diff --git a/rmgpy/rmg/pdep.py b/rmgpy/rmg/pdep.py index 0e1398e51a..bd0a2ab09d 100644 --- a/rmgpy/rmg/pdep.py +++ b/rmgpy/rmg/pdep.py @@ -816,14 +816,6 @@ def update(self, reaction_model, pdep_settings): spec.conformer = Conformer(E0=spec.get_thermo_data().E0) E0.append(spec.conformer.E0.value_si) - # Use the average E0 as the reference energy (`energy_correction`) for the network - # The `energy_correction` will be added to the free energies and enthalpies for each - # configuration in the network. - energy_correction = -np.array(E0).mean() - for spec in self.reactants + self.products + self.isomers: - spec.energy_correction = energy_correction - self.energy_correction = energy_correction - # Determine transition state energies on potential energy surface # In the absence of any better information, we simply set it to # be the reactant ground-state energy + the activation energy @@ -851,9 +843,9 @@ def update(self, reaction_model, pdep_settings): 'type "{2!s}".'.format(rxn, self.index, rxn.kinetics.__class__)) rxn.fix_barrier_height(force_positive=True) if rxn.network_kinetics is None: - E0 = sum([spec.conformer.E0.value_si for spec in rxn.reactants]) + rxn.kinetics.Ea.value_si + energy_correction + E0 = sum([spec.conformer.E0.value_si for spec in rxn.reactants]) + rxn.kinetics.Ea.value_si else: - E0 = sum([spec.conformer.E0.value_si for spec in rxn.reactants]) + rxn.network_kinetics.Ea.value_si + energy_correction + E0 = sum([spec.conformer.E0.value_si for spec in rxn.reactants]) + rxn.network_kinetics.Ea.value_si rxn.transition_state = rmgpy.species.TransitionState(conformer=Conformer(E0=(E0 * 0.001, "kJ/mol"))) # Set collision model