pmutt.reaction.Reaction

class pmutt.reaction.Reaction(reactants, reactants_stoich, products, products_stoich, transition_state=None, transition_state_stoich=None, notes=None)

Bases: _pmuttBase

Represents a chemical reaction

reactants

Reactants

Type:: list of pmutt model objects

reactants_stoich

Stoichiometric quantities of reactants

Type:: list of float

products

Products

Type:: list of pmutt model objects

products_stoich

Stoichiometric quantities of products

Type:: list of float

transition_state

Transition state specie. Default is None

Type:: pmutt model object, optional

transition_state_stoich

Stoichiometric quantities of transition state species. Default is None

Type:: list of float, optional

notes

Other notes such as the source of the reaction. Default is None

Type:: str or dict, optional

Notes

Specie-specific parameters can be passed by having a key named after the specie mapping onto a dictionary whose keys are the parameters to pass.

e.g. For the reaction: H2 + 0.5O2 = H2O, the pressures can be specified independently using the following dictionary. In this example arbitrary values were used so the quantity evaluated may be meaningless.

kwargs = {
    'T': 298.,
    'H2_kwargs': {'P': 2.},
    'O2_kwargs': {'P': 1.},
    'H2O_kwargs': {'P': 1.,}
}

__init__(reactants, reactants_stoich, products, products_stoich, transition_state=None, transition_state_stoich=None, notes=None)

Methods

`__init__`(reactants, reactants_stoich, ...[, ...])
`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`([T, rev, m, use_q])	Gets pre-exponential factor between reactants (or products) and transition state in 1/s
`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[, rev])	Gets change in Gibbs energy between reactants/products and the transition state
`get_G_state`(state, units, T, **kwargs)	Gets the Gibbs energy at a state
`get_GoRT_act`([rev])	Gets change in dimensionless Gibbs energy between reactants/products and the transition state
`get_GoRT_state`(state, **kwargs)	Gets dimensionless Gibbs energy at a state
`get_H_act`(units, T[, rev])	Gets change in enthalpy between reactants/products and the transition state
`get_H_state`(state, units, T, **kwargs)	Gets the enthalpy at a state
`get_HoRT_act`([rev])	Gets change in dimensionless enthalpy between reactants/products and the transition state
`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_dict`()	Represents object as dictionary with JSON-accepted datatypes
`to_string`([species_delimiter, ...])	Writes the Reaction object as a stoichiometric reaction

Attributes

`products`
`products_stoich`
`reactants`
`reactants_stoich`
`transition_state`
`transition_state_stoich`

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, raise_error=True, raise_warning=True)

Create a reaction object using the reaction string

Parameters:

reaction_str (str) – Reaction string.
species (dict or list) – Dictionary using the names as keys. If you have a list of species it will automatically be converted to a dictionary.
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
raise_error (bool, optional) – If True, raises an error if the transition state is not located in species. Default is True
raise_warning (bool, optional) – Only relevant if raise_error is False. Raises a warning if the transition state is not located in species. If a warning is raised, the Reaction will try to be initialized without the transition state. Default is True

Returns:

Reaction

Return type:

Reaction object

Raises:

KeyError – Raised if species does not contain an entry for the reactants, products or transition state in reaction_str

get_A(T=298.15, rev=False, m=0, use_q=True, **kwargs)

Gets pre-exponential factor between reactants (or products) and transition state in 1/s

\(A = \frac {k_B T} {h} \frac {q^{TS}}{q^{initial state}} \exp (m)\) if use_q = True

\(A = \frac {k_B T} {h} \exp\bigg(\frac {\Delta S^{TS}}{R}+m \bigg)\) if use_q = False

Parameters:

rev (bool, optional) – Reverse direction. If True, uses products as initial state instead of reactants. Default is False
T (float, optional) – Temperature in K. Default is standard temperature.
m (int, optional) – Molecularity of gas-phase species in the reaction. Condensed-phase reactions and unimolecular gas-phase reactions should have a value of 1. Bimolecular gas-phase reactions should have a value of 2. If None specified, m will be calculated (assuming all species in the initial state arw gas phase). To get the transition-state estimate of the pre-exponential factor, set to 0 (default).
use_q (bool, optional) – If True, uses ratio of partition functions to calculate A (Note: include_ZPE=False). If False, uses the entropy of activation to calculate A.
kwargs (keyword arguments) – Parameters required to calculate pre-exponential factor. See class docstring to see how to pass specific parameters to different species.

Returns:

A – Pre-exponential factor

Return type: