and formation energies using reference species.
`from_dict`(json_obj)	Recreate an object from the JSON representation.
`get_AoRT`(descriptors, T)
`get_Cp`(units, **kwargs)	Calculate the heat capacity (constant P)
`get_CpoR`()	Default method to calculate the dimensionless heat capacity at constant pressure.
`get_Cv`(units, **kwargs)	Calculate the heat capacity (constant V)
`get_CvoR`()	Default method to calculate the dimensionless heat capacity at constant volume.
`get_F`(units[, T])	Calculate the Helmholtz energy
`get_FoRT`(**kwargs)	Calculates the dimensionless Helmholtz energy
`get_G`(units[, T])	Calculate the Gibbs energy
`get_GoRT`(descriptors, T)	Calculates the dimensionless Gibbs free energy
`get_H`(units[, T])	Calculate the enthalpy
`get_HoRT`(descriptors[, T])	Returns the offset due to the descriptor composition of a specie.
`get_S`(units, **kwargs)	Calculate the entropy
`get_SoR`()	Default method to calculate the dimensionless entropy.
`get_U`(units[, T])	Calculate the internal energy
`get_UoRT`()	Default method to calculate the dimensionless internal energy.
`get_descriptors`()	Returns the descriptors in references.
`get_descriptors_matrix`()	Creates the descriptors matrix required for calculating the offset.
`get_q`()	Default method to calculate the partition coefficient.
`index`(name)
`insert`(obj)
`pop`([obj])
`remove`(obj)
`to_dict`()	Represents object as dictionary with JSON-accepted datatypes

append(obj)

clear_offset(): Removes all entries from descriptor offset dictionary.

extend(seq)

fit_HoRT_offset(): Calculate the descriptoral offset between DFT and formation energies using reference species.

classmethod from_dict(json_obj)

Recreate an object from the JSON representation.

Parameters:: json_obj (dict) – JSON representation
Returns:: References
Return type:: References object

get_AoRT(descriptors, T)

get_Cp(units, **kwargs)

Calculate the heat capacity (constant P)

Parameters:

units (str) – Units as string. See R() for accepted units.
kwargs (keyword arguments) – Parameters needed by get_CpoR

Returns:

Cp – Heat capacity (constant P) in appropriate units

Return type:

float

get_CpoR()

Default method to calculate the dimensionless heat capacity at constant pressure.

Returns:: CpoR – Returns 0
Return type:: float

get_Cv(units, **kwargs)

Calculate the heat capacity (constant V)

Parameters:

units (str) – Units as string. See R() for accepted units.
kwargs (keyword arguments) – Parameters needed by get_CvoR

Returns:

Cv – Heat capacity (constant V) in appropriate units

Return type:

float

get_CvoR()

Default method to calculate the dimensionless heat capacity at constant volume.

Returns:: CvoR – Returns 0
Return type:: float

get_F(units, T=298.15, **kwargs)

Calculate the Helmholtz energy

Parameters:

units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).
T (float, optional) – Temperature in K. Default is 298.15 K
kwargs (keyword arguments) – Parameters needed by get_FoRT

Returns:

F – Hemholtz energy in appropriate units

Return type:

float

get_FoRT(**kwargs)

Calculates the dimensionless Helmholtz energy

Parameters:: kwargs (keyword arguments) – Parameters needed by get_UoRT and get_SoR
Returns:: FoRT – Dimensionless Helmholtz energy
Return type:: float

get_G(units, T=298.15, **kwargs)

Calculate the Gibbs energy

Parameters:

units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).
T (float, optional) – Temperature in K. Default is 298.15 K
kwargs (keyword arguments) – Parameters needed by get_GoRT

Returns:

G – Gibbs energy in appropriate units

Return type:

float

get_GoRT(descriptors, T)

Calculates the dimensionless Gibbs free energy

Parameters:: kwargs (keyword arguments) – Parameters needed by get_HoRT and get_SoR
Returns:: GoRT – Dimensionless Gibbs free energy
Return type:: float

get_H(units, T=298.15, **kwargs)

Calculate the enthalpy

Parameters:

units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).
T (float, optional) – Temperature in K. Default is 298.15 K
kwargs (keyword arguments) – Parameters needed by get_HoRT

Returns:

H – Enthalpy in appropriate units

Return type:

float

get_HoRT(descriptors, T=None)

Returns the offset due to the descriptor composition of a specie. The offset is defined as follows:

\(HoRT_{exp} = HoRT_{dft} + offset\)

Parameters:

descriptors (dict) – Dictionary where the keys are decriptors and the values are the number of each descriptor in a formula unit
T (float or (N,) numpy.ndarray, optional) – Temperature in K. If not specified, adjusts using T_ref

Returns:

HoRT – Offset to add to potentialenergy (in eV) to adjust to References

Return type:

float

get_S(units, **kwargs)

Calculate the entropy

Parameters:

units (str) – Units as string. See R() for accepted units.
kwargs (keyword arguments) – Parameters needed by get_SoR

Returns:

S – Entropy in appropriate units

Return type:

float

get_SoR()

Default method to calculate the dimensionless entropy.

Returns:: SoR – Returns 0
Return type:: float

get_U(units, T=298.15, **kwargs)

Calculate the internal energy

Parameters:

units (str) – Units as string. See R() for accepted units but omit the ‘/K’ (e.g. J/mol).
T (float, optional) – Temperature in K. Default is 298.15 K
kwargs (keyword arguments) – Parameters needed by get_UoRT

Returns:

U – Internal energy in appropriate units

Return type:

float

get_UoRT()

Default method to calculate the dimensionless internal energy.

Returns:: UoRT – Returns 0
Return type:: float

get_descriptors()

Returns the descriptors in references.

Returns:: descriptors – Unique descriptors in reference species
Return type:: tuple

get_descriptors_matrix()

Creates the descriptors matrix required for calculating the offset. The descriptors are sorted in alphabetical order.

Returns:: descriptor matrix – Rows correspond to reference species. Columns correspond to descriptors
Return type:: (M,N) numpy.ndarray

get_q()

Default method to calculate the partition coefficient.

Returns:: q – Returns 1
Return type:: float

index(name)

insert(obj)

pop(obj=-1)

remove(obj)

to_dict()

Represents object as dictionary with JSON-accepted datatypes

Returns:: obj_dict
Return type:: dict