[Reactor] Fix behavior of componentIndex with ambigous names

The name 'H' can mean either the species by that name or the entahlpy
of the reactor, in the case of ConstPressureReactor, and the previous
behavior always returned the index of the enthalpy.

This changes the behavior to preferentially return the species, and
adds alternative names for reactor state variables that are less
likely to generate namespace collisions: 'mass', 'volume',
'int_energy', 'enthalpy', 'temperature', 'distance', 'velocity'. The
single character names are still supported.

Resolves Issue 193.

include/cantera/zeroD/Reactor.h

@@ -151,6 +151,12 @@ protected:
     //! Reset the reaction rate multipliers
     virtual void resetSensitivity(double* params);
 
+    //! Return the index in the solution vector for this reactor of the species
+    //! named *nm*, in either the homogeneous phase or a surface phase, relative
+    //! to the start of the species terms. Used to implement componentIndex for
+    //! specific reactor implementations.
+    virtual size_t speciesIndex(const std::string& nm) const;
+
     //! Pointer to the homogeneous Kinetics object that handles the reactions
     Kinetics*   m_kin;
 

interfaces/cython/cantera/test/test_reactor.py

@@ -617,16 +617,16 @@ class TestConstPressureReactor(utilities.CanteraTest):
             mfc2 = ct.MassFlowController(env, self.r2, mdot=0.05)
 
         if add_surf:
-            interface1 = ct.Interface('diamond.xml', 'diamond_100',
+            self.interface1 = ct.Interface('diamond.xml', 'diamond_100',
                                       (self.gas1, solid))
-            interface2 = ct.Interface('diamond.xml', 'diamond_100',
+            self.interface2 = ct.Interface('diamond.xml', 'diamond_100',
                                       (self.gas2, solid))
 
-            C = np.zeros(interface1.n_species)
+            C = np.zeros(self.interface1.n_species)
             C[0] = 0.3
             C[4] = 0.7
-            self.w1.left.kinetics = interface1
-            self.w2.left.kinetics = interface2
+            self.w1.left.kinetics = self.interface1
+            self.w2.left.kinetics = self.interface2
             self.w1.left.coverages = C
             self.w2.left.coverages = C
 
@@ -636,6 +636,19 @@ class TestConstPressureReactor(utilities.CanteraTest):
         self.net2.set_max_time_step(0.05)
         self.net2.max_err_test_fails = 10
 
+    def test_component_index(self):
+        self.create_reactors(add_surf=True)
+        for (gas,net,iface,r) in ((self.gas1, self.net1, self.interface1, self.r1),
+                                  (self.gas2, self.net2, self.interface2, self.r2)):
+            net.step(1.0)
+
+            N0 = net.n_vars - gas.n_species - iface.n_species
+            N1 = net.n_vars - iface.n_species
+            for i, name in enumerate(gas.species_names):
+                self.assertEqual(i + N0, r.component_index(name))
+            for i, name in enumerate(iface.species_names):
+                self.assertEqual(i + N1, r.component_index(name))
+
     def integrate(self, surf=False):
         for t in np.arange(0.5, 50, 1.0):
             self.net1.advance(t)

src/zeroD/ConstPressureReactor.cpp

@@ -223,34 +223,16 @@ void ConstPressureReactor::evalEqs(doublereal time, doublereal* y,
 
 size_t ConstPressureReactor::componentIndex(const string& nm) const
 {
-    if (nm == "m") {
-        return 0;
-    }
-    if (nm == "H") {
-        return 1;
-    }
-    // check for a gas species name
-    size_t k = m_thermo->speciesIndex(nm);
+    size_t k = speciesIndex(nm);
     if (k != npos) {
         return k + 2;
+    } else if (nm == "m" || nm == "mass") {
+        return 0;
+    } else if (nm == "H" || nm == "enthalpy") {
+        return 1;
+    } else {
+        return npos;
     }
-
-    // check for a wall species
-    size_t walloffset = 0, kp = 0;
-    thermo_t* th;
-    for (size_t m = 0; m < m_nwalls; m++) {
-        if (m_wall[m]->kinetics(m_lr[m])) {
-            kp = m_wall[m]->kinetics(m_lr[m])->reactionPhaseIndex();
-            th = &m_wall[m]->kinetics(m_lr[m])->thermo(kp);
-            k = th->speciesIndex(nm);
-            if (k != npos) {
-                return k + 2 + m_nsp + walloffset;
-            } else {
-                walloffset += th->nSpecies();
-            }
-        }
-    }
-    return npos;
 }
 
 }

src/zeroD/FlowReactor.cpp

@@ -118,16 +118,14 @@ void FlowReactor::evalEqs(doublereal time, doublereal* y,
 
 size_t FlowReactor::componentIndex(const string& nm) const
 {
-    if (nm == "X") {
-        return 0;
-    }
-    if (nm == "U") {
-        return 1;
-    }
     // check for a gas species name
     size_t k = m_thermo->speciesIndex(nm);
     if (k != npos) {
         return k + 2;
+    } else if (nm == "X" || nm == "distance") {
+        return 0;
+    } else if (nm == "U" || nm == "velocity") {
+        return 1;
     } else {
         return npos;
     }

src/zeroD/IdealGasConstPressureReactor.cpp

@@ -231,12 +231,16 @@ void IdealGasConstPressureReactor::evalEqs(doublereal time, doublereal* y,
 
 size_t IdealGasConstPressureReactor::componentIndex(const string& nm) const
 {
-    if (nm == "T") {
+    size_t k = speciesIndex(nm);
+    if (k != npos) {
+        return k + 2;
+    } else if (nm == "m" || nm == "mass") {
+        return 0;
+    } else if (nm == "T" || nm == "temperature") {
         return 1;
     } else {
-        return ConstPressureReactor::componentIndex(nm);
+        return npos;
     }
-
 }
 
 }

src/zeroD/IdealGasReactor.cpp

@@ -251,10 +251,17 @@ void IdealGasReactor::evalEqs(doublereal time, doublereal* y,
 
 size_t IdealGasReactor::componentIndex(const string& nm) const
 {
-    if (nm == "T") {
+    size_t k = speciesIndex(nm);
+    if (k != npos) {
+        return k + 3;
+    } else if (nm == "m" || nm == "mass") {
+        return 0;
+    } else if (nm == "V" || nm == "volume") {
+        return 1;
+    } else if (nm == "T" || nm == "temperature") {
         return 2;
     } else {
-        return Reactor::componentIndex(nm);
+        return npos;
     }
 }
 

src/zeroD/Reactor.cpp

@@ -318,22 +318,12 @@ std::vector<std::pair<void*, int> > Reactor::getSensitivityOrder() const
     return order;
 }
 
-size_t Reactor::componentIndex(const string& nm) const
+size_t Reactor::speciesIndex(const string& nm) const
 {
-    if (nm == "m") {
-        return 0;
-    }
-    if (nm == "V") {
-        return 1;
-    }
-    if (nm == "U") {
-        return 2;
-    }
-
     // check for a gas species name
     size_t k = m_thermo->speciesIndex(nm);
     if (k != npos) {
-        return k + 3;
+        return k;
     }
 
     // check for a wall species
@@ -345,7 +335,7 @@ size_t Reactor::componentIndex(const string& nm) const
             th = &m_wall[m]->kinetics(m_lr[m])->thermo(kp);
             k = th->speciesIndex(nm);
             if (k != npos) {
-                return k + 3 + m_nsp + walloffset;
+                return k + m_nsp + walloffset;
             } else {
                 walloffset += th->nSpecies();
             }
@@ -354,6 +344,22 @@ size_t Reactor::componentIndex(const string& nm) const
     return npos;
 }
 
+size_t Reactor::componentIndex(const string& nm) const
+{
+    size_t k = speciesIndex(nm);
+    if (k != npos) {
+        return k + 3;
+    } else if (nm == "m" || nm == "mass") {
+        return 0;
+    } else if (nm == "V" || nm == "volume") {
+        return 1;
+    } else if (nm == "U" || nm == "int_energy") {
+        return 2;
+    } else {
+        return npos;
+    }
+}
+
 void Reactor::applySensitivity(double* params)
 {
     if (!params) {