[Reactor] ReactorNet::addReactor takes a reference instead of a pointer

This reflects how the function is usually used. The old signature is now
deprecated, as is the extra argument for transfering "ownership" to the
ReactorNet object.

include/cantera/zeroD/ReactorNet.h

@@ -114,6 +114,13 @@ public:
     //@}
 
     //! Add the reactor *r* to this reactor network.
+    void addReactor(Reactor& r);
+
+    //! Add the reactor *r* to this reactor network.
+    /**
+     *  @deprecated To be removed after Cantera 2.2. Use addReactor(Reactor&)
+     *  instead.
+     */
     void addReactor(Reactor* r, bool iown = false);
 
     //! Return a reference to the *n*-th reactor in this network. The reactor

interfaces/cython/cantera/_cantera.pxd

@@ -324,7 +324,7 @@ cdef extern from "cantera/zeroD/flowControllers.h":
 cdef extern from "cantera/zeroD/ReactorNet.h":
     cdef cppclass CxxReactorNet "Cantera::ReactorNet":
         CxxReactorNet()
-        void addReactor(CxxReactor*)
+        void addReactor(CxxReactor&)
         void advance(double) except +
         double step(double) except +
         double time()

interfaces/cython/cantera/reactor.pyx

@@ -732,7 +732,7 @@ cdef class ReactorNet:
     def add_reactor(self, Reactor r):
         """Add a reactor to the network."""
         self._reactors.append(r)
-        self.net.addReactor(r.reactor)
+        self.net.addReactor(deref(r.reactor))
 
     def advance(self, double t):
         """

samples/cxx/combustor/combustor.cpp

@@ -98,7 +98,7 @@ void runexample()
 
     // the simulation only contains one reactor
     ReactorNet sim;
-    sim.addReactor(&combustor);
+    sim.addReactor(combustor);
 
     // take single steps to 6 s, writing the results to a CSV file
     // for later plotting.

samples/cxx/kinetics1/kinetics1.cpp

@@ -74,7 +74,7 @@ int kinetics1(int np, void* p)
     // create a container object to run the simulation
     // and add the reactor to it
     ReactorNet sim;
-    sim.addReactor(&r, false);
+    sim.addReactor(&r);
 
     // main loop
     clock_t t0 = clock();        // save start time

src/clib/ctreactor.cpp

@@ -304,7 +304,7 @@ extern "C" {
     {
         try {
             NetworkCabinet::item(i).addReactor(
-                &dynamic_cast<Reactor&>(ReactorCabinet::item(n)));
+                dynamic_cast<Reactor&>(ReactorCabinet::item(n)));
             return 0;
         } catch (...) {
             return handleAllExceptions(-1, ERR);

src/zeroD/ReactorNet.cpp

@@ -163,6 +163,12 @@ double ReactorNet::step(doublereal time)
 
 void ReactorNet::addReactor(Reactor* r, bool iown)
 {
+    warn_deprecated("ReactorNet::addReactor(Reactor*)",
+        "To be removed after Cantera 2.2. Use 'addReactor(Reactor&) instead'.");
+    if (iown) {
+        warn_deprecated("ReactorNet::addReactor",
+            "Ownership of Reactors by ReactorNet is deprecated.");
+    }
     r->setNetwork(this);
     if (r->type() >= ReactorType) {
         m_reactors.push_back(r);
@@ -174,6 +180,13 @@ void ReactorNet::addReactor(Reactor* r, bool iown)
     }
 }
 
+void ReactorNet::addReactor(Reactor& r)
+{
+    r.setNetwork(this);
+    m_reactors.push_back(&r);
+    m_iown.push_back(false);
+}
+
 void ReactorNet::eval(doublereal t, doublereal* y,
                       doublereal* ydot, doublereal* p)
 {

test_problems/cxx_ex/kinetics_example1.cpp

@@ -76,7 +76,7 @@ int kinetics_example1(int job)
         // and add the reactor to it
         ReactorNet* sim_ptr = new ReactorNet();
         sim_ptr->setVerbose(false);
-        sim_ptr->addReactor(&r);
+        sim_ptr->addReactor(r);
 
         double tm;
         double dt = 1.e-5;    // interval at which output is written

test_problems/cxx_ex/kinetics_example3.cpp

@@ -73,7 +73,7 @@ int kinetics_example3(int job)
         // and add the reactor to it
         ReactorNet& sim = *(new ReactorNet());
         sim.setVerbose(false);
-        sim.addReactor(&r);
+        sim.addReactor(r);
 
         double tm;
         double dt = 1.e-5;    // interval at which output is written

test_problems/cxx_ex/rxnpath_example1.cpp

@@ -120,7 +120,7 @@ int rxnpath_example1(int job)
         // create a container object to run the simulation
         // and add the reactor to it
         ReactorNet& sim = *(new ReactorNet());
-        sim.addReactor(&r);
+        sim.addReactor(r);
 
         // create a reaction path diagram builder
         ReactionPathBuilder b;