pymatgen.analysis.reaction_calculator module

class BalancedReaction(reactants_coeffs, products_coeffs)

Bases: monty.json.MSONable

An object representing a complete chemical reaction.

Reactants and products to be specified as dict of {Composition: coeff}.

Parameters:

• ({Composition (products_coeffs) – float}): Reactants as dict of {Composition: amt}.
• ({Composition – float}): Products as dict of {Composition: amt}.

TOLERANCE = 1e-06

all_comp

List of all compositions in the reaction.

as_dict()

as_entry(energies)

Returns a ComputedEntry representation of the reaction. :return:

calculate_energy(energies)

Calculates the energy of the reaction.

Parameters:({Composition (energies) – float}): Energy for each composition. E.g ., {comp1: energy1, comp2: energy2}. Returns:reaction energy as a float.

coeffs

Final coefficients of the calculated reaction

elements

List of elements in the reaction

classmethod from_dict(d)

static from_string(rxn_string)

Generates a balanced reaction from a string. The reaction must already be balanced.

Parameters:rxn_string – The reaction string. For example, “4 Li + O2-> 2Li2O” Returns:BalancedReaction

get_coeff(comp)

Returns coefficient for a particular composition

get_el_amount(element)

Returns the amount of the element in the reaction.

Parameters:element (Element/Specie) – Element in the reaction Returns:Amount of that element in the reaction.

normalize_to(comp, factor=1)

Normalizes the reaction to one of the compositions. By default, normalizes such that the composition given has a coefficient of 1. Another factor can be specified.

Parameters:

• comp (Composition) – Composition to normalize to
• factor (float) – Factor to normalize to. Defaults to 1.

normalize_to_element(element, factor=1)

Normalizes the reaction to one of the elements. By default, normalizes such that the amount of the element is 1. Another factor can be specified.

Parameters:

• element (Element/Specie) – Element to normalize to.
• factor (float) – Factor to normalize to. Defaults to 1.

normalized_repr

A normalized representation of the reaction. All factors are converted to lowest common factors.

normalized_repr_and_factor()

Normalized representation for a reaction For example, 4 Li + 2 O -> 2Li2O becomes 2 Li + O -> Li2O

products

List of products

reactants

List of reactants

class ComputedReaction(reactant_entries, product_entries)

Bases: pymatgen.analysis.reaction_calculator.Reaction

Convenience class to generate a reaction from ComputedEntry objects, with some additional attributes, such as a reaction energy based on computed energies.

Parameters:

• reactant_entries ([ComputedEntry]) – List of reactant_entries.
• product_entries ([ComputedEntry]) – List of product_entries.

all_entries

Equivalent of all_comp but returns entries, in the same order as the coefficients.

as_dict()

calculated_reaction_energy

classmethod from_dict(d)

class Reaction(reactants, products)

Bases: pymatgen.analysis.reaction_calculator.BalancedReaction

A more flexible class representing a Reaction. The reaction amounts will be automatically balanced. Reactants and products can swap sides so that all coefficients are positive. Normalizes so that the FIRST product (or products, if underdetermined) has a coefficient of one.

Reactants and products to be specified as list of pymatgen.core.structure.Composition. e.g., [comp1, comp2]

Parameters:

• reactants ([Composition]) – List of reactants.
• products ([Composition]) – List of products.

as_dict()

copy()

Returns a copy of the Reaction object.

classmethod from_dict(d)

exception ReactionError(msg)

Bases: Exception

Exception class for Reactions. Allows more information in exception messages to cover situations not covered by standard exception classes.