Add to_cantera_kinetics for SurfaceArrhenius and StickingCoefficient kinetics classes

rmgpy/kinetics/surface.pyx

@@ -285,6 +285,36 @@ cdef class StickingCoefficient(KineticsModel):
 
         return string
 
+    def to_cantera_kinetics(self):
+        """
+        Converts the RMG StickingCoefficient object to a cantera StickingArrheniusRate
+
+        Inputs for both are (A,b,E)  where A is dimensionless, b is dimensionless, and E is in J/kmol
+
+        """
+
+        import cantera as ct
+        import rmgpy.quantity
+
+        assert type(self._A) == rmgpy.quantity.ScalarQuantity, "A factor must be a ScalarQuantity"
+        A = self._A.value_si
+        b = self._n.value_si
+        E = self._Ea.value_si * 1000  # convert from J/mol to J/kmol
+
+        return ct.StickingArrheniusRate(A, b, E)
+
+
+    def set_cantera_kinetics(self, ct_reaction, species_list):
+        """
+        Passes in a cantera Reaction() object and sets its
+        rate to a Cantera ArrheniusRate object.
+        """
+        import cantera as ct
+        assert isinstance(ct_reaction.rate, ct.StickingArrheniusRate), "Must have a Cantera StickingArrheniusRate attribute"
+
+        # Set the rate parameter to a cantera Arrhenius object
+        ct_reaction.rate = self.to_cantera_kinetics()
+
 ################################################################################
 cdef class StickingCoefficientBEP(KineticsModel):
     """
@@ -570,6 +600,54 @@ cdef class SurfaceArrhenius(Arrhenius):
         return (SurfaceArrhenius, (self.A, self.n, self.Ea, self.T0, self.Tmin, self.Tmax, self.Pmin, self.Pmax,
                                    self.coverage_dependence, self.uncertainty, self.comment))
 
+    def to_cantera_kinetics(self):
+        """
+        Converts the RMG SurfaceArrhenius object to a cantera InterfaceArrheniusRate
+        Inputs are (A,b,E)  where A is in units of m^2/kmol/s, b is dimensionless, and E is in J/kmol
+
+        There are no surface falloff reaction types in Cantera, so that isn't implemented here
+        """
+
+        import cantera as ct
+
+        rate_units_dimensionality = {'1/s': 0,
+                                     's^-1': 0,
+                                     'm^2/(mol*s)': 1,
+                                     'm^4/(mol^2*s)': 2,
+                                     'cm^2/(mol*s)': 1,
+                                     'cm^4/(mol^2*s)': 2,
+                                     'm^2/(molecule*s)': 1,
+                                     'm^4/(molecule^2*s)': 2,
+                                     'cm^2/(molecule*s)': 1,
+                                     'cm^4/(molecule^2*s)': 2,
+                                     }
+
+        if self._T0.value_si != 1:
+            A = self._A.value_si / (self._T0.value_si) ** self._n.value_si
+        else:
+            A = self._A.value_si
+
+        try:
+            A *= 1000 ** rate_units_dimensionality[self._A.units]
+        except KeyError:
+            raise Exception('Arrhenius A-factor units {0} not found among accepted units for converting to '
+                            'Cantera Arrhenius object.'.format(self._A.units))
+
+        b = self._n.value_si
+        E = self._Ea.value_si * 1000  # convert from J/mol to J/kmol
+        return ct.InterfaceArrheniusRate(A, b, E)
+
+    def set_cantera_kinetics(self, ct_reaction, species_list):
+        """
+        Passes in a cantera Reaction() object and sets its
+        rate to a Cantera InterfaceArrheniusRate object.
+        """
+        import cantera as ct
+        assert isinstance(ct_reaction.rate, ct.InterfaceArrheniusRate), "Must have a Cantera InterfaceArrheniusRate attribute"
+
+        # Set the rate parameter to a cantera Arrhenius object
+        ct_reaction.rate = self.to_cantera_kinetics()
+
 ################################################################################
 
 cdef class SurfaceArrheniusBEP(ArrheniusEP):

rmgpy/reaction.py

@@ -288,7 +288,10 @@
         if self.kinetics:
             if isinstance(self.kinetics, Arrhenius):
                 # Create an Elementary Reaction
-                ct_reaction = ct.Reaction(reactants=ct_reactants, products=ct_products, rate=ct.ArrheniusRate())
+                if isinstance(self.kinetics, SurfaceArrhenius):  # SurfaceArrhenius inherits from Arrhenius
+                    ct_reaction = ct.Reaction(reactants=ct_reactants, products=ct_products, rate=ct.InterfaceArrheniusRate())
+                else:
+                    ct_reaction = ct.Reaction(reactants=ct_reactants, products=ct_products, rate=ct.ArrheniusRate())
             elif isinstance(self.kinetics, MultiArrhenius):
                 # Return a list of elementary reactions which are duplicates
                 ct_reaction = [ct.Reaction(reactants=ct_reactants, products=ct_products, rate=ct.ArrheniusRate())
@@ -356,6 +359,9 @@
                         reactants=ct_reactants, products=ct_products, rate=rate
                     )
 
+            elif isinstance(self.kinetics, StickingCoefficient):
+                ct_reaction = ct.Reaction(reactants=ct_reactants, products=ct_products, rate=ct.StickingArrheniusRate())
+
             else:
                 raise NotImplementedError('Unable to set cantera kinetics for {0}'.format(self.kinetics))