[Python] Add setters for constructing elementary and third-body reactions

This allows creating reactions of these types without needing an XML or
CTI input file.

interfaces/cython/cantera/reaction.pyx

@@ -94,40 +94,56 @@ cdef class Reaction:
     property reactants:
         def __get__(self):
             return comp_map_to_dict(self.reaction.reactants)
+        def __set__(self, reactants):
+            self.reaction.reactants = comp_map(reactants)
 
     property products:
         def __get__(self):
             return comp_map_to_dict(self.reaction.products)
+        def __set__(self, products):
+            self.reaction.products = comp_map(products)
 
     property orders:
         def __get__(self):
             return comp_map_to_dict(self.reaction.orders)
+        def __set__(self, orders):
+            self.reaction.orders = comp_map(orders)
 
     property ID:
         def __get__(self):
             return pystr(self.reaction.id)
+        def __set__(self, ID):
+            self.reaction.id = stringify(ID)
 
     property reversible:
         def __get__(self):
             return self.reaction.reversible
+        def __set__(self, reversible):
+            self.reaction.reversible = reversible
 
     property duplicate:
         def __get__(self):
             return self.reaction.duplicate
+        def __set__(self, duplicate):
+             self.reaction.duplicate = duplicate
 
     property allow_nonreactant_orders:
         def __get__(self):
             return self.reaction.allow_nonreactant_orders
+        def __set__(self, allow):
+            self.reaction.allow_nonreactant_orders = allow
 
     property allow_negative_orders:
         def __get__(self):
             return self.reaction.allow_negative_orders
+        def __set__(self, allow):
+            self.reaction.allow_negative_orders = allow
 
 
 cdef class Arrhenius:
-    def __cinit__(self, A=0, b=0, E=0, init=True):
+    def __cinit__(self, A=0, b=0, E=0, Ta=0, init=True):
         if init:
-            self.rate = new CxxArrhenius(A, b, E)
+            self.rate = new CxxArrhenius(A, b, E / gas_constant)
             self.reaction = None
 
     def __dealloc__(self):
@@ -155,7 +171,7 @@ cdef wrapArrhenius(CxxArrhenius* rate, Reaction reaction):
 
 cdef copyArrhenius(CxxArrhenius* rate):
     r = Arrhenius(rate.preExponentialFactor(), rate.temperatureExponent(),
-                  rate.activationEnergy_R())
+                  rate.activationEnergy_R() * gas_constant)
     return r
 
 
@@ -166,6 +182,9 @@ cdef class ElementaryReaction(Reaction):
         def __get__(self):
             cdef CxxElementaryReaction* r = <CxxElementaryReaction*>self.reaction
             return wrapArrhenius(&(r.rate), self)
+        def __set__(self, Arrhenius rate):
+            cdef CxxElementaryReaction* r = <CxxElementaryReaction*>self.reaction
+            r.rate = deref(rate.rate)
 
 
 cdef class ThirdBodyReaction(ElementaryReaction):
@@ -177,10 +196,14 @@ cdef class ThirdBodyReaction(ElementaryReaction):
     property efficiencies:
         def __get__(self):
             return comp_map_to_dict(self.tbr().third_body.efficiencies)
+        def __set__(self, eff):
+            self.tbr().third_body.efficiencies = comp_map(eff)
 
     property default_efficiency:
         def __get__(self):
             return self.tbr().third_body.default_efficiency
+        def __set__(self, default_eff):
+            self.tbr().third_body.default_efficiency = default_eff
 
     def efficiency(self, species):
         return self.tbr().third_body.efficiency(stringify(species))

interfaces/cython/cantera/test/test_kinetics.py

@@ -597,6 +597,9 @@ class TestReaction(utilities.CanteraTest):
     @classmethod
     def setUpClass(cls):
         cls.gas = ct.Solution('h2o2.xml')
+        cls.gas.X = 'H2:0.1, H2O:0.2, O2:0.7, O:1e-4, OH:1e-5, H:2e-5'
+        cls.gas.TP = 900, 2*ct.one_atm
+        cls.species = ct.Species.listFromFile('h2o2.xml')
 
     def test_fromCti(self):
         r = ct.Reaction.fromCti('''three_body_reaction('2 O + M <=> O2 + M',
@@ -640,3 +643,34 @@ class TestReaction(utilities.CanteraTest):
         eq2 = [self.gas.reaction(i).equation
                for i in range(self.gas.n_reactions)]
         self.assertEqual(eq1, eq2)
+
+    def test_elementary(self):
+        r = ct.ElementaryReaction()
+        r.reactants = {'O':1, 'H2':1}
+        r.products = {'H':1, 'OH':1}
+        r.rate = ct.Arrhenius(3.87e1, 2.7, 6260*1000*4.184)
+
+        gas2 = ct.Solution(thermo='IdealGas', kinetics='GasKinetics',
+                           species=self.species, reactions=[r])
+        gas2.TPX = self.gas.TPX
+
+        self.assertNear(gas2.forward_rate_constants[0],
+                        self.gas.forward_rate_constants[2])
+        self.assertNear(gas2.net_rates_of_progress[0],
+                        self.gas.net_rates_of_progress[2])
+
+    def test_thirdbody(self):
+        r = ct.ThirdBodyReaction()
+        r.reactants = {'O':1, 'H':1}
+        r.products = {'OH':1}
+        r.rate = ct.Arrhenius(5e11, -1.0, 0.0)
+        r.efficiencies = {'AR':0.7, 'H2':2.0, 'H2O':6.0}
+
+        gas2 = ct.Solution(thermo='IdealGas', kinetics='GasKinetics',
+                           species=self.species, reactions=[r])
+        gas2.TPX = self.gas.TPX
+
+        self.assertNear(gas2.forward_rate_constants[0],
+                        self.gas.forward_rate_constants[1])
+        self.assertNear(gas2.net_rates_of_progress[0],
+                        self.gas.net_rates_of_progress[1])