[Samples] Fix compilation errors and warnings in the C++ examples

samples/cxx/bvp/BoundaryValueProblem.h

@@ -6,6 +6,7 @@
 #define BVP_H
 
 #include "cantera/onedim.h"
+#include <fstream>
 
 /// Namespace for the boundary value problem package.
 namespace BVP
@@ -113,18 +114,19 @@ class BoundaryValueProblem : public Cantera::Domain1D
      *  @param n Component number.
      *  @param c Component parameter values
      */
-    void setComponent(int n, Component& c) {
+    void setComponent(size_t n, Component& c) {
         if (m_sim == 0) {
             start();
         }
-        if (n < 0 || n >= m_nv) {
+        if (n >= m_nv) {
             throw Cantera::CanteraError("BoundaryValueProblem::setComponent",
                                         "Illegal solution component number");
         }
         // set the upper and lower bounds for this component
         setBounds(n, c.lower, c.upper);
         // set the error tolerances
-        setTolerances(n, c.rtol, c.atol);
+        setSteadyTolerances(c.rtol, c.atol, n);
+        setTransientTolerances(c.rtol, c.atol, n);
         // specify whether this component should be considered in
         // refining the grid
         m_refiner->setActive(n, c.refine);
@@ -209,15 +211,15 @@ class BoundaryValueProblem : public Cantera::Domain1D
      * True if n is the index of the left-most grid point (zero),
      * false otherwise.
      */
-    bool isLeft(int n) const {
+    bool isLeft(size_t n) const {
         return (n == 0);
     }
 
     /**
      * True if \a n is the index of the right-most grid point, false
      * otherwise.
      */
-    bool isRight(int n) const {
+    bool isRight(size_t n) const {
         return (n == nPoints() - 1);
     }
 

samples/cxx/combustor/combustor.cpp

@@ -19,7 +19,6 @@ void runexample()
 
     // use reaction mechanism GRI-Mech 3.0
     IdealGasMix gas("gri30.cti", "gri30");
-    int nsp = gas.nSpecies();
 
     // create a reservoir for the fuel inlet, and set to pure methane.
     Reservoir fuel_in;
@@ -105,7 +104,6 @@ void runexample()
     double tfinal = 1.0;
     double tnow = 0.0;
     double tres;
-    int k;
 
     std::ofstream f("combustor_cxx.csv");
     std::vector<size_t> k_out;

samples/cxx/demo.cpp

@@ -13,6 +13,7 @@
 
 #include "cantera/IdealGasMix.h"    // defines class IdealGasMix
 #include "cantera/transport.h"      // transport properties
+#include <cstdio>
 
 // All Cantera kernel names are in namespace Cantera. You can either
 // reference everything as Cantera::<name>, or include the following

samples/cxx/kinetics1/kinetics1.cpp

@@ -48,7 +48,7 @@ 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);
+    sim.addReactor(r);
 
     // main loop
     clock_t t0 = clock();        // save start time