pmutt.statmech.StatMech

class pmutt.statmech.StatMech(name=None, trans_model=<pmutt.statmech.EmptyMode object>, vib_model=<pmutt.statmech.EmptyMode object>, rot_model=<pmutt.statmech.EmptyMode object>, elec_model=<pmutt.statmech.EmptyMode object>, nucl_model=<pmutt.statmech.EmptyMode object>, misc_models=None, elements=None, references=None, smiles=None, notes=None, **kwargs)

Bases: _ModelBase

Base class for statistical mechanic models.

name

Name of the specie. Default is None

Type:

str, optional

trans_model

Deals with translational modes. Default is EmptyMode

Type:

pmutt.statmech.trans object, optional

vib_model

Deals with vibrational modes. Default is EmptyMode

Type:

pmutt.statmech.vib object, optional

rot_model

Deals with rotational modes. Default is EmptyMode

Type:

pmutt.statmech.rot object, optional

elec_model

Deals with electronic modes. Default is EmptyMode

Type:

pmutt.statmech.elec object, optional

nucl_model

Deals with nuclear modes. Default is EmptyMode

Type:

pmutt.statmech.nucl object

elements

Composition of the species. Default is None. Keys of dictionary are elements, values are stoichiometric values in a formula unit. e.g. CH3OH can be represented as: {‘C’: 1, ‘H’: 4, ‘O’: 1,}.

Type:

dict, optional

references

Contains references to adjust HoRT. If not specified then HoRT_dft will be used without adjustment. Default is None

Type:

References, optional

misc_models

Extra models that do not fit in the above attributes. Commonly used models would be pmutt.statmech and pmutt.mixture models

Type:

list of pmutt model objects, optional

smiles

Smiles representation of species

Type:

str, optional

notes

Any additional details you would like to include such as computational set up. Default is None

Type:

str, optional

__init__(name=None, trans_model=<pmutt.statmech.EmptyMode object>, vib_model=<pmutt.statmech.EmptyMode object>, rot_model=<pmutt.statmech.EmptyMode object>, elec_model=<pmutt.statmech.EmptyMode object>, nucl_model=<pmutt.statmech.EmptyMode object>, misc_models=None, elements=None, references=None, smiles=None, notes=None, **kwargs)

Methods

__init__([name, trans_model, vib_model, ...])

from_dict(json_obj)

Recreate an object from the JSON representation.

get_Cp(units[, verbose, raise_error, ...])

Calculate the heat capacity (constant P)

get_CpoR([verbose, raise_error, ...])

Dimensionless heat capacity (constant P)

get_Cv(units[, verbose, raise_error, ...])

Calculate the heat capacity (constant V)

get_CvoR([verbose, raise_error, ...])

Dimensionless heat capacity (constant V)

get_E(units[, T, raise_error, ...])

Calculate the electronic energy

get_EoRT([T, include_ZPE, raise_error, ...])

Dimensionless electronic energy

get_F(units[, T, verbose, raise_error, ...])

Calculate the Helmholtz energy

get_FoRT([verbose, raise_error, ...])

Dimensionless Helmholtz energy

get_G(units[, T, verbose, raise_error, ...])

Calculate the Gibbs energy

get_GoRT([verbose, raise_error, ...])

Dimensionless Gibbs energy

get_H(units[, T, raise_error, ...])

Calculate the enthalpy

get_HoRT([verbose, raise_error, ...])

Dimensionless enthalpy

get_S(units[, verbose, raise_error, ...])

Calculate the entropy

get_Selements()

Calculate the dimensionless entropy of the elements in the molecule

get_SoR([verbose, raise_error, ...])

Dimensionless entropy

get_U(units[, T, verbose, raise_error, ...])

Calculate the internal energy

get_UoRT([verbose, raise_error, ...])

Dimensionless internal energy

get_q([verbose, raise_error, raise_warning, ...])

Partition function

get_quantity(method_name[, raise_error, ...])

Generic method to get any quantity from modes.

to_dict()

Represents object as dictionary with JSON-accepted datatypes
classmethod from_dict(json_obj)

Recreate an object from the JSON representation.

Parameters:

json_obj (dict) – JSON representation

Returns:

StatMech

Return type:

StatMech object

get_Cp(units, verbose=False, raise_error=True, raise_warning=True, use_references=True, **kwargs)

Calculate the heat capacity (constant P)

Parameters:

  • units (str) – Units as string. See R() for accepted units.

  • verbose (bool, optional) – If False, returns the total heat capacity. If True, returns contribution of each mode.

  • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

  • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

  • use_references (bool, optional) – If True, adds contribution from references. Default is True

  • kwargs (key-word arguments) – Parameters passed to each mode

Returns:

Cp – Heat capacity. N represents the number of misc models. If verbose is True, contribution to each mode are as follows: [trans, vib, rot, elec, nucl, misc_models (if any)]

Return type:

float or (N+5,) numpy.ndarray

get_CpoR(verbose=False, raise_error=True, raise_warning=True, use_references=True, **kwargs)

Dimensionless heat capacity (constant P)

Parameters:

  • verbose (bool, optional) – If False, returns the total heat capacity. If True, returns contribution of each mode.

  • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

  • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

  • use_references (bool, optional) – If True, adds contribution from references. Default is True

  • kwargs (key-word arguments) – Parameters passed to each mode

Returns:

CpoR – Dimensionless heat capacity. N represents the number of misc models. If verbose is True, contribution to each mode are as follows: [trans, vib, rot, elec, nucl, misc_models (if any)]

Return type:

float or (N+5,) numpy.ndarray

get_Cv(units, verbose=False, raise_error=True, raise_warning=True, use_references=True, **kwargs)

Calculate the heat capacity (constant V)

Parameters:

  • units (str) – Units as string. See R() for accepted units.

  • verbose (bool, optional) – If False, returns the total heat capacity. If True, returns contribution of each mode.

  • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

  • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

  • use_references (bool, optional) – If True, adds contribution from references. Default is True

  • kwargs (key-word arguments) – Parameters passed to each mode

Returns:

Cv – Heat capacity. N represents the number of misc models. If verbose is True, contribution to each mode are as follows: [trans, vib, rot, elec, nucl, misc_models (if any)]

Return type:

float or (N+5,) numpy.ndarray

get_CvoR(verbose=False, raise_error=True, raise_warning=True, use_references=True, **kwargs)

Dimensionless heat capacity (constant V)

Parameters:

  • verbose (bool, optional) – If False, returns the total heat capacity. If True, returns contribution of each mode.

  • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

  • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

  • use_references (bool, optional) – If True, adds contribution from references. Default is True

  • kwargs (key-word arguments) – Parameters passed to each mode

Returns:

CvoR – Dimensionless heat capacity. N represents the number of misc models. If verbose is True, contribution to each mode are as follows: [trans, vib, rot, elec, nucl, misc_models (if any)]

Return type:

float or (N+5,) numpy.ndarray

get_E(units, T=298.15, raise_error=True, raise_warning=True, include_ZPE=False, **kwargs)

Calculate the electronic 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. If the electronic mode is GroundStateElec, then the output is insensitive to this input. Default is 298.15 K

  • include_ZPE (bool, optional) – If True, includes the zero point energy. Default is False

  • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

  • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

  • kwargs (key-word arguments) – Parameters passed to each mode

Returns:

E – Electronic energy

Return type:

float

get_EoRT(T=298.15, include_ZPE=False, raise_error=True, raise_warning=True, **kwargs)

Dimensionless electronic energy

Parameters:

  • T (float, optional) – Temperature in K. If the electronic mode is GroundStateElec, then the output is insensitive to this input. Default is 298.15 K

  • include_ZPE (bool, optional) – If True, includes the zero point energy. Default is False

  • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

  • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

  • kwargs (key-word arguments) – Parameters passed to electronic mode

Returns:

EoRT – Dimensionless electronic energy

Return type:

float

get_F(units, T=298.15, verbose=False, raise_error=True, raise_warning=True, use_references=True, S_elements=None, **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

  • verbose (bool, optional) – If False, returns the Helmholtz energy. If True, returns contribution of each mode.

  • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

  • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

  • use_references (bool, optional) – If True, adds contribution from references. Default is True

  • S_elements (bool, optional) – Includes the entropy of the elements to compute an entropy of formation. Defauly is None

  • kwargs (key-word arguments) – Parameters passed to each mode

Returns:

F – Helmholtz energy. N represents the number of misc models. If verbose is True, contribution to each mode are as follows: [trans, vib, rot, elec, nucl, misc_models (if any)]

Return type:

float or (N+5,) numpy.ndarray

get_FoRT(verbose=False, raise_error=True, raise_warning=True, use_references=True, S_elements=None, **kwargs)

Dimensionless Helmholtz energy

Parameters:

  • verbose (bool, optional) – If False, returns the total Helmholtz energy. If True, returns contribution of each mode.

  • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

  • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

  • use_references (bool, optional) – If True, adds contribution from references. Default is True

  • S_elements (bool, optional) – Includes the entropy of the elements to compute an entropy of formation. Defauly is None

  • kwargs (key-word arguments) – Parameters passed to each mode

Returns:

FoRT – Dimensionless Helmoltz energy. N represents the number of misc models. If verbose is True, contribution to each mode are as follows: [trans, vib, rot, elec, nucl, misc_models (if any)]

Return type:

float or (N+5,) numpy.ndarray

get_G(units, T=298.15, verbose=False, raise_error=True, raise_warning=True, use_references=True, S_elements=None, **kwargs)

Calculate the Gibbs energy

Parameters:

  • verbose (bool, optional) – If False, returns the Gibbs energy. If True, returns contribution of each mode.

  • 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

  • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

  • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

  • S_elements (bool, optional) – Includes the entropy of the elements to compute an entropy of formation. Defauly is None

  • kwargs (key-word arguments) – Parameters passed to each mode

Returns:

G – Gibbs energy. N represents the number of misc models. If verbose is True, contribution to each mode are as follows: [trans, vib, rot, elec, nucl, misc_models (if any)]

Return type:

float or (N+5,) numpy.ndarray

get_GoRT(verbose=False, raise_error=True, raise_warning=True, use_references=True, S_elements=None, **kwargs)

Dimensionless Gibbs energy

Parameters:

  • verbose (bool, optional) – If False, returns the total Gibbs energy. If True, returns contribution of each mode.

  • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

  • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

  • use_references (bool, optional) – If True, adds contribution from references. Default is True

  • S_elements (bool, optional) – Includes the entropy of the elements to compute an entropy of formation. Defauly is None

  • kwargs (key-word arguments) – Parameters passed to each mode

Returns:

GoRT – Dimensionless Gibbs energy. N represents the number of misc models. If verbose is True, contribution to each mode are as follows: [trans, vib, rot, elec, nucl, misc_models (if any)]

Return type:

float or (N+5,) numpy.ndarray

get_H(units, T=298.15, raise_error=True, raise_warning=True, verbose=False, use_references=True, **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

  • verbose (bool, optional) – If False, returns the enthalpy. If True, returns contribution of each mode.

  • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

  • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

  • use_references (bool, optional) – If True, adds contribution from references. Default is True

  • kwargs (key-word arguments) – Parameters passed to each mode

Returns:

H – Enthalpy. N represents the number of misc models. If verbose is True, contribution to each mode are as follows: [trans, vib, rot, elec, nucl, misc_models (if any)]

Return type:

float or (N+5,) numpy.ndarray

get_HoRT(verbose=False, raise_error=True, raise_warning=True, use_references=True, **kwargs)

Dimensionless enthalpy

Parameters:

  • verbose (bool, optional) – If False, returns the total enthalpy. If True, returns contribution of each mode.

  • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

  • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

  • use_references (bool, optional) – If True, adds contribution from references. Default is True

  • kwargs (key-word arguments) – Parameters passed to each mode

Returns:

HoRT – Dimensionless enthalpy. N represents the number of misc models. If verbose is True, contribution to each mode are as follows: [trans, vib, rot, elec, nucl, misc_models (if any)]

Return type:

float or (N+5,) numpy.ndarray

get_S(units, verbose=False, raise_error=True, raise_warning=True, use_references=True, S_elements=None, **kwargs)

Calculate the entropy

Parameters:

  • units (str) – Units as string. See R() for accepted units.

  • verbose (bool, optional) – If False, returns the entropy. If True, returns contribution of each mode.

  • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

  • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

  • use_references (bool, optional) – If True, adds contribution from references. Default is True

  • S_elements (bool, optional) – Includes the entropy of the elements to compute an entropy of formation. Defauly is None

  • kwargs (key-word arguments) – Parameters passed to each mode

Returns:

S – Entropy. N represents the number of misc models. If verbose is True, contribution to each mode are as follows: [trans, vib, rot, elec, nucl, misc_models (if any)]

Return type:

float or (N+5,) numpy.ndarray

get_Selements()

Calculate the dimensionless entropy of the elements in the molecule

Parameters:

None –

Returns:

SoR – Entropy

Return type:

float

get_SoR(verbose=False, raise_error=True, raise_warning=True, use_references=True, S_elements=None, **kwargs)

Dimensionless entropy

Parameters:

  • verbose (bool, optional) – If False, returns the total entropy. If True, returns contribution of each mode.

  • kwargs (key-word arguments) – Parameters passed to each mode

  • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

  • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

  • use_references (bool, optional) – If True, adds contribution from references. Default is True

  • S_elements (bool, optional) – Includes the entropy of the elements to compute an entropy of formation. Defauly is None

Returns:

SoR – Dimensionless entropy. N represents the number of misc models. If verbose is True, contribution to each mode are as follows: [trans, vib, rot, elec, nucl, misc_models (if any)]

Return type:

float or (N+5,) numpy.ndarray

get_U(units, T=298.15, verbose=False, raise_error=True, raise_warning=True, use_references=True, **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

  • verbose (bool, optional) – If False, returns the internal energy. If True, returns contribution of each mode.

  • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

  • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

  • use_references (bool, optional) – If True, adds contribution from references. Default is True

  • kwargs (key-word arguments) – Parameters passed to each mode

Returns:

U – Internal energy. N represents the number of misc models. If verbose is True, contribution to each mode are as follows: [trans, vib, rot, elec, nucl, misc_models (if any)]

Return type:

float or (N+5,) numpy.ndarray

get_UoRT(verbose=False, raise_error=True, raise_warning=True, use_references=True, **kwargs)

Dimensionless internal energy

Parameters:

  • verbose (bool, optional) – If False, returns the total internal energy. If True, returns contribution of each mode.

  • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

  • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

  • use_references (bool, optional) – If True, adds contribution from references. Default is True

  • kwargs (key-word arguments) – Parameters passed to each mode

Returns:

UoRT – Dimensionless internal energy. N represents the number of misc models. If verbose is True, contribution to each mode are as follows: [trans, vib, rot, elec, nucl, misc_models (if any)]

Return type:

float or (N+5,) numpy.ndarray

get_q(verbose=False, raise_error=True, raise_warning=True, use_references=True, **kwargs)

Partition function

Parameters:

  • verbose (bool, optional) – If False, returns the product of partition functions. If True, returns contributions of each mode

  • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

  • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

  • use_references (bool, optional) – If True, adds contribution from references. Default is True

  • kwargs (key-word arguments) – Parameters passed to each mode

Returns:

q – Partition function. N represents the number of misc models. If verbose is True, contribution to each mode are as follows: [trans, vib, rot, elec, nucl, misc_models (if any)]

Return type:

float or (N+5,) numpy.ndarray

get_quantity(method_name, raise_error=True, raise_warning=True, operation='sum', verbose=False, use_references=True, **kwargs)

Generic method to get any quantity from modes.

Parameters:

  • method_name (str) – Name of method to use to calculate quantity. Calculates any quantity as long as the relevant objects have the same method name

  • raise_error (bool, optional) – If True, raises an error if any of the modes do not have the quantity of interest. Default is True

  • raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if any of the modes do not have the quantity of interest. Default is True

  • operation (str, optional) –

    Operation to apply when combining the modes. Supported options include:

    • sum (Default)

    • prod

  • use_references (bool, optional) – If True, adds contribution from references. Default is True

  • verbose (bool, optional) – If False, returns the total Gibbs energy. If True, returns contribution of each mode.

  • kwargs (key-word arguments) – Parameters passed to each mode

Returns:

quantity – Desired quantity. N represents the number of misc models. If verbose is True, contribution to each mode are as follows: [trans, vib, rot, elec, nucl, references, misc_models (if any)]

Return type:

float or (N+6,) numpy.ndarray

to_dict()

Represents object as dictionary with JSON-accepted datatypes

Returns:

obj_dict

Return type:

dict