pmutt.omkm.reaction.SurfaceReaction

class pmutt.omkm.reaction.SurfaceReaction(id=None, is_adsorption=False, A=None, beta=None, Ea=None, sticking_coeff=None, direction=None, use_motz_wise=False, **kwargs)

Bases: Reaction

Expresses OpenMKM surface reaction in Cantera CTI format reaction. Inherits from Reaction.

id

ID of the reaction. Default is None

Type:: str, optional

is_adsorption

If True, the reaction represents an adsorption. Default is False

Type:: bool, optional

A

Pre-exponential constant. If not specified, uses reaction to determine value.

Type:: float, optional

beta

Power to raise the temperature in the rate expression. Default is 1 if is_adsorption is False, 0 if is_adsorption is True.

Type:: float, optional

Ea

Activation energy in kcal/mol. If not specified, uses reaction to determine value.

Type:: float, optional

sticking_coeff

Sticking coefficient. Only relevant if is_adsorption is True. Default is 0.5 if is_adsorption is True, None if is_adsorption is False.

Type:: float, optional

direction

Direction of the reaction. Used for BEP relationships. Accepted options are ‘cleavage’ and ‘synthesis’.

Type:: str, optional

use_motz_wise

Used when generating OpenMKM YAML file. If True, uses Motz-Wise correction to sticking coefficient. Only applicable to adsorption reactions. Default is False.

Type:: bool, optional

kwargs

Keyword arguments used to initialize the reactants, transition state and products

Type:: keyword arguments

__init__(id=None, is_adsorption=False, A=None, beta=None, Ea=None, sticking_coeff=None, direction=None, use_motz_wise=False, **kwargs)

Methods

`__init__`([id, is_adsorption, A, beta, Ea, ...])
`check_element_balance`()	Checks the reactants, products and transition state elemental composition
`from_dict`(json_obj)	Recreate an object from the JSON representation.
`from_string`(reaction_str, species[, ...])	Create a reaction object using the reaction string
`get_A`([sden_operation, include_entropy, T, ...])	Calculates the preexponential factor in the Cantera format
`get_Cp_act`(units[, rev])	Gets change in heat capacity (constant P) between reactants/products and the transition state
`get_Cp_state`(state, units, **kwargs)	Gets the heat capacity at constant pressure at a state
`get_CpoR_act`([rev])	Gets change in dimensionless heat capacity between reactants/products and the transition state
`get_CpoR_state`(state, **kwargs)	Gets dimensionless heat capacity at constant pressure at a state
`get_Cv_act`(units[, rev])	Gets change in heat capacity (constant V) between reactants/products and the transition state
`get_Cv_state`(state, units, **kwargs)	Gets the heat capacity at constant volume at a state
`get_CvoR_act`([rev])	Gets change in dimensionless heat capacity (constant V) between reactants/products and the transition state
`get_CvoR_state`(state, **kwargs)	Gets dimensionless heat capacity at constant volume at a state
`get_E_act`(units, T[, rev, del_m])	Gets act energy between reactants (or products) and transition state
`get_E_state`(state, units[, T, include_ZPE])	Gets the electronic energy at a state
`get_EoRT_act`([rev, del_m])	Gets dimensionless Arrhenius activation energy between reactants (or products) and transition state
`get_EoRT_state`(state[, include_ZPE])	Gets dimensionless electronic energy at a state
`get_F_act`(units, T[, rev])	Gets change in Helmholtz energy between reactants/products and the transition state
`get_F_state`(state, units, T, **kwargs)	Gets the Helholtz energy at a state
`get_FoRT_act`([rev])	Gets change in dimensionless Helmholtz energy between reactants/products and transition state
`get_FoRT_state`(state, **kwargs)	Gets dimensionless Helmholtz energy at a state
`get_G_act`(units, T[, P, rev])	Calculates the Gibbs energy of activation.
`get_G_state`(state, units, T, **kwargs)	Gets the Gibbs energy at a state
`get_GoRT_act`([rev, act])	Calculates the dimensionless Gibbs energy of activation.
`get_GoRT_state`(state, **kwargs)	Gets dimensionless Gibbs energy at a state
`get_H_act`(units, T[, rev])	Calculates the enthalpy of activation.
`get_H_state`(state, units, T, **kwargs)	Gets the enthalpy at a state
`get_HoRT_act`([rev])	Calculates the dimensionless enthalpy of activation.
`get_HoRT_state`(state, **kwargs)	Gets dimensionless enthalpy at a state
`get_Keq`([rev, act])	Gets equilibrium constant between reactants and products
`get_S_act`(units[, rev])	Gets change in entropy between reactants/products and the transition state
`get_S_state`(state, units, **kwargs)	Gets the entropy at a state
`get_SoR_act`([rev])	Gets change in dimensionless entropy between reactants/products and the transition state
`get_SoR_state`(state, **kwargs)	Gets dimensionless entropy at a state
`get_U_act`(units, T[, rev])	Gets change in internal energy between reactants/products and the transition state
`get_U_state`(state, units, T, **kwargs)	Gets the internal energy at a state
`get_UoRT_act`([rev])	Gets change in dimensionless internal energy between reactants/products and the transition state
`get_UoRT_state`(state, **kwargs)	Gets dimensionless internal energy at a state
`get_delta_Cp`(units[, rev, act])	Gets change in heat capacity (constant P) between reactants and products
`get_delta_CpoR`([rev, act])	Gets change in dimensionless heat capacity between reactants and products
`get_delta_Cv`(units[, rev, act])	Gets change in heat capacity (constant V) between reactants and products
`get_delta_CvoR`([rev, act])	Gets change in dimensionless heat capacity (constant V) between reactants and products
`get_delta_E`(units, T[, rev, act])	Gets change in electronic energy between reactants and products
`get_delta_EoRT`([rev, act])	Gets change in dimensionless electronic energy between reactants and products
`get_delta_F`(units, T[, rev, act])	Gets change in Helmholtz energy between reactants and products
`get_delta_FoRT`([rev, act])	Gets change in dimensionless Helmholtz energy between reactants and products
`get_delta_G`(units, T[, rev, act])	Gets change in Gibbs energy between reactants and products
`get_delta_GoRT`([rev, act])	Gets change in dimensionless Gibbs energy between reactants and products
`get_delta_H`(units, T[, rev, act])	Gets change in enthalpy between reactants and products
`get_delta_HoRT`([rev, act])	Gets change in dimensionless enthalpy between reactants and products
`get_delta_S`(units[, rev, act])	Gets change in entropy between reactants and products
`get_delta_SoR`([rev, act])	Gets change in dimensionless entropy between reactants and products
`get_delta_U`(units, T[, rev, act])	Gets change in internal energy between reactants and products
`get_delta_UoRT`([rev, act])	Gets change in dimensionless internal energy between reactants and products
`get_delta_q`([rev, act])	Gets change in partition function between reactants and products
`get_delta_quantity`(initial_state, ...)	Helper method to calculate the change in thermodynamic quantity between states
`get_q_act`([rev, include_ZPE])	Gets change in partition function between reactants/products and the transition state
`get_q_state`(state, **kwargs)	Gets partition function at a state
`get_species`([include_TS, key])	Returns the unique species included in the reaction.
`get_state_quantity`(state, method_name, **kwargs)	Helper method to calculate the thermodynamic quantity of the state
`to_cti`([T, P, quantity_unit, length_unit, ...])	Writes the object in Cantera's CTI format.
`to_dict`()	Represents object as dictionary with JSON-accepted datatypes
`to_omkm_yaml`([T, P, quantity_unit, ...])	Writes the object in Cantera's YAML format.
`to_string`([species_delimiter, ...])	Writes the Reaction object as a stoichiometric reaction

Attributes

`beta`
`id`
`products`
`products_stoich`
`reactants`
`reactants_stoich`
`sticking_coeff`
`transition_state`
`transition_state_stoich`

property beta

check_element_balance()

Checks the reactants, products and transition state elemental composition

Raises:: ValueError – Raised if the reactants, products and/or transition state element composition does not agree.

classmethod from_dict(json_obj)

Recreate an object from the JSON representation.

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

classmethod from_string(reaction_str, species, species_delimiter='+', reaction_delimiter='=', notes=None, A=None, beta=1, Ea=None, is_adsorption=False, sticking_coeff=0.5, direction=None, id=None, use_motz_wise=False)

Create a reaction object using the reaction string

Parameters:

reaction_str (str) – Reaction string.
species (dict) – Dictionary using the names as keys. If you have a list of species, use pmutt.pmutt_list_to_dict to make a dict.
species_delimiter (str, optional) – Delimiter that separate species. Leading and trailing spaces will be trimmed. Default is ‘+’
reaction_delimiter (str, optional) – Delimiter that separate states of the reaction. Leading and trailing spaces will be trimmed. Default is ‘=’
notes (str or dict, optional) – Other notes such as the source of the reaction. Default is None
A (float, optional) – Pre-exponential constant. If not specified, uses reaction to determine value.
beta (float, optional) – Power to raise the temperature in the rate expression. Default is 1 if is_adsorption is False, 0 if is_adsorption is True.
Ea (float, optional) – Activation energy. If not specified, uses reaction to determine value.
is_adsorption (bool, optional) – If True, the reaction represents an adsorption. Default is False
sticking_coeff (float, optional) – Sticking coefficient. Only relevant if is_adsorption is True. Default is 0.5
gas_phase (bool) – True if the reaction has only gas-phase species. This attribute is determined based on the reactants and products
use_motz_wise (bool, optional) – Used when generating OpenMKM YAML file. If True, uses Motz-Wise correction to sticking coefficient. Only applicable to adsorption reactions. Default is False.

Returns:

SurfaceReaction

Return type:

SurfaceReaction object

get_A(sden_operation='sum', include_entropy=True, T=298.15, units='molec/cm2', **kwargs)

Calculates the preexponential factor in the Cantera format

Parameters:

sden_operation (str, optional) – Site density operation to use. Default is ‘min’
include_entropy (bool, optional) – If True, includes the entropy of activation. Default is True
T (float, optional) – Temperature in K. Default is 298.15 K
units (str or Units, optional) – Units for A. If Units class specified, determines the units for A. Default is ‘molec/cm2’
kwargs (keyword arguments) – Parameters required to calculate pre-exponential factor

get_Cp_act(units, rev=False, **kwargs)

Gets change in heat capacity (constant P) between reactants/products and the transition state

Parameters:

units (str) – Units as string. See R() for accepted units.
rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False
kwargs (keyword arguments) – Parameters required to calculate heat capacity. See class docstring to see how to pass specific parameters to different species.

Returns:

delta_Cp – Change in heat capacity between reactants/products and the transition state

Return type: