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Remove incorrectly calculated and applied energy_correction from pdep.py #2791

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Remove incorrectly calculated and applied energy_correction from pdep.py #2791

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12 changes: 2 additions & 10 deletions rmgpy/rmg/pdep.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down
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