fixup! several potential related changes in reaction.py

Author: davidfarinajr

rmgpy/reaction.pxd

@@ -85,9 +85,9 @@ cdef class Reaction:
 
     cpdef double get_entropy_of_reaction(self, double T)
 
-    cpdef double get_free_energy_of_reaction(self, double T, potential=?)
+    cpdef double get_free_energy_of_reaction(self, double T, double potential=?)
 
-    cpdef double get_equilibrium_constant(self, double T, potential=?, str type=?)
+    cpdef double get_equilibrium_constant(self, double T, double potential=?, str type=?)
 
     cpdef np.ndarray get_enthalpies_of_reaction(self, np.ndarray Tlist)
 

rmgpy/reaction.py

@@ -564,7 +564,7 @@ def get_entropy_of_reaction(self, T):
             dSrxn += product.get_entropy(T)
         return dSrxn
 
-    def get_free_energy_of_reaction(self, T, potential=None):
+    def get_free_energy_of_reaction(self, T, potential=0):
         """
         Return the Gibbs free energy of reaction in J/mol evaluated at
         temperature `T` in K and potential in Volts (if applicable)
@@ -573,7 +573,7 @@ def get_free_energy_of_reaction(self, T, potential=None):
         dGrxn = 0.0
 
         if self.is_charge_transfer_reaction() and self.V0:
-            dGrxn = -1 * abs(self.ne) * constants.F * self.V0.value_si # G = -nFE0 in J/mol
+            dGrxn = -1 * abs(self.ne) * constants.F * self.V0.value_si # G = -nFE0 in J/mol, not sure about sign
         else:
             for reactant in self.reactants:
                 if not reactant.is_electron():
@@ -590,12 +590,12 @@ def get_free_energy_of_reaction(self, T, potential=None):
                         logging.error("Problem with product {!r} in reaction {!s}".format(reactant, self))
                         raise
 
-        if self.is_charge_transfer_reaction() and potential is not None:
-            dGrxn += (dGrxn - self.ne * constants.F * potential)    # Not sure about sign here or equation G = -nFE0 + nF(V0-V)
-                                                                    # where nF(V0-V) is from applied potential
+        if self.is_charge_transfer_reaction() and potential != 0:
+            dGrxn -=  self.ne * constants.F * potential    # Not sure about sign here
+
         return dGrxn
 
-    def get_equilibrium_constant(self, T, potential=None, type='Kc'):
+    def get_equilibrium_constant(self, T, potential=0, type='Kc'):
         """
         Return the equilibrium constant for the reaction at the specified
         temperature `T` in K and (electrochemical) potential in volts (if applicable).