Use lowest energy Configuration for energy_correction.

As noted in #2791
the energy_correction was not actually an average of the Configuration energies
because some Configurations (reactants and products) are bimolecular.
This corrects the calculation, but also switches to using the MINIMUM
rather than the average, so that the lowest should end up at zero.

Author: rwest

rmgpy/rmg/pdep.py

@@ -788,38 +788,34 @@ def update(self, reaction_model, pdep_settings, requires_rms=False):
         # Log the network being updated
         logging.info("Updating {0!s}".format(self))
 
-        E0 = []
         # Generate states data for unimolecular isomers and reactants if necessary
         for isomer in self.isomers:
             spec = isomer.species[0]
             if not spec.has_statmech():
                 spec.generate_statmech()
-            E0.append(spec.conformer.E0.value_si)
         for reactants in self.reactants:
             for spec in reactants.species:
                 if not spec.has_statmech():
                     spec.generate_statmech()
-                E0.append(spec.conformer.E0.value_si)
         # Also generate states data for any path reaction reactants, so we can
         # always apply the ILT method in the direction the kinetics are known
         for reaction in self.path_reactions:
             for spec in reaction.reactants:
                 if not spec.has_statmech():
                     spec.generate_statmech()
-                E0.append(spec.conformer.E0.value_si)
         # While we don't need the frequencies for product channels, we do need
         # the E0, so create a conformer object with the E0 for the product
         # channel species if necessary
         for products in self.products:
             for spec in products.species:
                 if spec.conformer is None:
                     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
+        # Use the lowest 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()
+        energy_correction = -min(sum(spec.conformer.E0.value_si for spec in stationary_point.species)
+                                 for stationary_point in self.reactants + self.isomers + self.products)
         for spec in self.reactants + self.products + self.isomers:
             spec.energy_correction = energy_correction
         self.energy_correction = energy_correction