Merge bug fixes from the 2.0 maintenance branch

SConstruct

@@ -230,6 +230,8 @@ else:
     defaults.singleLibrary = False
 
 defaults.fsLayout = 'compact' if env['OS'] == 'Windows' else 'standard'
+defaults.env_vars = 'LD_LIBRARY_PATH' if 'LD_LIBRARY_PATH' in os.environ else ''
+defaults.python_prefix = '$prefix' if env['OS'] != 'Windows' else ''
 
 # **************************************
 # *** Read user-configurable options ***
@@ -279,11 +281,12 @@ opts.AddVariables(
         '', PathVariable.PathAccept),
     PathVariable(
         'python_prefix',
-        """If you want to install the Cantera Python package somewhere other
-           than the default 'site-packages' directory within the Python library
-           directory, then set this to the desired directory. This is useful
-           when you do not have write access to the Python library directory.""",
-        '', PathVariable.PathAccept),
+        """Use this option if you want to install the Cantera Python package to
+           an alternate location. On Unix-like systems, the default is the same
+           as the $prefix option. If this option is set to the empty string (the
+           default on Windows), then the Package will be installed to the system
+           default 'site-packages' directory.""",
+        defaults.python_prefix, PathVariable.PathAccept),
     EnumVariable(
         'matlab_toolbox',
         """This variable controls whether the Matlab toolbox will be built. If
@@ -396,7 +399,7 @@ opts.AddVariables(
      """Environment variables to propagate through to SCons. Either the
         string "all" or a comma separated list of variable names, e.g.
         'LD_LIBRARY_PATH,HOME'""",
-     ''),
+     defaults.env_vars),
     ('cxx_flags',
      'Compiler flags passed to the C++ compiler only.',
      defaults.cxxFlags),
@@ -1186,6 +1189,7 @@ build_cantera = Alias('build', finish_build)
 Default('build')
 
 def postInstallMessage(target, source, env):
+    env['python_module_loc'] = env.subst(env['python_module_loc'])
     print """
 Cantera has been successfully installed.
 

include/cantera/kinetics/ReactionData.h

@@ -19,6 +19,7 @@ public:
     //! Default constructor
     ReactionData() {
         reactionType = ELEMENTARY_RXN;
+        validate = false;
         number = 0;
         rxn_number = 0;
         reversible = true;
@@ -41,6 +42,7 @@ public:
      */
     int reactionType;
 
+    bool validate;
     int number;
     int rxn_number;
     std::vector<size_t> reactants;

include/cantera/kinetics/RxnRates.h

@@ -165,7 +165,7 @@ public:
             m_logA = log(m_A);
         }
 
-        const vector_fp& data = rdata.auxRateCoeffParameters;
+        const vector_fp& data = rdata.rateCoeffParameters;
         if (data.size() >= 7) {
             for (size_t n = 3; n < data.size()-3; n += 4) {
                 addCoverageDependence(size_t(data[n]), data[n+1],
@@ -420,6 +420,10 @@ public:
         n2_.resize(maxRates_);
         Ea1_.resize(maxRates_);
         Ea2_.resize(maxRates_);
+
+        if (rdata.validate) {
+            validate();
+        }
     }
 
     //! Update concentration-dependent parts of the rate coefficient.
@@ -469,7 +473,7 @@ public:
         if (m1_ == 1) {
             log_k1 = A1_[0] + n1_[0] * logT - Ea1_[0] * recipT;
         } else {
-            double k = 0.0;
+            double k = 1e-300; // non-zero to make log(k) finite
             for (size_t m = 0; m < m1_; m++) {
                 k += A1_[m] * exp(n1_[m] * logT - Ea1_[m] * recipT);
             }
@@ -479,7 +483,7 @@ public:
         if (m2_ == 1) {
             log_k2 = A2_[0] + n2_[0] * logT - Ea2_[0] * recipT;
         } else {
-            double k = 0.0;
+            double k = 1e-300; // non-zero to make log(k) finite
             for (size_t m = 0; m < m2_; m++) {
                 k += A2_[m] * exp(n2_[m] * logT - Ea2_[m] * recipT);
             }
@@ -506,6 +510,32 @@ public:
         return false;
     }
 
+    //! Check to make sure that the rate expression is finite over a range of
+    //! temperatures at each interpolation pressure. This is potentially an
+    //! issue when one of the Arrhenius expressions at a particular pressure
+    //! has a negative pre-exponential factor.
+    void validate() {
+        double T[] = {1.0, 10.0, 100.0, 1000.0, 10000.0};
+        for (pressureIter iter = pressures_.begin();
+             iter->first < 1000;
+             iter++)
+        {
+            update_C(&iter->first);
+            for (size_t i=0; i < 5; i++) {
+                double k = updateRC(log(T[i]), 1.0/T[i]);
+                if (!(k >= 0)) {
+                    // k is NaN. Increment the iterator so that the error
+                    // message will correctly indicate that the problematic rate
+                    // expression is at the higher of the adjacent pressures.
+                    throw CanteraError("Plog::validate",
+                                       "Invalid rate coefficient at P = " +
+                                       fp2str(exp((++iter)->first)) +
+                                       ", T = " + fp2str(T[i]));
+                }
+            }
+        }
+    }
+
 protected:
     //! log(p) to (index range) in A_, n, Ea vectors
     std::map<double, std::pair<size_t, size_t> > pressures_;

interfaces/python/Cantera/Reactor.py

@@ -432,7 +432,7 @@ class FlowReactor(ReactorBase):
             self.setMassFlowRate(mdot)
 
     def setMassFlowRate(self, mdot):
-        _cantera.flowReactor_setMassFlowRate(self.__reactor_id, mdot)
+        _cantera.flowReactor_setMassFlowRate(self.reactor_id(), mdot)
 
 
 class ConstPressureReactor(ReactorBase):

src/kinetics/importKinetics.cpp

@@ -689,6 +689,7 @@ bool rxninfo::installReaction(int iRxn, const XML_Node& r, Kinetics& kin,
     // xml data. Then, when we have collected everything we add the reaction to
     // the kinetics object, kin, at the end of the routine.
     ReactionData rdata;
+    rdata.validate = validate_rxn;
 
     // Check to see if the reaction is specified to be a duplicate of another
     // reaction. It's an error if the reaction is a duplicate and this is not