Fixed A-factor correction for SurfaceChargeTransfer

Added solvent correction for SurfaceChargeTransfer

Author: ssun30

rmgpy/reaction.py

@@ -996,7 +996,7 @@ def fix_barrier_height(self, force_positive=False, solvent="", apply_solvation_c
 
         if self.kinetics is None:
             raise KineticsError("Cannot fix barrier height for reactions with no kinetics attribute")
-        
+
         if isinstance(self.kinetics, Marcus):
             if apply_solvation_correction and solvent:
                 self.apply_solvent_correction(solvent)
@@ -1039,7 +1039,7 @@ def fix_barrier_height(self, force_positive=False, solvent="", apply_solvation_c
                     logging.info("For reaction {0!s} Ea raised from {1:.1f} to {2:.1f} kJ/mol.".format(
                         self, self.kinetics.Ea.value_si / 1000., Ea / 1000.))
                     self.kinetics.Ea.value_si = Ea
-            if isinstance(self.kinetics, (Arrhenius, StickingCoefficient, ArrheniusChargeTransfer)):  # SurfaceArrhenius is a subclass of Arrhenius
+            if isinstance(self.kinetics, (Arrhenius, StickingCoefficient, ArrheniusChargeTransfer, SurfaceChargeTransfer)):  # SurfaceArrhenius is a subclass of Arrhenius
                 if apply_solvation_correction and solvent and self.kinetics.solute:
                     self.apply_solvent_correction(solvent)
                 Ea = self.kinetics.Ea.value_si

rmgpy/rmg/reactors.py

@@ -601,22 +601,20 @@ def to_rms(obj, species_names=None, rms_species_list=None, rmg_species=None):
         A = obj._A.value_si
         if obj._T0.value_si != 1.0:
             A /= ((obj._T0.value_si) ** obj._n.value_si)
-        # if obj._V0.value_si != 0.0:
-        #     A *= np.exp(obj._alpha.value_si*obj._electrons.value_si*constants.F*obj.V0.value_si/constants.R/300)
         n = obj._n.value_si
         Ea = obj._Ea.value_si
-        q = obj._alpha.value_si*obj._electrons.value_si    
-        return rms.Arrheniusq(A, n, Ea, q, rms.EmptyRateUncertainty())
+        q = obj._alpha.value_si*obj._electrons.value_si
+        V0 = obj._V0.value_si
+        return rms.Arrheniusq(A, n, Ea, q, V0, rms.EmptyRateUncertainty())
     elif isinstance(obj, SurfaceChargeTransfer):
         A = obj._A.value_si
         if obj._T0.value_si != 1.0:
             A /= ((obj._T0.value_si) ** obj._n.value_si)
-        # if obj._V0.value_si != 0.0:
-        #     A *= np.exp(obj._alpha.value_si*obj._electrons.value_si*constants.F*obj.V0.value_si/constants.R/300)
         n = obj._n.value_si
         Ea = obj._Ea.value_si
         q = obj._alpha.value_si*obj._electrons.value_si
-        return rms.Arrheniusq(A, n, Ea, q, rms.EmptyRateUncertainty())
+        V0 = obj._V0.value_si
+        return rms.Arrheniusq(A, n, Ea, q, V0, rms.EmptyRateUncertainty())
     elif isinstance(obj, Marcus):
         A = obj._A.value_si
         n = obj._n.value_si
@@ -725,7 +723,7 @@ def to_rms(obj, species_names=None, rms_species_list=None, rmg_species=None):
             else:
                 atomnums[atm.element.symbol] = 1
         bondnum = len(mol.get_all_edges())
-        
+
         if not obj.molecule[0].contains_surface_site():
             rad = rms.getspeciesradius(atomnums, bondnum)
             diff = rms.StokesDiffusivity(rad)