diff --git a/Cantera/python/src/methods.h b/Cantera/python/src/methods.h
index ce7560f21..026e974ec 100644
--- a/Cantera/python/src/methods.h
+++ b/Cantera/python/src/methods.h
@@ -85,46 +85,8 @@ static PyMethodDef ct_methods[] = {
     {"ct_print", ct_print,  METH_VARARGS},
     {"ct_refcnt", ct_refcnt,  METH_VARARGS},
     {"readlog", ct_readlog,  METH_VARARGS},
-    //{"ck2cti", ct_ck2cti,  METH_VARARGS},
     {"buildSolutionFromXML", ct_buildSolutionFromXML, METH_VARARGS},
 
-//     {"Flow", py_flow_new,  METH_VARARGS},
-//     {"flow_delete", py_flow_delete,  METH_VARARGS},
-//     {"flow_setupgrid", py_flow_setupgrid,  METH_VARARGS},
-//     {"flow_setthermo", py_flow_setthermo,  METH_VARARGS},
-//     {"flow_setkinetics", py_flow_setkinetics,  METH_VARARGS},
-//     {"flow_settransport", py_flow_settransport,  METH_VARARGS},
-//     {"flow_setpressure", py_flow_setpressure,  METH_VARARGS},
-//     {"flow_solvespecies", py_flow_solvespecies,  METH_VARARGS},
-//     {"flow_settemperature", py_flow_settemperature,  METH_VARARGS},
-//     {"flow_setenergyfactor", py_flow_setenergyfactor,  METH_VARARGS},
-//     {"flow_setmassfraction", py_flow_setmassfraction,  METH_VARARGS},
-//     {"flow_settolerances", py_flow_settolerances,  METH_VARARGS},
-//     {"flow_energy", py_flow_energy,  METH_VARARGS},
-//     {"flow_showsolution", py_flow_showsolution,  METH_VARARGS},
-//     {"flow_resize", py_flow_resize,  METH_VARARGS},
-//     {"flow_outputtec", py_flow_outputtec,  METH_VARARGS},
-//     {"flow_restore", py_flow_restore,  METH_VARARGS},
-//     {"flow_setfixedpoint", py_flow_setfixedpoint,  METH_VARARGS},
-//     {"flow_setboundaries", py_flow_setboundaries,  METH_VARARGS},
-//     {"copy", py_copy,  METH_VARARGS},
-//     {"bdry_new", py_bdry_new,  METH_VARARGS},
-//     {"bdry_del", py_bdry_delete,  METH_VARARGS},
-//     {"bdry_set", py_bdry_set,  METH_VARARGS},
-//     {"onedim_solve", py_onedim_solve,  METH_VARARGS},
-//     {"onedim_new", py_onedim_new,  METH_VARARGS},
-//     {"onedim_del", py_onedim_delete,  METH_VARARGS},
-//     {"onedim_setnewtonoptions", py_onedim_setnewtonoptions,  METH_VARARGS},
-//     {"onedim_ssnorm", py_onedim_ssnorm,  METH_VARARGS},
-//     {"onedim_setsteadymode", py_onedim_setsteadymode,  METH_VARARGS},
-//     {"onedim_settransientmode", py_onedim_settransientmode,  METH_VARARGS},
-//     {"onedim_eval", py_onedim_eval,  METH_VARARGS},
-//     {"onedim_addflow", py_onedim_addflow,  METH_VARARGS},
-//     {"onedim_resize", py_onedim_resize,  METH_VARARGS},
-//     {"onedim_writestats", py_onedim_writestats,  METH_VARARGS},
-//     {"onedim_timestep", py_onedim_timestep,  METH_VARARGS},
-//     {"onedim_save", py_onedim_save,  METH_VARARGS},
-
     {"domain_clear", py_domain_clear, METH_VARARGS},
     {"domain_del", py_domain_del, METH_VARARGS},
     {"domain_type", py_domain_type, METH_VARARGS},
diff --git a/Cantera/src/InterfaceKinetics.cpp b/Cantera/src/InterfaceKinetics.cpp
index 80fc65640..f82181106 100644
--- a/Cantera/src/InterfaceKinetics.cpp
+++ b/Cantera/src/InterfaceKinetics.cpp
@@ -27,183 +27,6 @@ using namespace std;
 
 namespace Cantera {
 
-
-    ///////////////////////////////////////////////////////////
-    //
-    //    class SurfPhase methods
-    //
-    ///////////////////////////////////////////////////////////
-
-    SurfPhase::
-    SurfPhase(doublereal n0):
-	ThermoPhase(),
-	m_n0(n0),
-	m_logn0(0.0),
-	m_tmin(0.0),
-	m_tmax(0.0),
-	m_press(OneAtm),
-	m_tlast(0.0) 
-    {
-	if (n0 > 0.0) m_logn0 = log(n0);
-        setNDim(2);
-    }
-
-    doublereal SurfPhase::
-    enthalpy_mole() const {
-        if (m_n0 <= 0.0) return 0.0; 
-        _updateThermo();
-        return mean_X(m_h0.begin());
-    }
-
-    SurfPhase::
-    ~SurfPhase() { }
-
-    /**
-     * For a surface phase, the pressure is not a relevant
-     * thermodynamic variable, and so the enthalpy is equal to the
-     * internal energy.
-     */
-    doublereal SurfPhase::
-    intEnergy_mole() const { return enthalpy_mole(); }
-
-    void SurfPhase::
-    getStandardChemPotentials(doublereal* mu0) const {
-        _updateThermo();
-        copy(m_mu0.begin(), m_mu0.end(), mu0);
-    }
-
-    void SurfPhase::
-    getActivityConcentrations(doublereal* c) const { 
-        getConcentrations(c); 
-    }
-
-    doublereal SurfPhase::
-    standardConcentration(int k) const {
-        return m_n0/size(k); 
-    }
-
-    doublereal SurfPhase::
-    logStandardConc(int k) const {
-        return m_logn0 - m_logsize[k];
-    }
-
-    void SurfPhase::
-    setParameters(int n, doublereal* c) {
-        m_n0 = c[0];
-	if (m_n0 <= 0.0) {
-	  throw CanteraError("SurfPhase::setParameters",
-			     "Bad value for parameter");
-	}
-        m_logn0 = log(m_n0);
-    }
-
-    void SurfPhase::
-    initThermo() {
-        m_h0.resize(m_kk);
-        m_s0.resize(m_kk);
-        m_cp0.resize(m_kk);
-        m_mu0.resize(m_kk);
-        m_work.resize(m_kk);
-        m_pe.resize(m_kk, 0.0);
-        vector_fp cov(m_kk, 0.0);
-        cov[0] = 1.0;
-        setCoverages(cov.begin());
-        m_logsize.resize(m_kk);
-        for (int k = 0; k < m_kk; k++) 
-            m_logsize[k] = log(size(k));
-    }
-
-    void SurfPhase::
-    setPotentialEnergy(int k, doublereal pe) {
-        m_pe[k] = pe;
-        _updateThermo(true);
-    }
-
-    void SurfPhase::
-    setSiteDensity(doublereal n0) {
-        doublereal x = n0;
-        setParameters(1, &x);
-    }
-
-
-    //void SurfPhase::
-    //setElectricPotential(doublereal V) {
-    //    for (int k = 0; k < m_kk; k++) {
-    //        m_pe[k] = charge(k)*Faraday*V;
-    //    }
-    //    _updateThermo(true);
-    //}
-
-    /**
-     * Set the coverage fractions to a specified 
-     * state. This routine converts to concentrations
-     * in kmol/m2, using m_n0, the surface site density,
-     * and size(k), which is defined to be the number of
-     * surface sites occupied by the kth molecule.
-     * It then calls State::setConcentrations to set the
-     * internal concentration in the object.
-     */
-    void SurfPhase::
-    setCoverages(const doublereal* theta) {
-        for (int k = 0; k < m_kk; k++) {
-            m_work[k] = m_n0*theta[k]/size(k);
-        }
-	/*
-	 * Call the State:: class function
-	 * setConcentrations.
-	 */
-        setConcentrations(m_work.begin());
-    }
-
-    void SurfPhase::
-    getCoverages(doublereal* theta) const {
-        getConcentrations(theta);
-        for (int k = 0; k < m_kk; k++) {
-            theta[k] *= size(k)/m_n0; 
-        }
-    }
-
-    void SurfPhase::
-    setCoveragesByName(string cov) {
-        int kk = nSpecies();
-        int k;
-        compositionMap cc;
-        for (k = 0; k < kk; k++) { 
-            cc[speciesName(k)] = -1.0;
-        }
-        parseCompString(cov, cc);
-        doublereal c;
-        vector_fp cv(kk, 0.0);
-        for (k = 0; k < kk; k++) { 
-            c = cc[speciesName(k)];
-            if (c > 0.0) cv[k] = c;
-        }
-        setCoverages(cv.begin());
-    }
-
-
-    void SurfPhase::
-    _updateThermo(bool force) const {
-        doublereal tnow = temperature();
-        if (m_tlast != tnow || force) {
-            m_spthermo->update(tnow, m_cp0.begin(), m_h0.begin(), 
-                m_s0.begin());
-            m_tlast = tnow;
-            doublereal rt = GasConstant * tnow;
-            int k;
-            //doublereal deltaE;
-            for (k = 0; k < m_kk; k++) {
-                m_h0[k] *= rt;
-                m_s0[k] *= GasConstant;
-                m_cp0[k] *= GasConstant;
-                //deltaE = m_pe[k];
-                //m_h0[k] += deltaE;
-                m_mu0[k] = m_h0[k] - tnow*m_s0[k];
-            }
-            m_tlast = tnow;
-        }
-    }
-
     //////////////////////////////////////////////////////////////////
 
     /**
@@ -314,34 +137,35 @@ namespace Cantera {
     void InterfaceKinetics::updateKc() {
         int i, irxn;
         vector_fp& m_rkc = m_kdata->m_rkcn;
-
-        int n, nsp, k, ik=0;
-        doublereal rt = GasConstant*thermo(0).temperature();
-        doublereal rrt = 1.0/rt;
-        int np = nPhases();
-        for (n = 0; n < np; n++) {
-            thermo(n).getStandardChemPotentials(m_mu0.begin() + m_start[n]);
-            nsp = thermo(n).nSpecies();
-            for (k = 0; k < nsp; k++) {
-                m_mu0[ik] -= rt*thermo(n).logStandardConc(k);
-                m_mu0[ik] += Faraday * m_phi[n] * thermo(n).charge(k);
-                ik++;
-            }
-        }
-
         fill(m_rkc.begin(), m_rkc.end(), 0.0);
 
-        // compute Delta mu^0 for all reversible reactions
-        m_reactantStoich.decrementReactions(m_mu0.begin(), m_rkc.begin()); 
-        m_revProductStoich.incrementReactions(m_mu0.begin(), m_rkc.begin());
+        if (m_nrev > 0) {
 
-        for (i = 0; i < m_nrev; i++) {
-            irxn = m_revindex[i];
-            m_rkc[irxn] = exp(m_rkc[irxn]*rrt);
-        }
+            int n, nsp, k, ik=0;
+            doublereal rt = GasConstant*thermo(0).temperature();
+            doublereal rrt = 1.0/rt;
+            int np = nPhases();
+            for (n = 0; n < np; n++) {
+                thermo(n).getStandardChemPotentials(m_mu0.begin() + m_start[n]);
+                nsp = thermo(n).nSpecies();
+                for (k = 0; k < nsp; k++) {
+                    m_mu0[ik] -= rt*thermo(n).logStandardConc(k);
+                    m_mu0[ik] += Faraday * m_phi[n] * thermo(n).charge(k);
+                    ik++;
+                }
+            }
 
-        for (i = 0; i != m_nirrev; ++i) {
-            m_rkc[ m_irrev[i] ] = 0.0;
+            // compute Delta mu^0 for all reversible reactions
+            m_reactantStoich.decrementReactions(m_mu0.begin(), m_rkc.begin()); 
+            m_revProductStoich.incrementReactions(m_mu0.begin(), m_rkc.begin());
+
+            for (i = 0; i < m_nrev; i++) {
+                irxn = m_revindex[i];
+                m_rkc[irxn] = exp(m_rkc[irxn]*rrt);
+            }
+            for (i = 0; i != m_nirrev; ++i) {
+                m_rkc[ m_irrev[i] ] = 0.0;
+            }
         }
     }
 
@@ -491,6 +315,10 @@ namespace Cantera {
     addReaction(const ReactionData& r) {
 
         int nr = r.reactants.size();
+
+        // a global reaction is idnetified as one with 
+        // a reactant stoichiometric coefficient not equal 
+        // to the molecularity for some reactant
         bool isglobal = false;
         for (int n = 0; n < nr; n++) {
             if (r.rstoich[n] != int(r.order[n])) {
diff --git a/Cantera/src/Makefile.in b/Cantera/src/Makefile.in
index ee96d2dd9..492369a8e 100755
--- a/Cantera/src/Makefile.in
+++ b/Cantera/src/Makefile.in
@@ -33,7 +33,7 @@ KINETICS   = GRI_30_Kinetics.o KineticsFactory.o GasKinetics.o FalloffFactory.o
              ReactionStoichMgr.o $(THERMO)
 
 # heterogeneous kinetics
-HETEROKIN = InterfaceKinetics.o ImplicitSurfChem.o $(THERMO)
+HETEROKIN = InterfaceKinetics.o ImplicitSurfChem.o SurfPhase.o $(THERMO)
 
 # support for importing from Chemkin-compatible reaction mechanisms
 CK         = $(KINETICS)
@@ -51,8 +51,8 @@ SOLVERS    = CVode.o  BandMatrix.o
 FLOW1D     =  $(KINETICS) $(SOLVERS)
 
 
-EVERYTHING = $(KINETICS) $(HETEROKIN) $(EQUIL) $(CK) $(TRANSPORT) $(REACTOR) $(RPATH) \
-             $(SOLVERS) $(FLOW1D)
+EVERYTHING = $(KINETICS) $(HETEROKIN) $(ELECTROCHEM) $(EQUIL) $(CK) \
+             $(TRANSPORT) $(REACTOR) $(RPATH) $(SOLVERS) $(FLOW1D)
 
 
 all:  @KERNEL@ lib
diff --git a/Cantera/src/NasaPoly1.h b/Cantera/src/NasaPoly1.h
index 9cc9ff0e7..12309ebc3 100755
--- a/Cantera/src/NasaPoly1.h
+++ b/Cantera/src/NasaPoly1.h
@@ -31,7 +31,7 @@ namespace Cantera {
      * \f]
      * \f[
      * \frac{h^0(T)}{RT} = a_0 + \frac{a_1}{2} T + \frac{a_2}{3} T^2 
-     + \frac{a_3}{4} T^3 + \frac{a_4}{5} T^4  + a_5.
+     * + \frac{a_3}{4} T^3 + \frac{a_4}{5} T^4  + \frac{a_5}{T}.
      * \f]
      * \f[
      * \frac{s^0(T)}{R} = a_0\ln T + a_1 T + \frac{a_2}{2} T^2 
@@ -61,26 +61,34 @@ namespace Cantera {
 
         virtual ~NasaPoly1(){}
       
-        doublereal minTemp() const { return m_lowT;}
-        doublereal maxTemp() const { return m_highT;}
+        doublereal minTemp() const     { return m_lowT;}
+        doublereal maxTemp() const     { return m_highT;}
         doublereal refPressure() const { return m_Pref; }
       
+        /**
+         * Update the properties for this species. This method is called 
+         * with a pointer to an array containing the functions of temperature needed by this 
+         * parameterization, and three pointers to arrays where the computed property values
+         * should be written. This method updates only one value in each array.  
+         */
         void updateProperties(const doublereal* tt, 
             doublereal* cp_R, doublereal* h_RT, doublereal* s_R) const {
           
-            doublereal ct0 = m_coeff[2];
-            doublereal ct1 = m_coeff[3]*tt[0];
-            doublereal ct2 = m_coeff[4]*tt[1];
-            doublereal ct3 = m_coeff[5]*tt[2];
-            doublereal ct4 = m_coeff[6]*tt[3];
+            doublereal ct0 = m_coeff[2];          // a0 
+            doublereal ct1 = m_coeff[3]*tt[0];    // a1 * T
+            doublereal ct2 = m_coeff[4]*tt[1];    // a2 * T^2
+            doublereal ct3 = m_coeff[5]*tt[2];    // a3 * T^3
+            doublereal ct4 = m_coeff[6]*tt[3];    // a4 * T^4
  
             doublereal cp, h, s;
             cp = ct0 + ct1 + ct2 + ct3 + ct4;
             h = ct0 + 0.5*ct1 + OneThird*ct2 + 0.25*ct3 + 0.2*ct4
-                + m_coeff[0]*tt[4];
+                + m_coeff[0]*tt[4];               // last term is a5/T
             s = ct0*tt[5] + ct1 + 0.5*ct2 + OneThird*ct3
-                +0.25*ct4 + m_coeff[1];
+                +0.25*ct4 + m_coeff[1];           // last term is a6
 
+            // return the computed properties in the location in the output 
+            // arrays for this species
             cp_R[m_index] = cp;
             h_RT[m_index] = h;
             s_R[m_index] = s;
@@ -88,9 +96,11 @@ namespace Cantera {
 
     protected:
         
-        doublereal m_lowT, m_highT, m_Pref;
-        int m_index;
-        array_fp m_coeff;
+        doublereal m_lowT;     // lowest valid temperature
+        doublereal m_highT;    // highest valid temperature
+        doublereal m_Pref;     // standard-state pressure
+        int m_index;           // species index
+        array_fp m_coeff;      // array of polynomial coefficients
     
     private:
 
diff --git a/Cantera/src/NasaThermo.h b/Cantera/src/NasaThermo.h
index 63c4cae13..d706c7fbe 100755
--- a/Cantera/src/NasaThermo.h
+++ b/Cantera/src/NasaThermo.h
@@ -3,9 +3,9 @@
  */
 
 /*
- * $author$
- * $revision$
- * $date$
+ * $Author$
+ * $Revision$
+ * $Date$
  */
 
 
@@ -57,12 +57,12 @@ namespace Cantera {
 
         /**
          * Install parameterization for a species.
-         * @param index  Species index
-         * @param type   ignored, since only NASA type is supported
-         * @param c      coefficients. These are
-         * - c[0] midpoint temperature
-         * - c[1] - c[7] coefficients for low T range
-         * - c[8] - c[14] coefficients for high T range
+         * @param index    Species index
+         * @param type     ignored, since only NASA type is supported
+         * @param c        coefficients. These are
+         * - c[0]          midpoint temperature
+         * - c[1] - c[7]   coefficients for low T range
+         * - c[8] - c[14]  coefficients for high T range
          */
         virtual void install(int index, int type, const doublereal* c, 
             doublereal minTemp, doublereal maxTemp, doublereal refPressure) { 
@@ -105,6 +105,10 @@ namespace Cantera {
             m_low_map[index] = &m_low[igrp-1].back();
         }
 
+
+        /** 
+         * update the properties for only one species.
+         */
         virtual void update_one(int k, doublereal t, doublereal* cp_R, 
             doublereal* h_RT, doublereal* s_R) const {
 
@@ -127,6 +131,7 @@ namespace Cantera {
             doublereal* h_RT, doublereal* s_R) const {
             int i;
 
+            // load functions of temperature into m_t vector
             m_t[0] = t;
             m_t[1] = t*t;
             m_t[2] = m_t[1]*t;
@@ -134,6 +139,7 @@ namespace Cantera {
             m_t[4] = 1.0/t;
             m_t[5] = log(t);
 
+            // iterate over the groups
             vector<NasaPoly1>::const_iterator _begin, _end;
             for (i = 0; i != m_ngroups; i++) {
                 if (t > m_tmid[i]) {
@@ -149,6 +155,13 @@ namespace Cantera {
             }
         }
                 
+        /**
+         * Return the lowest temperature at which the thermodynamic
+         * parameterization is valid.  If no argument is supplied, the
+         * value is the one for which all species parameterizations
+         * are valid. Otherwise, if an integer argument is given, the
+         * value applies only to the species with that index.
+         */
         virtual doublereal minTemp(int k=-1) const {
             if (k < 0)
                 return m_tlow_max;
@@ -187,8 +200,11 @@ namespace Cantera {
 #endif
 
 // $Log$
-// Revision 1.1  2003-04-14 17:57:51  dggoodwin
-// Initial revision
+// Revision 1.2  2003-11-01 04:50:35  dggoodwin
+// *** empty log message ***
+//
+// Revision 1.1.1.1  2003/04/14 17:57:51  dggoodwin
+// Initial import.
 //
 // Revision 1.16  2003/01/13 10:14:32  dgg
 // *** empty log message ***
diff --git a/Cantera/src/SpeciesThermo.h b/Cantera/src/SpeciesThermo.h
index e4c671170..0a1d73ca7 100755
--- a/Cantera/src/SpeciesThermo.h
+++ b/Cantera/src/SpeciesThermo.h
@@ -34,10 +34,9 @@ namespace Cantera {
     //////////////////////// class SpeciesThermo ////////////////////
 
     /**
-     * Virtual base class for the species thermo
-     * manager classes. This class defines the interface which all
-     * subclasses must implement.
-     * @ingroup spthermo 
+     * Virtual base class for the species thermo manager classes. This
+     * class defines the interface which all subclasses must
+     * implement.  @ingroup spthermo
      */
 
     class SpeciesThermo {
diff --git a/Cantera/src/ct2ctml.cpp b/Cantera/src/ct2ctml.cpp
index ed9c5e6ad..33c513585 100644
--- a/Cantera/src/ct2ctml.cpp
+++ b/Cantera/src/ct2ctml.cpp
@@ -111,7 +111,7 @@ namespace ctml {
         //char line[90];
         //if (ierr != 0) {
         try {
-            char ch;
+            char ch=0;
             string s = "";
             ifstream ferr("ct2ctml.log");
             if (ferr) {
diff --git a/Cantera/src/importCTML.cpp b/Cantera/src/importCTML.cpp
index 97cdf54fe..f326591b8 100755
--- a/Cantera/src/importCTML.cpp
+++ b/Cantera/src/importCTML.cpp
@@ -103,12 +103,13 @@ namespace Cantera {
         XML_Node *db, *doc;
         split(file_ID, fname, idstr);
         if (fname == "") {
-	  if (!root) return 0;
-	  db = root->findID(idstr, 3);
+            if (!root) throw CanteraError("get_XML_Node","no file name given. file_ID = "+file_ID);
+            db = root->findID(idstr, 3);
         } else {
 	  doc = get_XML_File(fname);
-	  if (!doc) return 0;
+	  if (!doc) throw CanteraError("get_XML_Node", "get_XML_File failed trying to open "+fname);
 	  db = doc->findID(idstr, 3);
+          if (!db) throw CanteraError("get_XML_Node", "id tag "+idstr+" not found.");
         }
         return db;
     }
diff --git a/Cantera/src/mix_defs.h b/Cantera/src/mix_defs.h
index 832e46b82..e829a5bd8 100755
--- a/Cantera/src/mix_defs.h
+++ b/Cantera/src/mix_defs.h
@@ -35,11 +35,13 @@ namespace Cantera {
     const int cSurf = 3;           //  SurfPhase in SurfPhase.h 
     const int cMetal = 4;          //  MetalPhase in MetalPhase.h
     const int cSolidCompound = 5;  //  SolidCompound in SolidCompound.h
+    const int cEdge = 6;
 
     // kinetic manager types
     const int cGasKinetics = 2;
     const int cGRI30 = 3;
     const int cInterfaceKinetics = 4;
+    const int cLineKinetics = 5;
 }
 
 #endif
diff --git a/Cantera/src/oneD/Domain1D.h b/Cantera/src/oneD/Domain1D.h
index 191a39ee4..16ecbb226 100644
--- a/Cantera/src/oneD/Domain1D.h
+++ b/Cantera/src/oneD/Domain1D.h
@@ -398,11 +398,12 @@ namespace Cantera {
         virtual void setupGrid(int n, const doublereal* z) {}
 
         /**
-         * Writes some or all initial solution values into array x,
-         * which is the solution vector for this domain. This allows
-         * initial values that have been set prior to installing this
-         * domain into the container to be written to the global
-         * solution vector.
+         * Writes some or all initial solution values into the global
+         * solution array, beginning at the location pointed to by
+         * x. This method is called by the Sim1D constructor, and
+         * allows default values or ones that have been set locally
+         * prior to installing this domain into the container to be
+         * written to the global solution vector.
          */
         virtual void _getInitialSoln(doublereal* x) {
             throw CanteraError("Domain1D::_getInitialSoln",
@@ -410,13 +411,19 @@ namespace Cantera {
         }
 
         /**
-         * Perform any necessary domain-specific initialization using 
-         * local solution vector x.
+         * In some cases, a domain may need to set parameters that
+         * depend on the initial solution estimate. In such cases, the
+         * parameters may be set in method _finalize. This method is
+         * called just before the Newton solver is called, and the x
+         * array is guaranteed to be the local solution vector for
+         * this domain that will be used as the initial guess. If no
+         * such parameters need to be set, then method _finalize does
+         * not need to be overloaded.
          */ 
-        virtual void _finalize(const doublereal* x) {
-            throw CanteraError("Domain1D::_finalize",
-                "base class method _finalize called!");
-        }
+        virtual void _finalize(const doublereal* x) {}
+        //throw CanteraError("Domain1D::_finalize",
+        //      "base class method _finalize called!");
+        //}
 
 
     protected:
diff --git a/Cantera/src/oneD/MultiJac.cpp b/Cantera/src/oneD/MultiJac.cpp
index 07faecfd1..1a4123a02 100644
--- a/Cantera/src/oneD/MultiJac.cpp
+++ b/Cantera/src/oneD/MultiJac.cpp
@@ -20,6 +20,8 @@
 #endif
 
 #include <vector>
+#include <math.h>
+
 using namespace std;
 
 #include "MultiJac.h"
@@ -93,10 +95,12 @@ namespace Cantera {
                         for (m = 0; m < mv; m++) {
                             value(m+iloc,ipt) = (m_r1[m+iloc] 
                                 - resid0[m+iloc])*rdx;
-                            //if (m == 15) {
-                            //    cout << "perturbed " << n << " " << value(m+iloc,ipt) <<  " " << m_r1[m+iloc]
-                            //         << " " << resid0[m+iloc] << " " << rdx << endl;
-                            //}
+                            if (__isnand(value(m+iloc,ipt))) {
+                                cout << "NaN detected at i, j, n, m: " << i 
+                                     << " " << j << " " << n << " " <<  m << 
+                                    " " << m_r1[m+iloc] << " " << resid0[m+iloc]
+                                     << " " << rdx << endl;
+                            }
                         }
                     }
                 }
diff --git a/Cantera/src/oneD/MultiNewton.cpp b/Cantera/src/oneD/MultiNewton.cpp
index 27b521550..f57bdd061 100644
--- a/Cantera/src/oneD/MultiNewton.cpp
+++ b/Cantera/src/oneD/MultiNewton.cpp
@@ -145,7 +145,7 @@ namespace Cantera {
 			       "Jacobian is singular for domain "+
 			       dom.id() + ", component "
 			       +dom.componentName(comp)+" at point "
-			       +int2str(pt));
+			       +int2str(pt)+"\nsee file bandmatrix.csv\n");
 	  }
 	  else if (iok < 0)   
 	    throw CanteraError("MultiNewton::step",
diff --git a/Cantera/src/transport/MixTransport.cpp b/Cantera/src/transport/MixTransport.cpp
index 09e29e4c1..b1550a144 100755
--- a/Cantera/src/transport/MixTransport.cpp
+++ b/Cantera/src/transport/MixTransport.cpp
@@ -52,7 +52,6 @@ namespace Cantera {
     bool MixTransport::init(TransportParams& tr) {
 
         // constant substance attributes
-        //m_phase = tr.mix;
         m_thermo = tr.thermo;
         m_nsp   = m_thermo->nSpecies();
         m_tmin  = m_thermo->minTemp();
diff --git a/Cantera/src/transport/TransportBase.h b/Cantera/src/transport/TransportBase.h
index a8a8998ec..0feacb2c8 100755
--- a/Cantera/src/transport/TransportBase.h
+++ b/Cantera/src/transport/TransportBase.h
@@ -24,11 +24,12 @@
 #include "../ctexceptions.h"
 #include "../Array.h"
 #include "../stringUtils.h"
-//#include "Phase.h"
 #include "../ThermoPhase.h"
 
 namespace Cantera {
 
+    // exception class
+
     class NotImplemented : public CanteraError {
     public:
         NotImplemented(string method) : CanteraError("Transport",
@@ -53,24 +54,21 @@ namespace Cantera {
 
 
     /**
-     * Base class for transport property managers. 
-     * All classes that compute transport properties derive from this
-     * class.  Class Transport is meant to be used as a base class
-     * only. It is possible to instantiate it, but its methods throw
-     * exceptions if called.
-     * @see MultiTransport
-     * @see MixTransport
+     * Base class for transport property managers.  All classes that
+     * compute transport properties derive from this class.  Class
+     * Transport is meant to be used as a base class only. It is
+     * possible to instantiate it, but its methods throw exceptions if
+     * called.
      */
     class Transport {
 
     public:
 
         /**
-         * Transport model. Each transport manager may implement a
-         * different transport model, defined as the set of equations
-         * used to compute the transport properties. This virtual
-         * method returns an integer flag that identifies the
-         * transport model implemented.
+         * Transport model. The transport model is the set of
+         * equations used to compute the transport properties. This
+         * virtual method returns an integer flag that identifies the
+         * transport model implemented. The base class returns 0.
          */
         virtual int model() {return 0;}
 
@@ -86,7 +84,6 @@ namespace Cantera {
 
         /**
          * Returns true if the transport manager is ready for use.
-         * When first created, ready() returns false, since  
          */
         bool ready() { return m_ready; }
 
@@ -107,8 +104,7 @@ namespace Cantera {
          
 
         /**
-         * The mixture viscosity in Pa-s. 
-         * @see \ref viscositySection
+         * The viscosity in Pa-s. 
          */
         virtual doublereal viscosity() 
             { return err("viscosity"); }
@@ -128,7 +124,6 @@ namespace Cantera {
          * applications where bulk viscosity is important, it is
          * possible to create a transport manager that computes it by
          * overloading this method.
-         * @see bulkViscositySection
          */
         virtual doublereal bulkViscosity()  
             { return err("bulkViscosity"); }
@@ -136,13 +131,12 @@ namespace Cantera {
         
         /**
          * The thermal conductivity in W/m/K. 
-         * @see thermalConductivitySection
          */
         virtual doublereal thermalConductivity()
             { return err("thermalConductivity"); }
 
         /**
-         * The electrical conductivity (mho/m).
+         * The electrical conductivity (Siemens/m).
          */
         virtual doublereal electricalConductivity()
             { return err("electricalConductivity"); }
@@ -150,14 +144,10 @@ namespace Cantera {
         /**
          * Electrical mobilities. Units: [m^2/V/s].
          */
-        void getMobilities(vector_fp& mobil) {
-            if (mobil.size() < m_nmin) sizeError(mobil.size(), m_nmin);
-            getMobilities(mobil.begin());
-        }
-
         virtual void getMobilities(doublereal* mobil)
             { err("getMobilities"); }
 
+
         //@}
 
 
@@ -168,16 +158,6 @@ namespace Cantera {
         doublereal* grad_T, int ldx, const doublereal* grad_X,
             int ldf, doublereal* fluxes) { err("getSpeciesFluxes"); }
 
-        /**
-         * Get the species mass fluxes, given the gradients.
-         */
-        void getSpeciesFluxes(int ndim, vector_fp& grad_T, const Array2D& grad_X,
-            Array2D& fluxes) { 
-            getSpeciesFluxes(ndim, grad_T.begin(), grad_X.nRows(), grad_X.begin(),
-                fluxes.nRows(), fluxes.begin());
-        }
-                                  
-
 
         /**
          * Thermal diffusion coefficients. Units: [kg/m/sec].
@@ -191,10 +171,6 @@ namespace Cantera {
          * diffusion coefficients.  Dimension dt at least as large as
          * the number of species.
          */
-        void getThermalDiffCoeffs(vector_fp& dt) {
-            if (dt.size() < m_nmin) sizeError(dt.size(),m_nmin);
-            getThermalDiffCoeffs(dt.begin());
-        }
         virtual void getThermalDiffCoeffs(doublereal* dt) 
             { err("getThermalDiffCoeffs"); }
 
@@ -202,11 +178,6 @@ namespace Cantera {
         /**
          * Binary diffusion coefficients. Units: [m^2/s].
          */
-        void getBinaryDiffCoeffs(Array2D& d) {
-            if (d.nRows() < m_nmin || d.nColumns() < m_nmin) 
-                sizeError(d.nRows(), m_nmin, d.nColumns(), m_nmin);
-            getBinaryDiffCoeffs(d.nRows(), d.begin());
-        }
         virtual void getBinaryDiffCoeffs(int ld, doublereal* d) 
             { err("getBinaryDiffCoeffs"); }
 
@@ -217,11 +188,6 @@ namespace Cantera {
          * model, then this method returns the array of multicomponent
          * diffusion coefficients.
          */
-        void getMultiDiffCoeffs(Array2D& d) {
-            if (d.nRows() < m_nmin || d.nColumns() < m_nmin) 
-                sizeError(d.nRows(), m_nmin, d.nColumns(), m_nmin);
-            getMultiDiffCoeffs(d.nRows(), d.begin());
-        }
         virtual void getMultiDiffCoeffs(int ld, doublereal* d) 
             { err("getMultiDiffCoeffs"); }
 
@@ -232,20 +198,21 @@ namespace Cantera {
          * diffusion model, then this method returns the array of
          * mixture-averaged diffusion coefficients.
          */
-        void getMixDiffCoeffs(vector_fp& d) {
-            if (d.size() < m_nmin) 
-                sizeError(d.size(), m_nmin);
-            getMixDiffCoeffs(d.begin());
-        }
         virtual void getMixDiffCoeffs(doublereal* d) 
             { err("getMixDiffCoeffs"); }
 
+#ifdef INCL_CBAR
         doublereal meanThermalSpeed(int k) const {
             doublereal t = m_thermo->temperature();
             doublereal mw = m_thermo->molecularWeight(k);
             return sqrt(8.0 * GasConstant * t /(Pi * mw));
         }
+#endif
 
+        /**
+         * Set transport model parameters. This method may be
+         * overloaded in subclasses to set model-specific parameters.
+         */
         virtual void setParameters(int type, int k, doublereal* p) 
             { err("setParameters"); }
 
@@ -262,6 +229,7 @@ namespace Cantera {
         Transport(thermo_t* thermo=0) 
             : m_thermo(thermo), m_ready(false), m_nmin(0), m_index(-1) {}
 
+
     protected:
 
         /**
@@ -286,7 +254,7 @@ namespace Cantera {
                 m_nmin = m_thermo->nSpecies();
             }
             else 
-                throw CanteraError("Transport::setPhase",
+                throw CanteraError("Transport::setThermo",
                     "the phase object cannot be changed after "
                     "the transport manager has been constructed.");
         }
@@ -307,12 +275,12 @@ namespace Cantera {
         //@}
 
 
-        //phase_t*  m_phase;  ///< pointer to the object representing the phase 
         thermo_t*  m_thermo;  ///< pointer to the object representing the phase 
-        bool      m_ready;  ///< false initially, true if ready to use
+        bool      m_ready;  ///< true if finalize has been called
         size_t    m_nmin;   ///< number of species
         int       m_index;  
 
+
     private:
 
         /**
@@ -321,27 +289,17 @@ namespace Cantera {
          * is being used that does not implement all virtual methods,
          * and one of those methods was called by the application
          * program. For example, a transport manager that computes the
-         * thermal conductivity of a solid may not overload the
-         * viscosity() method, since the viscosity is meaningless. If the
-         * application invokes the viscosity() method, the base class
-         * method will be called, resulting in an exception being
-         * thrown.
+         * thermal conductivity of a solid may not define the
+         * viscosity() method, since the viscosity is in this case
+         * meaningless. If the application invokes the viscosity()
+         * method, the base class method will be called, resulting in
+         * an exception being thrown.
          */
         doublereal err(string msg) const { 
             throw NotImplemented(msg);
             return 0.0;
         }
 
-        void sizeError(int nr, int nrmin, int nc=-1, int ncmin=-1) {
-            string msg;
-            msg = "Array size (" + int2str(nr);
-            if (nc > 0) msg += "," + int2str(nc);
-            msg += ") is too small. Dimension at least (" + int2str(nrmin);
-            if (nc > 0) msg += "," + int2str(ncmin);
-            msg += ").";
-            throw CanteraError("Transport", msg);
-        }
-
     };
 
     typedef Transport transport_t;
diff --git a/Makefile.in b/Makefile.in
index 59669e0b4..017359eae 100755
--- a/Makefile.in
+++ b/Makefile.in
@@ -14,10 +14,11 @@ build_clib = @BUILD_CLIB@
 build_python = @BUILD_PYTHON@
 build_matlab = @BUILD_MATLAB@
 os_is_win = @OS_IS_WIN@
+incl_user_code = @INCL_USER_CODE@
 
 LIBDIR=@LIB_DIR@
 
-all: kernel cxxlib hdr-collect clib python matlab utils
+all: kernel user cxxlib hdr-collect clib python matlab utils
 
 win: python matlab
 
@@ -34,6 +35,11 @@ kernel: info
 	cd ext; @MAKE@
 	cd Cantera/src; @MAKE@
 
+user:
+ifeq ($(incl_user_code),1)
+	cd Cantera/user; @MAKE@
+endif
+
 clib: 
 	cd Cantera/clib/src; @MAKE@
 	ranlib @buildlib@/*.a
diff --git a/config/configure b/config/configure
index 35e8f7fe4..a2a92fa6d 100755
--- a/config/configure
+++ b/config/configure
@@ -1084,6 +1084,13 @@ if test -z "$PIC"; then PIC='-fPIC'; fi
 
 #if test -z "$LCXX_END_LIBS"; then LCXX_END_LIBS='-lm'; fi
 
+#########################################################
+#  User Code
+#########################################################
+USERDIR=""
+INCL_USER_CODE=0
+if test -n "$USER_SRC_DIR"; then USERDIR=$USER_SRC_DIR; INCL_USER_CODE=1; fi
+
 #########################################################
 #  The Cantera Kernel
 #########################################################
@@ -1247,7 +1254,7 @@ if test -z "$PYTHON_CMD"; then
 do
   # Extract the first word of "$ac_prog", so it can be a program name with args.
 set dummy $ac_prog; ac_word=$2
-echo "$as_me:1250: checking for $ac_word" >&5
+echo "$as_me:1257: checking for $ac_word" >&5
 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
 if test "${ac_cv_path_PYTHON_CMD+set}" = set; then
   echo $ECHO_N "(cached) $ECHO_C" >&6
@@ -1264,7 +1271,7 @@ for ac_dir in $ac_dummy; do
   test -z "$ac_dir" && ac_dir=.
   if $as_executable_p "$ac_dir/$ac_word"; then
    ac_cv_path_PYTHON_CMD="$ac_dir/$ac_word"
-   echo "$as_me:1267: found $ac_dir/$ac_word" >&5
+   echo "$as_me:1274: found $ac_dir/$ac_word" >&5
    break
 fi
 done
@@ -1275,10 +1282,10 @@ fi
 PYTHON_CMD=$ac_cv_path_PYTHON_CMD
 
 if test -n "$PYTHON_CMD"; then
-  echo "$as_me:1278: result: $PYTHON_CMD" >&5
+  echo "$as_me:1285: result: $PYTHON_CMD" >&5
 echo "${ECHO_T}$PYTHON_CMD" >&6
 else
-  echo "$as_me:1281: result: no" >&5
+  echo "$as_me:1288: result: no" >&5
 echo "${ECHO_T}no" >&6
 fi
 
@@ -1309,7 +1316,7 @@ if test "$BUILD_MATLAB_TOOLBOX" != "n"; then
   if test -z "$MATLAB_CMD"; then
     # Extract the first word of "matlab", so it can be a program name with args.
 set dummy matlab; ac_word=$2
-echo "$as_me:1312: checking for $ac_word" >&5
+echo "$as_me:1319: checking for $ac_word" >&5
 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
 if test "${ac_cv_path_MATLAB_CMD+set}" = set; then
   echo $ECHO_N "(cached) $ECHO_C" >&6
@@ -1326,7 +1333,7 @@ for ac_dir in $ac_dummy; do
   test -z "$ac_dir" && ac_dir=.
   if $as_executable_p "$ac_dir/$ac_word"; then
    ac_cv_path_MATLAB_CMD="$ac_dir/$ac_word"
-   echo "$as_me:1329: found $ac_dir/$ac_word" >&5
+   echo "$as_me:1336: found $ac_dir/$ac_word" >&5
    break
 fi
 done
@@ -1338,10 +1345,10 @@ fi
 MATLAB_CMD=$ac_cv_path_MATLAB_CMD
 
 if test -n "$MATLAB_CMD"; then
-  echo "$as_me:1341: result: $MATLAB_CMD" >&5
+  echo "$as_me:1348: result: $MATLAB_CMD" >&5
 echo "${ECHO_T}$MATLAB_CMD" >&6
 else
-  echo "$as_me:1344: result: no" >&5
+  echo "$as_me:1351: result: no" >&5
 echo "${ECHO_T}no" >&6
 fi
 
@@ -1363,7 +1370,7 @@ if test -n "$ac_tool_prefix"; then
   do
     # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
 set dummy $ac_tool_prefix$ac_prog; ac_word=$2
-echo "$as_me:1366: checking for $ac_word" >&5
+echo "$as_me:1373: checking for $ac_word" >&5
 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
 if test "${ac_cv_prog_CXX+set}" = set; then
   echo $ECHO_N "(cached) $ECHO_C" >&6
@@ -1378,7 +1385,7 @@ for ac_dir in $ac_dummy; do
   test -z "$ac_dir" && ac_dir=.
   $as_executable_p "$ac_dir/$ac_word" || continue
 ac_cv_prog_CXX="$ac_tool_prefix$ac_prog"
-echo "$as_me:1381: found $ac_dir/$ac_word" >&5
+echo "$as_me:1388: found $ac_dir/$ac_word" >&5
 break
 done
 
@@ -1386,10 +1393,10 @@ fi
 fi
 CXX=$ac_cv_prog_CXX
 if test -n "$CXX"; then
-  echo "$as_me:1389: result: $CXX" >&5
+  echo "$as_me:1396: result: $CXX" >&5
 echo "${ECHO_T}$CXX" >&6
 else
-  echo "$as_me:1392: result: no" >&5
+  echo "$as_me:1399: result: no" >&5
 echo "${ECHO_T}no" >&6
 fi
 
@@ -1402,7 +1409,7 @@ if test -z "$CXX"; then
 do
   # Extract the first word of "$ac_prog", so it can be a program name with args.
 set dummy $ac_prog; ac_word=$2
-echo "$as_me:1405: checking for $ac_word" >&5
+echo "$as_me:1412: checking for $ac_word" >&5
 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
 if test "${ac_cv_prog_ac_ct_CXX+set}" = set; then
   echo $ECHO_N "(cached) $ECHO_C" >&6
@@ -1417,7 +1424,7 @@ for ac_dir in $ac_dummy; do
   test -z "$ac_dir" && ac_dir=.
   $as_executable_p "$ac_dir/$ac_word" || continue
 ac_cv_prog_ac_ct_CXX="$ac_prog"
-echo "$as_me:1420: found $ac_dir/$ac_word" >&5
+echo "$as_me:1427: found $ac_dir/$ac_word" >&5
 break
 done
 
@@ -1425,10 +1432,10 @@ fi
 fi
 ac_ct_CXX=$ac_cv_prog_ac_ct_CXX
 if test -n "$ac_ct_CXX"; then
-  echo "$as_me:1428: result: $ac_ct_CXX" >&5
+  echo "$as_me:1435: result: $ac_ct_CXX" >&5
 echo "${ECHO_T}$ac_ct_CXX" >&6
 else
-  echo "$as_me:1431: result: no" >&5
+  echo "$as_me:1438: result: no" >&5
 echo "${ECHO_T}no" >&6
 fi
 
@@ -1440,27 +1447,27 @@ test -n "$ac_ct_CXX" || ac_ct_CXX="g++"
 fi
 
 # Provide some information about the compiler.
-echo "$as_me:1443:" \
+echo "$as_me:1450:" \
      "checking for C++ compiler version" >&5
 ac_compiler=`set X $ac_compile; echo $2`
-{ (eval echo "$as_me:1446: \"$ac_compiler --version </dev/null >&5\"") >&5
+{ (eval echo "$as_me:1453: \"$ac_compiler --version </dev/null >&5\"") >&5
   (eval $ac_compiler --version </dev/null >&5) 2>&5
   ac_status=$?
-  echo "$as_me:1449: \$? = $ac_status" >&5
+  echo "$as_me:1456: \$? = $ac_status" >&5
   (exit $ac_status); }
-{ (eval echo "$as_me:1451: \"$ac_compiler -v </dev/null >&5\"") >&5
+{ (eval echo "$as_me:1458: \"$ac_compiler -v </dev/null >&5\"") >&5
   (eval $ac_compiler -v </dev/null >&5) 2>&5
   ac_status=$?
-  echo "$as_me:1454: \$? = $ac_status" >&5
+  echo "$as_me:1461: \$? = $ac_status" >&5
   (exit $ac_status); }
-{ (eval echo "$as_me:1456: \"$ac_compiler -V </dev/null >&5\"") >&5
+{ (eval echo "$as_me:1463: \"$ac_compiler -V </dev/null >&5\"") >&5
   (eval $ac_compiler -V </dev/null >&5) 2>&5
   ac_status=$?
-  echo "$as_me:1459: \$? = $ac_status" >&5
+  echo "$as_me:1466: \$? = $ac_status" >&5
   (exit $ac_status); }
 
 cat >conftest.$ac_ext <<_ACEOF
-#line 1463 "configure"
+#line 1470 "configure"
 #include "confdefs.h"
 
 int
@@ -1476,13 +1483,13 @@ ac_clean_files="$ac_clean_files a.out a.exe"
 # Try to create an executable without -o first, disregard a.out.
 # It will help us diagnose broken compilers, and finding out an intuition
 # of exeext.
-echo "$as_me:1479: checking for C++ compiler default output" >&5
+echo "$as_me:1486: checking for C++ compiler default output" >&5
 echo $ECHO_N "checking for C++ compiler default output... $ECHO_C" >&6
 ac_link_default=`echo "$ac_link" | sed 's/ -o *conftest[^ ]*//'`
-if { (eval echo "$as_me:1482: \"$ac_link_default\"") >&5
+if { (eval echo "$as_me:1489: \"$ac_link_default\"") >&5
   (eval $ac_link_default) 2>&5
   ac_status=$?
-  echo "$as_me:1485: \$? = $ac_status" >&5
+  echo "$as_me:1492: \$? = $ac_status" >&5
   (exit $ac_status); }; then
   # Find the output, starting from the most likely.  This scheme is
 # not robust to junk in `.', hence go to wildcards (a.*) only as a last
@@ -1505,34 +1512,34 @@ done
 else
   echo "$as_me: failed program was:" >&5
 cat conftest.$ac_ext >&5
-{ { echo "$as_me:1508: error: C++ compiler cannot create executables" >&5
+{ { echo "$as_me:1515: error: C++ compiler cannot create executables" >&5
 echo "$as_me: error: C++ compiler cannot create executables" >&2;}
    { (exit 77); exit 77; }; }
 fi
 
 ac_exeext=$ac_cv_exeext
-echo "$as_me:1514: result: $ac_file" >&5
+echo "$as_me:1521: result: $ac_file" >&5
 echo "${ECHO_T}$ac_file" >&6
 
 # Check the compiler produces executables we can run.  If not, either
 # the compiler is broken, or we cross compile.
-echo "$as_me:1519: checking whether the C++ compiler works" >&5
+echo "$as_me:1526: checking whether the C++ compiler works" >&5
 echo $ECHO_N "checking whether the C++ compiler works... $ECHO_C" >&6
 # FIXME: These cross compiler hacks should be removed for Autoconf 3.0
 # If not cross compiling, check that we can run a simple program.
 if test "$cross_compiling" != yes; then
   if { ac_try='./$ac_file'
-  { (eval echo "$as_me:1525: \"$ac_try\"") >&5
+  { (eval echo "$as_me:1532: \"$ac_try\"") >&5
   (eval $ac_try) 2>&5
   ac_status=$?
-  echo "$as_me:1528: \$? = $ac_status" >&5
+  echo "$as_me:1535: \$? = $ac_status" >&5
   (exit $ac_status); }; }; then
     cross_compiling=no
   else
     if test "$cross_compiling" = maybe; then
 	cross_compiling=yes
     else
-	{ { echo "$as_me:1535: error: cannot run C++ compiled programs.
+	{ { echo "$as_me:1542: error: cannot run C++ compiled programs.
 If you meant to cross compile, use \`--host'." >&5
 echo "$as_me: error: cannot run C++ compiled programs.
 If you meant to cross compile, use \`--host'." >&2;}
@@ -1540,24 +1547,24 @@ If you meant to cross compile, use \`--host'." >&2;}
     fi
   fi
 fi
-echo "$as_me:1543: result: yes" >&5
+echo "$as_me:1550: result: yes" >&5
 echo "${ECHO_T}yes" >&6
 
 rm -f a.out a.exe conftest$ac_cv_exeext
 ac_clean_files=$ac_clean_files_save
 # Check the compiler produces executables we can run.  If not, either
 # the compiler is broken, or we cross compile.
-echo "$as_me:1550: checking whether we are cross compiling" >&5
+echo "$as_me:1557: checking whether we are cross compiling" >&5
 echo $ECHO_N "checking whether we are cross compiling... $ECHO_C" >&6
-echo "$as_me:1552: result: $cross_compiling" >&5
+echo "$as_me:1559: result: $cross_compiling" >&5
 echo "${ECHO_T}$cross_compiling" >&6
 
-echo "$as_me:1555: checking for executable suffix" >&5
+echo "$as_me:1562: checking for executable suffix" >&5
 echo $ECHO_N "checking for executable suffix... $ECHO_C" >&6
-if { (eval echo "$as_me:1557: \"$ac_link\"") >&5
+if { (eval echo "$as_me:1564: \"$ac_link\"") >&5
   (eval $ac_link) 2>&5
   ac_status=$?
-  echo "$as_me:1560: \$? = $ac_status" >&5
+  echo "$as_me:1567: \$? = $ac_status" >&5
   (exit $ac_status); }; then
   # If both `conftest.exe' and `conftest' are `present' (well, observable)
 # catch `conftest.exe'.  For instance with Cygwin, `ls conftest' will
@@ -1573,25 +1580,25 @@ for ac_file in `(ls conftest.exe; ls conftest; ls conftest.*) 2>/dev/null`; do
   esac
 done
 else
-  { { echo "$as_me:1576: error: cannot compute EXEEXT: cannot compile and link" >&5
+  { { echo "$as_me:1583: error: cannot compute EXEEXT: cannot compile and link" >&5
 echo "$as_me: error: cannot compute EXEEXT: cannot compile and link" >&2;}
    { (exit 1); exit 1; }; }
 fi
 
 rm -f conftest$ac_cv_exeext
-echo "$as_me:1582: result: $ac_cv_exeext" >&5
+echo "$as_me:1589: result: $ac_cv_exeext" >&5
 echo "${ECHO_T}$ac_cv_exeext" >&6
 
 rm -f conftest.$ac_ext
 EXEEXT=$ac_cv_exeext
 ac_exeext=$EXEEXT
-echo "$as_me:1588: checking for object suffix" >&5
+echo "$as_me:1595: checking for object suffix" >&5
 echo $ECHO_N "checking for object suffix... $ECHO_C" >&6
 if test "${ac_cv_objext+set}" = set; then
   echo $ECHO_N "(cached) $ECHO_C" >&6
 else
   cat >conftest.$ac_ext <<_ACEOF
-#line 1594 "configure"
+#line 1601 "configure"
 #include "confdefs.h"
 
 int
@@ -1603,10 +1610,10 @@ main ()
 }
 _ACEOF
 rm -f conftest.o conftest.obj
-if { (eval echo "$as_me:1606: \"$ac_compile\"") >&5
+if { (eval echo "$as_me:1613: \"$ac_compile\"") >&5
   (eval $ac_compile) 2>&5
   ac_status=$?
-  echo "$as_me:1609: \$? = $ac_status" >&5
+  echo "$as_me:1616: \$? = $ac_status" >&5
   (exit $ac_status); }; then
   for ac_file in `(ls conftest.o conftest.obj; ls conftest.*) 2>/dev/null`; do
   case $ac_file in
@@ -1618,24 +1625,24 @@ done
 else
   echo "$as_me: failed program was:" >&5
 cat conftest.$ac_ext >&5
-{ { echo "$as_me:1621: error: cannot compute OBJEXT: cannot compile" >&5
+{ { echo "$as_me:1628: error: cannot compute OBJEXT: cannot compile" >&5
 echo "$as_me: error: cannot compute OBJEXT: cannot compile" >&2;}
    { (exit 1); exit 1; }; }
 fi
 
 rm -f conftest.$ac_cv_objext conftest.$ac_ext
 fi
-echo "$as_me:1628: result: $ac_cv_objext" >&5
+echo "$as_me:1635: result: $ac_cv_objext" >&5
 echo "${ECHO_T}$ac_cv_objext" >&6
 OBJEXT=$ac_cv_objext
 ac_objext=$OBJEXT
-echo "$as_me:1632: checking whether we are using the GNU C++ compiler" >&5
+echo "$as_me:1639: checking whether we are using the GNU C++ compiler" >&5
 echo $ECHO_N "checking whether we are using the GNU C++ compiler... $ECHO_C" >&6
 if test "${ac_cv_cxx_compiler_gnu+set}" = set; then
   echo $ECHO_N "(cached) $ECHO_C" >&6
 else
   cat >conftest.$ac_ext <<_ACEOF
-#line 1638 "configure"
+#line 1645 "configure"
 #include "confdefs.h"
 
 int
@@ -1650,16 +1657,16 @@ main ()
 }
 _ACEOF
 rm -f conftest.$ac_objext
-if { (eval echo "$as_me:1653: \"$ac_compile\"") >&5
+if { (eval echo "$as_me:1660: \"$ac_compile\"") >&5
   (eval $ac_compile) 2>&5
   ac_status=$?
-  echo "$as_me:1656: \$? = $ac_status" >&5
+  echo "$as_me:1663: \$? = $ac_status" >&5
   (exit $ac_status); } &&
          { ac_try='test -s conftest.$ac_objext'
-  { (eval echo "$as_me:1659: \"$ac_try\"") >&5
+  { (eval echo "$as_me:1666: \"$ac_try\"") >&5
   (eval $ac_try) 2>&5
   ac_status=$?
-  echo "$as_me:1662: \$? = $ac_status" >&5
+  echo "$as_me:1669: \$? = $ac_status" >&5
   (exit $ac_status); }; }; then
   ac_compiler_gnu=yes
 else
@@ -1671,19 +1678,19 @@ rm -f conftest.$ac_objext conftest.$ac_ext
 ac_cv_cxx_compiler_gnu=$ac_compiler_gnu
 
 fi
-echo "$as_me:1674: result: $ac_cv_cxx_compiler_gnu" >&5
+echo "$as_me:1681: result: $ac_cv_cxx_compiler_gnu" >&5
 echo "${ECHO_T}$ac_cv_cxx_compiler_gnu" >&6
 GXX=`test $ac_compiler_gnu = yes && echo yes`
 ac_test_CXXFLAGS=${CXXFLAGS+set}
 ac_save_CXXFLAGS=$CXXFLAGS
 CXXFLAGS="-g"
-echo "$as_me:1680: checking whether $CXX accepts -g" >&5
+echo "$as_me:1687: checking whether $CXX accepts -g" >&5
 echo $ECHO_N "checking whether $CXX accepts -g... $ECHO_C" >&6
 if test "${ac_cv_prog_cxx_g+set}" = set; then
   echo $ECHO_N "(cached) $ECHO_C" >&6
 else
   cat >conftest.$ac_ext <<_ACEOF
-#line 1686 "configure"
+#line 1693 "configure"
 #include "confdefs.h"
 
 int
@@ -1695,16 +1702,16 @@ main ()
 }
 _ACEOF
 rm -f conftest.$ac_objext
-if { (eval echo "$as_me:1698: \"$ac_compile\"") >&5
+if { (eval echo "$as_me:1705: \"$ac_compile\"") >&5
   (eval $ac_compile) 2>&5
   ac_status=$?
-  echo "$as_me:1701: \$? = $ac_status" >&5
+  echo "$as_me:1708: \$? = $ac_status" >&5
   (exit $ac_status); } &&
          { ac_try='test -s conftest.$ac_objext'
-  { (eval echo "$as_me:1704: \"$ac_try\"") >&5
+  { (eval echo "$as_me:1711: \"$ac_try\"") >&5
   (eval $ac_try) 2>&5
   ac_status=$?
-  echo "$as_me:1707: \$? = $ac_status" >&5
+  echo "$as_me:1714: \$? = $ac_status" >&5
   (exit $ac_status); }; }; then
   ac_cv_prog_cxx_g=yes
 else
@@ -1714,7 +1721,7 @@ ac_cv_prog_cxx_g=no
 fi
 rm -f conftest.$ac_objext conftest.$ac_ext
 fi
-echo "$as_me:1717: result: $ac_cv_prog_cxx_g" >&5
+echo "$as_me:1724: result: $ac_cv_prog_cxx_g" >&5
 echo "${ECHO_T}$ac_cv_prog_cxx_g" >&6
 if test "$ac_test_CXXFLAGS" = set; then
   CXXFLAGS=$ac_save_CXXFLAGS
@@ -1741,7 +1748,7 @@ for ac_declaration in \
    'void exit (int);'
 do
   cat >conftest.$ac_ext <<_ACEOF
-#line 1744 "configure"
+#line 1751 "configure"
 #include "confdefs.h"
 #include <stdlib.h>
 $ac_declaration
@@ -1754,16 +1761,16 @@ exit (42);
 }
 _ACEOF
 rm -f conftest.$ac_objext
-if { (eval echo "$as_me:1757: \"$ac_compile\"") >&5
+if { (eval echo "$as_me:1764: \"$ac_compile\"") >&5
   (eval $ac_compile) 2>&5
   ac_status=$?
-  echo "$as_me:1760: \$? = $ac_status" >&5
+  echo "$as_me:1767: \$? = $ac_status" >&5
   (exit $ac_status); } &&
          { ac_try='test -s conftest.$ac_objext'
-  { (eval echo "$as_me:1763: \"$ac_try\"") >&5
+  { (eval echo "$as_me:1770: \"$ac_try\"") >&5
   (eval $ac_try) 2>&5
   ac_status=$?
-  echo "$as_me:1766: \$? = $ac_status" >&5
+  echo "$as_me:1773: \$? = $ac_status" >&5
   (exit $ac_status); }; }; then
   :
 else
@@ -1773,7 +1780,7 @@ continue
 fi
 rm -f conftest.$ac_objext conftest.$ac_ext
   cat >conftest.$ac_ext <<_ACEOF
-#line 1776 "configure"
+#line 1783 "configure"
 #include "confdefs.h"
 $ac_declaration
 int
@@ -1785,16 +1792,16 @@ exit (42);
 }
 _ACEOF
 rm -f conftest.$ac_objext
-if { (eval echo "$as_me:1788: \"$ac_compile\"") >&5
+if { (eval echo "$as_me:1795: \"$ac_compile\"") >&5
   (eval $ac_compile) 2>&5
   ac_status=$?
-  echo "$as_me:1791: \$? = $ac_status" >&5
+  echo "$as_me:1798: \$? = $ac_status" >&5
   (exit $ac_status); } &&
          { ac_try='test -s conftest.$ac_objext'
-  { (eval echo "$as_me:1794: \"$ac_try\"") >&5
+  { (eval echo "$as_me:1801: \"$ac_try\"") >&5
   (eval $ac_try) 2>&5
   ac_status=$?
-  echo "$as_me:1797: \$? = $ac_status" >&5
+  echo "$as_me:1804: \$? = $ac_status" >&5
   (exit $ac_status); }; }; then
   break
 else
@@ -1824,7 +1831,7 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu
 if test -n "$ac_tool_prefix"; then
   # Extract the first word of "${ac_tool_prefix}gcc", so it can be a program name with args.
 set dummy ${ac_tool_prefix}gcc; ac_word=$2
-echo "$as_me:1827: checking for $ac_word" >&5
+echo "$as_me:1834: checking for $ac_word" >&5
 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
 if test "${ac_cv_prog_CC+set}" = set; then
   echo $ECHO_N "(cached) $ECHO_C" >&6
@@ -1839,7 +1846,7 @@ for ac_dir in $ac_dummy; do
   test -z "$ac_dir" && ac_dir=.
   $as_executable_p "$ac_dir/$ac_word" || continue
 ac_cv_prog_CC="${ac_tool_prefix}gcc"
-echo "$as_me:1842: found $ac_dir/$ac_word" >&5
+echo "$as_me:1849: found $ac_dir/$ac_word" >&5
 break
 done
 
@@ -1847,10 +1854,10 @@ fi
 fi
 CC=$ac_cv_prog_CC
 if test -n "$CC"; then
-  echo "$as_me:1850: result: $CC" >&5
+  echo "$as_me:1857: result: $CC" >&5
 echo "${ECHO_T}$CC" >&6
 else
-  echo "$as_me:1853: result: no" >&5
+  echo "$as_me:1860: result: no" >&5
 echo "${ECHO_T}no" >&6
 fi
 
@@ -1859,7 +1866,7 @@ if test -z "$ac_cv_prog_CC"; then
   ac_ct_CC=$CC
   # Extract the first word of "gcc", so it can be a program name with args.
 set dummy gcc; ac_word=$2
-echo "$as_me:1862: checking for $ac_word" >&5
+echo "$as_me:1869: checking for $ac_word" >&5
 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
 if test "${ac_cv_prog_ac_ct_CC+set}" = set; then
   echo $ECHO_N "(cached) $ECHO_C" >&6
@@ -1874,7 +1881,7 @@ for ac_dir in $ac_dummy; do
   test -z "$ac_dir" && ac_dir=.
   $as_executable_p "$ac_dir/$ac_word" || continue
 ac_cv_prog_ac_ct_CC="gcc"
-echo "$as_me:1877: found $ac_dir/$ac_word" >&5
+echo "$as_me:1884: found $ac_dir/$ac_word" >&5
 break
 done
 
@@ -1882,10 +1889,10 @@ fi
 fi
 ac_ct_CC=$ac_cv_prog_ac_ct_CC
 if test -n "$ac_ct_CC"; then
-  echo "$as_me:1885: result: $ac_ct_CC" >&5
+  echo "$as_me:1892: result: $ac_ct_CC" >&5
 echo "${ECHO_T}$ac_ct_CC" >&6
 else
-  echo "$as_me:1888: result: no" >&5
+  echo "$as_me:1895: result: no" >&5
 echo "${ECHO_T}no" >&6
 fi
 
@@ -1898,7 +1905,7 @@ if test -z "$CC"; then
   if test -n "$ac_tool_prefix"; then
   # Extract the first word of "${ac_tool_prefix}cc", so it can be a program name with args.
 set dummy ${ac_tool_prefix}cc; ac_word=$2
-echo "$as_me:1901: checking for $ac_word" >&5
+echo "$as_me:1908: checking for $ac_word" >&5
 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
 if test "${ac_cv_prog_CC+set}" = set; then
   echo $ECHO_N "(cached) $ECHO_C" >&6
@@ -1913,7 +1920,7 @@ for ac_dir in $ac_dummy; do
   test -z "$ac_dir" && ac_dir=.
   $as_executable_p "$ac_dir/$ac_word" || continue
 ac_cv_prog_CC="${ac_tool_prefix}cc"
-echo "$as_me:1916: found $ac_dir/$ac_word" >&5
+echo "$as_me:1923: found $ac_dir/$ac_word" >&5
 break
 done
 
@@ -1921,10 +1928,10 @@ fi
 fi
 CC=$ac_cv_prog_CC
 if test -n "$CC"; then
-  echo "$as_me:1924: result: $CC" >&5
+  echo "$as_me:1931: result: $CC" >&5
 echo "${ECHO_T}$CC" >&6
 else
-  echo "$as_me:1927: result: no" >&5
+  echo "$as_me:1934: result: no" >&5
 echo "${ECHO_T}no" >&6
 fi
 
@@ -1933,7 +1940,7 @@ if test -z "$ac_cv_prog_CC"; then
   ac_ct_CC=$CC
   # Extract the first word of "cc", so it can be a program name with args.
 set dummy cc; ac_word=$2
-echo "$as_me:1936: checking for $ac_word" >&5
+echo "$as_me:1943: checking for $ac_word" >&5
 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
 if test "${ac_cv_prog_ac_ct_CC+set}" = set; then
   echo $ECHO_N "(cached) $ECHO_C" >&6
@@ -1948,7 +1955,7 @@ for ac_dir in $ac_dummy; do
   test -z "$ac_dir" && ac_dir=.
   $as_executable_p "$ac_dir/$ac_word" || continue
 ac_cv_prog_ac_ct_CC="cc"
-echo "$as_me:1951: found $ac_dir/$ac_word" >&5
+echo "$as_me:1958: found $ac_dir/$ac_word" >&5
 break
 done
 
@@ -1956,10 +1963,10 @@ fi
 fi
 ac_ct_CC=$ac_cv_prog_ac_ct_CC
 if test -n "$ac_ct_CC"; then
-  echo "$as_me:1959: result: $ac_ct_CC" >&5
+  echo "$as_me:1966: result: $ac_ct_CC" >&5
 echo "${ECHO_T}$ac_ct_CC" >&6
 else
-  echo "$as_me:1962: result: no" >&5
+  echo "$as_me:1969: result: no" >&5
 echo "${ECHO_T}no" >&6
 fi
 
@@ -1972,7 +1979,7 @@ fi
 if test -z "$CC"; then
   # Extract the first word of "cc", so it can be a program name with args.
 set dummy cc; ac_word=$2
-echo "$as_me:1975: checking for $ac_word" >&5
+echo "$as_me:1982: checking for $ac_word" >&5
 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
 if test "${ac_cv_prog_CC+set}" = set; then
   echo $ECHO_N "(cached) $ECHO_C" >&6
@@ -1992,7 +1999,7 @@ if test "$ac_dir/$ac_word" = "/usr/ucb/cc"; then
   continue
 fi
 ac_cv_prog_CC="cc"
-echo "$as_me:1995: found $ac_dir/$ac_word" >&5
+echo "$as_me:2002: found $ac_dir/$ac_word" >&5
 break
 done
 
@@ -2014,10 +2021,10 @@ fi
 fi
 CC=$ac_cv_prog_CC
 if test -n "$CC"; then
-  echo "$as_me:2017: result: $CC" >&5
+  echo "$as_me:2024: result: $CC" >&5
 echo "${ECHO_T}$CC" >&6
 else
-  echo "$as_me:2020: result: no" >&5
+  echo "$as_me:2027: result: no" >&5
 echo "${ECHO_T}no" >&6
 fi
 
@@ -2028,7 +2035,7 @@ if test -z "$CC"; then
   do
     # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
 set dummy $ac_tool_prefix$ac_prog; ac_word=$2
-echo "$as_me:2031: checking for $ac_word" >&5
+echo "$as_me:2038: checking for $ac_word" >&5
 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
 if test "${ac_cv_prog_CC+set}" = set; then
   echo $ECHO_N "(cached) $ECHO_C" >&6
@@ -2043,7 +2050,7 @@ for ac_dir in $ac_dummy; do
   test -z "$ac_dir" && ac_dir=.
   $as_executable_p "$ac_dir/$ac_word" || continue
 ac_cv_prog_CC="$ac_tool_prefix$ac_prog"
-echo "$as_me:2046: found $ac_dir/$ac_word" >&5
+echo "$as_me:2053: found $ac_dir/$ac_word" >&5
 break
 done
 
@@ -2051,10 +2058,10 @@ fi
 fi
 CC=$ac_cv_prog_CC
 if test -n "$CC"; then
-  echo "$as_me:2054: result: $CC" >&5
+  echo "$as_me:2061: result: $CC" >&5
 echo "${ECHO_T}$CC" >&6
 else
-  echo "$as_me:2057: result: no" >&5
+  echo "$as_me:2064: result: no" >&5
 echo "${ECHO_T}no" >&6
 fi
 
@@ -2067,7 +2074,7 @@ if test -z "$CC"; then
 do
   # Extract the first word of "$ac_prog", so it can be a program name with args.
 set dummy $ac_prog; ac_word=$2
-echo "$as_me:2070: checking for $ac_word" >&5
+echo "$as_me:2077: checking for $ac_word" >&5
 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
 if test "${ac_cv_prog_ac_ct_CC+set}" = set; then
   echo $ECHO_N "(cached) $ECHO_C" >&6
@@ -2082,7 +2089,7 @@ for ac_dir in $ac_dummy; do
   test -z "$ac_dir" && ac_dir=.
   $as_executable_p "$ac_dir/$ac_word" || continue
 ac_cv_prog_ac_ct_CC="$ac_prog"
-echo "$as_me:2085: found $ac_dir/$ac_word" >&5
+echo "$as_me:2092: found $ac_dir/$ac_word" >&5
 break
 done
 
@@ -2090,10 +2097,10 @@ fi
 fi
 ac_ct_CC=$ac_cv_prog_ac_ct_CC
 if test -n "$ac_ct_CC"; then
-  echo "$as_me:2093: result: $ac_ct_CC" >&5
+  echo "$as_me:2100: result: $ac_ct_CC" >&5
 echo "${ECHO_T}$ac_ct_CC" >&6
 else
-  echo "$as_me:2096: result: no" >&5
+  echo "$as_me:2103: result: no" >&5
 echo "${ECHO_T}no" >&6
 fi
 
@@ -2105,37 +2112,37 @@ fi
 
 fi
 
-test -z "$CC" && { { echo "$as_me:2108: error: no acceptable cc found in \$PATH" >&5
+test -z "$CC" && { { echo "$as_me:2115: error: no acceptable cc found in \$PATH" >&5
 echo "$as_me: error: no acceptable cc found in \$PATH" >&2;}
    { (exit 1); exit 1; }; }
 
 # Provide some information about the compiler.
-echo "$as_me:2113:" \
+echo "$as_me:2120:" \
      "checking for C compiler version" >&5
 ac_compiler=`set X $ac_compile; echo $2`
-{ (eval echo "$as_me:2116: \"$ac_compiler --version </dev/null >&5\"") >&5
+{ (eval echo "$as_me:2123: \"$ac_compiler --version </dev/null >&5\"") >&5
   (eval $ac_compiler --version </dev/null >&5) 2>&5
   ac_status=$?
-  echo "$as_me:2119: \$? = $ac_status" >&5
+  echo "$as_me:2126: \$? = $ac_status" >&5
   (exit $ac_status); }
-{ (eval echo "$as_me:2121: \"$ac_compiler -v </dev/null >&5\"") >&5
+{ (eval echo "$as_me:2128: \"$ac_compiler -v </dev/null >&5\"") >&5
   (eval $ac_compiler -v </dev/null >&5) 2>&5
   ac_status=$?
-  echo "$as_me:2124: \$? = $ac_status" >&5
+  echo "$as_me:2131: \$? = $ac_status" >&5
   (exit $ac_status); }
-{ (eval echo "$as_me:2126: \"$ac_compiler -V </dev/null >&5\"") >&5
+{ (eval echo "$as_me:2133: \"$ac_compiler -V </dev/null >&5\"") >&5
   (eval $ac_compiler -V </dev/null >&5) 2>&5
   ac_status=$?
-  echo "$as_me:2129: \$? = $ac_status" >&5
+  echo "$as_me:2136: \$? = $ac_status" >&5
   (exit $ac_status); }
 
-echo "$as_me:2132: checking whether we are using the GNU C compiler" >&5
+echo "$as_me:2139: checking whether we are using the GNU C compiler" >&5
 echo $ECHO_N "checking whether we are using the GNU C compiler... $ECHO_C" >&6
 if test "${ac_cv_c_compiler_gnu+set}" = set; then
   echo $ECHO_N "(cached) $ECHO_C" >&6
 else
   cat >conftest.$ac_ext <<_ACEOF
-#line 2138 "configure"
+#line 2145 "configure"
 #include "confdefs.h"
 
 int
@@ -2150,16 +2157,16 @@ main ()
 }
 _ACEOF
 rm -f conftest.$ac_objext
-if { (eval echo "$as_me:2153: \"$ac_compile\"") >&5
+if { (eval echo "$as_me:2160: \"$ac_compile\"") >&5
   (eval $ac_compile) 2>&5
   ac_status=$?
-  echo "$as_me:2156: \$? = $ac_status" >&5
+  echo "$as_me:2163: \$? = $ac_status" >&5
   (exit $ac_status); } &&
          { ac_try='test -s conftest.$ac_objext'
-  { (eval echo "$as_me:2159: \"$ac_try\"") >&5
+  { (eval echo "$as_me:2166: \"$ac_try\"") >&5
   (eval $ac_try) 2>&5
   ac_status=$?
-  echo "$as_me:2162: \$? = $ac_status" >&5
+  echo "$as_me:2169: \$? = $ac_status" >&5
   (exit $ac_status); }; }; then
   ac_compiler_gnu=yes
 else
@@ -2171,19 +2178,19 @@ rm -f conftest.$ac_objext conftest.$ac_ext
 ac_cv_c_compiler_gnu=$ac_compiler_gnu
 
 fi
-echo "$as_me:2174: result: $ac_cv_c_compiler_gnu" >&5
+echo "$as_me:2181: result: $ac_cv_c_compiler_gnu" >&5
 echo "${ECHO_T}$ac_cv_c_compiler_gnu" >&6
 GCC=`test $ac_compiler_gnu = yes && echo yes`
 ac_test_CFLAGS=${CFLAGS+set}
 ac_save_CFLAGS=$CFLAGS
 CFLAGS="-g"
-echo "$as_me:2180: checking whether $CC accepts -g" >&5
+echo "$as_me:2187: checking whether $CC accepts -g" >&5
 echo $ECHO_N "checking whether $CC accepts -g... $ECHO_C" >&6
 if test "${ac_cv_prog_cc_g+set}" = set; then
   echo $ECHO_N "(cached) $ECHO_C" >&6
 else
   cat >conftest.$ac_ext <<_ACEOF
-#line 2186 "configure"
+#line 2193 "configure"
 #include "confdefs.h"
 
 int
@@ -2195,16 +2202,16 @@ main ()
 }
 _ACEOF
 rm -f conftest.$ac_objext
-if { (eval echo "$as_me:2198: \"$ac_compile\"") >&5
+if { (eval echo "$as_me:2205: \"$ac_compile\"") >&5
   (eval $ac_compile) 2>&5
   ac_status=$?
-  echo "$as_me:2201: \$? = $ac_status" >&5
+  echo "$as_me:2208: \$? = $ac_status" >&5
   (exit $ac_status); } &&
          { ac_try='test -s conftest.$ac_objext'
-  { (eval echo "$as_me:2204: \"$ac_try\"") >&5
+  { (eval echo "$as_me:2211: \"$ac_try\"") >&5
   (eval $ac_try) 2>&5
   ac_status=$?
-  echo "$as_me:2207: \$? = $ac_status" >&5
+  echo "$as_me:2214: \$? = $ac_status" >&5
   (exit $ac_status); }; }; then
   ac_cv_prog_cc_g=yes
 else
@@ -2214,7 +2221,7 @@ ac_cv_prog_cc_g=no
 fi
 rm -f conftest.$ac_objext conftest.$ac_ext
 fi
-echo "$as_me:2217: result: $ac_cv_prog_cc_g" >&5
+echo "$as_me:2224: result: $ac_cv_prog_cc_g" >&5
 echo "${ECHO_T}$ac_cv_prog_cc_g" >&6
 if test "$ac_test_CFLAGS" = set; then
   CFLAGS=$ac_save_CFLAGS
@@ -2241,16 +2248,16 @@ cat >conftest.$ac_ext <<_ACEOF
 #endif
 _ACEOF
 rm -f conftest.$ac_objext
-if { (eval echo "$as_me:2244: \"$ac_compile\"") >&5
+if { (eval echo "$as_me:2251: \"$ac_compile\"") >&5
   (eval $ac_compile) 2>&5
   ac_status=$?
-  echo "$as_me:2247: \$? = $ac_status" >&5
+  echo "$as_me:2254: \$? = $ac_status" >&5
   (exit $ac_status); } &&
          { ac_try='test -s conftest.$ac_objext'
-  { (eval echo "$as_me:2250: \"$ac_try\"") >&5
+  { (eval echo "$as_me:2257: \"$ac_try\"") >&5
   (eval $ac_try) 2>&5
   ac_status=$?
-  echo "$as_me:2253: \$? = $ac_status" >&5
+  echo "$as_me:2260: \$? = $ac_status" >&5
   (exit $ac_status); }; }; then
   for ac_declaration in \
    ''\
@@ -2262,7 +2269,7 @@ if { (eval echo "$as_me:2244: \"$ac_compile\"") >&5
    'void exit (int);'
 do
   cat >conftest.$ac_ext <<_ACEOF
-#line 2265 "configure"
+#line 2272 "configure"
 #include "confdefs.h"
 #include <stdlib.h>
 $ac_declaration
@@ -2275,16 +2282,16 @@ exit (42);
 }
 _ACEOF
 rm -f conftest.$ac_objext
-if { (eval echo "$as_me:2278: \"$ac_compile\"") >&5
+if { (eval echo "$as_me:2285: \"$ac_compile\"") >&5
   (eval $ac_compile) 2>&5
   ac_status=$?
-  echo "$as_me:2281: \$? = $ac_status" >&5
+  echo "$as_me:2288: \$? = $ac_status" >&5
   (exit $ac_status); } &&
          { ac_try='test -s conftest.$ac_objext'
-  { (eval echo "$as_me:2284: \"$ac_try\"") >&5
+  { (eval echo "$as_me:2291: \"$ac_try\"") >&5
   (eval $ac_try) 2>&5
   ac_status=$?
-  echo "$as_me:2287: \$? = $ac_status" >&5
+  echo "$as_me:2294: \$? = $ac_status" >&5
   (exit $ac_status); }; }; then
   :
 else
@@ -2294,7 +2301,7 @@ continue
 fi
 rm -f conftest.$ac_objext conftest.$ac_ext
   cat >conftest.$ac_ext <<_ACEOF
-#line 2297 "configure"
+#line 2304 "configure"
 #include "confdefs.h"
 $ac_declaration
 int
@@ -2306,16 +2313,16 @@ exit (42);
 }
 _ACEOF
 rm -f conftest.$ac_objext
-if { (eval echo "$as_me:2309: \"$ac_compile\"") >&5
+if { (eval echo "$as_me:2316: \"$ac_compile\"") >&5
   (eval $ac_compile) 2>&5
   ac_status=$?
-  echo "$as_me:2312: \$? = $ac_status" >&5
+  echo "$as_me:2319: \$? = $ac_status" >&5
   (exit $ac_status); } &&
          { ac_try='test -s conftest.$ac_objext'
-  { (eval echo "$as_me:2315: \"$ac_try\"") >&5
+  { (eval echo "$as_me:2322: \"$ac_try\"") >&5
   (eval $ac_try) 2>&5
   ac_status=$?
-  echo "$as_me:2318: \$? = $ac_status" >&5
+  echo "$as_me:2325: \$? = $ac_status" >&5
   (exit $ac_status); }; }; then
   break
 else
@@ -2354,7 +2361,7 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu
 # AFS /usr/afsws/bin/install, which mishandles nonexistent args
 # SVR4 /usr/ucb/install, which tries to use the nonexistent group "staff"
 # ./install, which can be erroneously created by make from ./install.sh.
-echo "$as_me:2357: checking for a BSD compatible install" >&5
+echo "$as_me:2364: checking for a BSD compatible install" >&5
 echo $ECHO_N "checking for a BSD compatible install... $ECHO_C" >&6
 if test -z "$INSTALL"; then
 if test "${ac_cv_path_install+set}" = set; then
@@ -2403,7 +2410,7 @@ fi
     INSTALL=$ac_install_sh
   fi
 fi
-echo "$as_me:2406: result: $INSTALL" >&5
+echo "$as_me:2413: result: $INSTALL" >&5
 echo "${ECHO_T}$INSTALL" >&6
 
 # Use test -z because SunOS4 sh mishandles braces in ${var-val}.
@@ -2427,7 +2434,7 @@ if test -n "$ac_tool_prefix"; then
   do
     # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
 set dummy $ac_tool_prefix$ac_prog; ac_word=$2
-echo "$as_me:2430: checking for $ac_word" >&5
+echo "$as_me:2437: checking for $ac_word" >&5
 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
 if test "${ac_cv_prog_F77+set}" = set; then
   echo $ECHO_N "(cached) $ECHO_C" >&6
@@ -2442,7 +2449,7 @@ for ac_dir in $ac_dummy; do
   test -z "$ac_dir" && ac_dir=.
   $as_executable_p "$ac_dir/$ac_word" || continue
 ac_cv_prog_F77="$ac_tool_prefix$ac_prog"
-echo "$as_me:2445: found $ac_dir/$ac_word" >&5
+echo "$as_me:2452: found $ac_dir/$ac_word" >&5
 break
 done
 
@@ -2450,10 +2457,10 @@ fi
 fi
 F77=$ac_cv_prog_F77
 if test -n "$F77"; then
-  echo "$as_me:2453: result: $F77" >&5
+  echo "$as_me:2460: result: $F77" >&5
 echo "${ECHO_T}$F77" >&6
 else
-  echo "$as_me:2456: result: no" >&5
+  echo "$as_me:2463: result: no" >&5
 echo "${ECHO_T}no" >&6
 fi
 
@@ -2466,7 +2473,7 @@ if test -z "$F77"; then
 do
   # Extract the first word of "$ac_prog", so it can be a program name with args.
 set dummy $ac_prog; ac_word=$2
-echo "$as_me:2469: checking for $ac_word" >&5
+echo "$as_me:2476: checking for $ac_word" >&5
 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
 if test "${ac_cv_prog_ac_ct_F77+set}" = set; then
   echo $ECHO_N "(cached) $ECHO_C" >&6
@@ -2481,7 +2488,7 @@ for ac_dir in $ac_dummy; do
   test -z "$ac_dir" && ac_dir=.
   $as_executable_p "$ac_dir/$ac_word" || continue
 ac_cv_prog_ac_ct_F77="$ac_prog"
-echo "$as_me:2484: found $ac_dir/$ac_word" >&5
+echo "$as_me:2491: found $ac_dir/$ac_word" >&5
 break
 done
 
@@ -2489,10 +2496,10 @@ fi
 fi
 ac_ct_F77=$ac_cv_prog_ac_ct_F77
 if test -n "$ac_ct_F77"; then
-  echo "$as_me:2492: result: $ac_ct_F77" >&5
+  echo "$as_me:2499: result: $ac_ct_F77" >&5
 echo "${ECHO_T}$ac_ct_F77" >&6
 else
-  echo "$as_me:2495: result: no" >&5
+  echo "$as_me:2502: result: no" >&5
 echo "${ECHO_T}no" >&6
 fi
 
@@ -2503,30 +2510,30 @@ done
 fi
 
 # Provide some information about the compiler.
-echo "$as_me:2506:" \
+echo "$as_me:2513:" \
      "checking for Fortran 77 compiler version" >&5
 ac_compiler=`set X $ac_compile; echo $2`
-{ (eval echo "$as_me:2509: \"$ac_compiler --version </dev/null >&5\"") >&5
+{ (eval echo "$as_me:2516: \"$ac_compiler --version </dev/null >&5\"") >&5
   (eval $ac_compiler --version </dev/null >&5) 2>&5
   ac_status=$?
-  echo "$as_me:2512: \$? = $ac_status" >&5
+  echo "$as_me:2519: \$? = $ac_status" >&5
   (exit $ac_status); }
-{ (eval echo "$as_me:2514: \"$ac_compiler -v </dev/null >&5\"") >&5
+{ (eval echo "$as_me:2521: \"$ac_compiler -v </dev/null >&5\"") >&5
   (eval $ac_compiler -v </dev/null >&5) 2>&5
   ac_status=$?
-  echo "$as_me:2517: \$? = $ac_status" >&5
+  echo "$as_me:2524: \$? = $ac_status" >&5
   (exit $ac_status); }
-{ (eval echo "$as_me:2519: \"$ac_compiler -V </dev/null >&5\"") >&5
+{ (eval echo "$as_me:2526: \"$ac_compiler -V </dev/null >&5\"") >&5
   (eval $ac_compiler -V </dev/null >&5) 2>&5
   ac_status=$?
-  echo "$as_me:2522: \$? = $ac_status" >&5
+  echo "$as_me:2529: \$? = $ac_status" >&5
   (exit $ac_status); }
 
 # If we don't use `.F' as extension, the preprocessor is not run on the
 # input file.
 ac_save_ext=$ac_ext
 ac_ext=F
-echo "$as_me:2529: checking whether we are using the GNU Fortran 77 compiler" >&5
+echo "$as_me:2536: checking whether we are using the GNU Fortran 77 compiler" >&5
 echo $ECHO_N "checking whether we are using the GNU Fortran 77 compiler... $ECHO_C" >&6
 if test "${ac_cv_f77_compiler_gnu+set}" = set; then
   echo $ECHO_N "(cached) $ECHO_C" >&6
@@ -2540,16 +2547,16 @@ else
       end
 _ACEOF
 rm -f conftest.$ac_objext
-if { (eval echo "$as_me:2543: \"$ac_compile\"") >&5
+if { (eval echo "$as_me:2550: \"$ac_compile\"") >&5
   (eval $ac_compile) 2>&5
   ac_status=$?
-  echo "$as_me:2546: \$? = $ac_status" >&5
+  echo "$as_me:2553: \$? = $ac_status" >&5
   (exit $ac_status); } &&
          { ac_try='test -s conftest.$ac_objext'
-  { (eval echo "$as_me:2549: \"$ac_try\"") >&5
+  { (eval echo "$as_me:2556: \"$ac_try\"") >&5
   (eval $ac_try) 2>&5
   ac_status=$?
-  echo "$as_me:2552: \$? = $ac_status" >&5
+  echo "$as_me:2559: \$? = $ac_status" >&5
   (exit $ac_status); }; }; then
   ac_compiler_gnu=yes
 else
@@ -2561,14 +2568,14 @@ rm -f conftest.$ac_objext conftest.$ac_ext
 ac_cv_f77_compiler_gnu=$ac_compiler_gnu
 
 fi
-echo "$as_me:2564: result: $ac_cv_f77_compiler_gnu" >&5
+echo "$as_me:2571: result: $ac_cv_f77_compiler_gnu" >&5
 echo "${ECHO_T}$ac_cv_f77_compiler_gnu" >&6
 ac_ext=$ac_save_ext
 G77=`test $ac_compiler_gnu = yes && echo yes`
 ac_test_FFLAGS=${FFLAGS+set}
 ac_save_FFLAGS=$FFLAGS
 FFLAGS=
-echo "$as_me:2571: checking whether $F77 accepts -g" >&5
+echo "$as_me:2578: checking whether $F77 accepts -g" >&5
 echo $ECHO_N "checking whether $F77 accepts -g... $ECHO_C" >&6
 if test "${ac_cv_prog_f77_g+set}" = set; then
   echo $ECHO_N "(cached) $ECHO_C" >&6
@@ -2580,16 +2587,16 @@ cat >conftest.$ac_ext <<_ACEOF
       end
 _ACEOF
 rm -f conftest.$ac_objext
-if { (eval echo "$as_me:2583: \"$ac_compile\"") >&5
+if { (eval echo "$as_me:2590: \"$ac_compile\"") >&5
   (eval $ac_compile) 2>&5
   ac_status=$?
-  echo "$as_me:2586: \$? = $ac_status" >&5
+  echo "$as_me:2593: \$? = $ac_status" >&5
   (exit $ac_status); } &&
          { ac_try='test -s conftest.$ac_objext'
-  { (eval echo "$as_me:2589: \"$ac_try\"") >&5
+  { (eval echo "$as_me:2596: \"$ac_try\"") >&5
   (eval $ac_try) 2>&5
   ac_status=$?
-  echo "$as_me:2592: \$? = $ac_status" >&5
+  echo "$as_me:2599: \$? = $ac_status" >&5
   (exit $ac_status); }; }; then
   ac_cv_prog_f77_g=yes
 else
@@ -2600,7 +2607,7 @@ fi
 rm -f conftest.$ac_objext conftest.$ac_ext
 
 fi
-echo "$as_me:2603: result: $ac_cv_prog_f77_g" >&5
+echo "$as_me:2610: result: $ac_cv_prog_f77_g" >&5
 echo "${ECHO_T}$ac_cv_prog_f77_g" >&6
 if test "$ac_test_FFLAGS" = set; then
   FFLAGS=$ac_save_FFLAGS
@@ -2638,7 +2645,7 @@ ac_ext=f
 ac_compile='$F77 -c $FFLAGS conftest.$ac_ext >&5'
 ac_link='$F77 -o conftest$ac_exeext $FFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
 ac_compiler_gnu=$ac_cv_f77_compiler_gnu
-echo "$as_me:2641: checking how to get verbose linking output from $F77" >&5
+echo "$as_me:2648: checking how to get verbose linking output from $F77" >&5
 echo $ECHO_N "checking how to get verbose linking output from $F77... $ECHO_C" >&6
 if test "${ac_cv_prog_f77_v+set}" = set; then
   echo $ECHO_N "(cached) $ECHO_C" >&6
@@ -2650,16 +2657,16 @@ cat >conftest.$ac_ext <<_ACEOF
       end
 _ACEOF
 rm -f conftest.$ac_objext
-if { (eval echo "$as_me:2653: \"$ac_compile\"") >&5
+if { (eval echo "$as_me:2660: \"$ac_compile\"") >&5
   (eval $ac_compile) 2>&5
   ac_status=$?
-  echo "$as_me:2656: \$? = $ac_status" >&5
+  echo "$as_me:2663: \$? = $ac_status" >&5
   (exit $ac_status); } &&
          { ac_try='test -s conftest.$ac_objext'
-  { (eval echo "$as_me:2659: \"$ac_try\"") >&5
+  { (eval echo "$as_me:2666: \"$ac_try\"") >&5
   (eval $ac_try) 2>&5
   ac_status=$?
-  echo "$as_me:2662: \$? = $ac_status" >&5
+  echo "$as_me:2669: \$? = $ac_status" >&5
   (exit $ac_status); }; }; then
   ac_cv_prog_f77_v=
 # Try some options frequently used verbose output
@@ -2681,7 +2688,7 @@ _ACEOF
 # flags.
 ac_save_FFLAGS=$FFLAGS
 FFLAGS="$FFLAGS $ac_verb"
-(eval echo $as_me:2684: \"$ac_link\") >&5
+(eval echo $as_me:2691: \"$ac_link\") >&5
 ac_f77_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'`
 echo "$ac_f77_v_output" >&5
 FFLAGS=$ac_save_FFLAGS
@@ -2713,21 +2720,21 @@ fi
   done
 done
 if test -z "$ac_cv_prog_f77_v"; then
-   { echo "$as_me:2716: WARNING: cannot determine how to obtain linking information from $F77" >&5
+   { echo "$as_me:2723: WARNING: cannot determine how to obtain linking information from $F77" >&5
 echo "$as_me: WARNING: cannot determine how to obtain linking information from $F77" >&2;}
 fi
 else
   echo "$as_me: failed program was:" >&5
 cat conftest.$ac_ext >&5
-{ echo "$as_me:2722: WARNING: compilation failed" >&5
+{ echo "$as_me:2729: WARNING: compilation failed" >&5
 echo "$as_me: WARNING: compilation failed" >&2;}
 fi
 rm -f conftest.$ac_objext conftest.$ac_ext
 
 fi
-echo "$as_me:2728: result: $ac_cv_prog_f77_v" >&5
+echo "$as_me:2735: result: $ac_cv_prog_f77_v" >&5
 echo "${ECHO_T}$ac_cv_prog_f77_v" >&6
-echo "$as_me:2730: checking for Fortran 77 libraries" >&5
+echo "$as_me:2737: checking for Fortran 77 libraries" >&5
 echo $ECHO_N "checking for Fortran 77 libraries... $ECHO_C" >&6
 if test "${ac_cv_flibs+set}" = set; then
   echo $ECHO_N "(cached) $ECHO_C" >&6
@@ -2753,7 +2760,7 @@ _ACEOF
 # flags.
 ac_save_FFLAGS=$FFLAGS
 FFLAGS="$FFLAGS $ac_cv_prog_f77_v"
-(eval echo $as_me:2756: \"$ac_link\") >&5
+(eval echo $as_me:2763: \"$ac_link\") >&5
 ac_f77_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'`
 echo "$ac_f77_v_output" >&5
 FFLAGS=$ac_save_FFLAGS
@@ -2908,7 +2915,7 @@ esac
 fi # test "x$FLIBS" = "x"
 
 fi
-echo "$as_me:2911: result: $ac_cv_flibs" >&5
+echo "$as_me:2918: result: $ac_cv_flibs" >&5
 echo "${ECHO_T}$ac_cv_flibs" >&6
 FLIBS="$ac_cv_flibs"
 
@@ -2969,7 +2976,7 @@ fi
 
 # SO is the extension of shared libraries `(including the dot!)
 # -- usually .so, .sl on HP-UX, .dll on Cygwin
-echo "$as_me:2972: checking SO" >&5
+echo "$as_me:2979: checking SO" >&5
 echo $ECHO_N "checking SO... $ECHO_C" >&6
 if test -z "$SO"
 then
@@ -2980,7 +2987,7 @@ then
 	*)	   SO=.so;;
 	esac
 fi
-echo "$as_me:2983: result: $SO" >&5
+echo "$as_me:2990: result: $SO" >&5
 echo "${ECHO_T}$SO" >&6
 
 ac_ext=cc
@@ -2989,7 +2996,7 @@ ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
 ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
 ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
 
-ac_config_files="$ac_config_files ../Cantera/Makefile ../Cantera/src/Makefile ../Cantera/src/zeroD/Makefile ../Cantera/src/oneD/Makefile ../Cantera/src/converters/Makefile ../Cantera/src/transport/Makefile ../Cantera/clib/src/Makefile ../Cantera/fortran/src/Makefile ../Cantera/fortran/f77demos/f77demos.mak ../Cantera/matlab/Makefile ../Cantera/python/Makefile ../Cantera/python/setup.py ../Cantera/cxx/Makefile ../Cantera/python/src/Makefile ../ext/lapack/Makefile ../ext/blas/Makefile ../ext/cvode/Makefile ../ext/math/Makefile ../ext/tpx/Makefile ../ext/Makefile ../ext/recipes/Makefile ../examples/Makefile ../examples/cxx/Makefile ../Makefile ../tools/Makefile ../tools/src/Makefile ../tools/src/sample.mak ../tools/templates/f77/demo.mak ../tools/templates/cxx/demo.mak ../tools/testtools/Makefile ../data/inputs/Makefile ../test_problems/Makefile ../test_problems/cxx_ex/Makefile ../test_problems/silane_equil/Makefile ../test_problems/surfkin/Makefile ../test_problems/diamondSurf/Makefile"
+ac_config_files="$ac_config_files ../Cantera/Makefile ../Cantera/src/Makefile ../Cantera/src/zeroD/Makefile ../Cantera/src/oneD/Makefile ../Cantera/src/converters/Makefile ../Cantera/src/transport/Makefile ../Cantera/clib/src/Makefile ../Cantera/fortran/src/Makefile ../Cantera/fortran/f77demos/f77demos.mak ../Cantera/matlab/Makefile ../Cantera/python/Makefile ../Cantera/python/setup.py ../Cantera/cxx/Makefile ../Cantera/user/Makefile ../Cantera/python/src/Makefile ../ext/lapack/Makefile ../ext/blas/Makefile ../ext/cvode/Makefile ../ext/math/Makefile ../ext/tpx/Makefile ../ext/Makefile ../ext/recipes/Makefile ../examples/Makefile ../examples/cxx/Makefile ../Makefile ../tools/Makefile ../tools/src/Makefile ../tools/src/sample.mak ../tools/templates/f77/demo.mak ../tools/templates/cxx/demo.mak ../tools/testtools/Makefile ../data/inputs/Makefile ../test_problems/Makefile ../test_problems/cxx_ex/Makefile ../test_problems/silane_equil/Makefile ../test_problems/surfkin/Makefile ../test_problems/diamondSurf/Makefile"
 
 test "x$prefix" = xNONE && prefix=$ac_default_prefix
 # Let make expand exec_prefix.
@@ -3015,7 +3022,7 @@ DEFS=-DHAVE_CONFIG_H
 : ${CONFIG_STATUS=./config.status}
 ac_clean_files_save=$ac_clean_files
 ac_clean_files="$ac_clean_files $CONFIG_STATUS"
-{ echo "$as_me:3018: creating $CONFIG_STATUS" >&5
+{ echo "$as_me:3025: creating $CONFIG_STATUS" >&5
 echo "$as_me: creating $CONFIG_STATUS" >&6;}
 cat >$CONFIG_STATUS <<_ACEOF
 #! $SHELL
@@ -3188,7 +3195,7 @@ cat >>$CONFIG_STATUS <<\EOF
     echo "$ac_cs_version"; exit 0 ;;
   --he | --h)
     # Conflict between --help and --header
-    { { echo "$as_me:3191: error: ambiguous option: $1
+    { { echo "$as_me:3198: error: ambiguous option: $1
 Try \`$0 --help' for more information." >&5
 echo "$as_me: error: ambiguous option: $1
 Try \`$0 --help' for more information." >&2;}
@@ -3207,7 +3214,7 @@ Try \`$0 --help' for more information." >&2;}
     ac_need_defaults=false;;
 
   # This is an error.
-  -*) { { echo "$as_me:3210: error: unrecognized option: $1
+  -*) { { echo "$as_me:3217: error: unrecognized option: $1
 Try \`$0 --help' for more information." >&5
 echo "$as_me: error: unrecognized option: $1
 Try \`$0 --help' for more information." >&2;}
@@ -3255,6 +3262,7 @@ do
   "../Cantera/python/Makefile" ) CONFIG_FILES="$CONFIG_FILES ../Cantera/python/Makefile" ;;
   "../Cantera/python/setup.py" ) CONFIG_FILES="$CONFIG_FILES ../Cantera/python/setup.py" ;;
   "../Cantera/cxx/Makefile" ) CONFIG_FILES="$CONFIG_FILES ../Cantera/cxx/Makefile" ;;
+  "../Cantera/user/Makefile" ) CONFIG_FILES="$CONFIG_FILES ../Cantera/user/Makefile" ;;
   "../Cantera/python/src/Makefile" ) CONFIG_FILES="$CONFIG_FILES ../Cantera/python/src/Makefile" ;;
   "../ext/lapack/Makefile" ) CONFIG_FILES="$CONFIG_FILES ../ext/lapack/Makefile" ;;
   "../ext/blas/Makefile" ) CONFIG_FILES="$CONFIG_FILES ../ext/blas/Makefile" ;;
@@ -3279,7 +3287,7 @@ do
   "../test_problems/surfkin/Makefile" ) CONFIG_FILES="$CONFIG_FILES ../test_problems/surfkin/Makefile" ;;
   "../test_problems/diamondSurf/Makefile" ) CONFIG_FILES="$CONFIG_FILES ../test_problems/diamondSurf/Makefile" ;;
   "../config.h" ) CONFIG_HEADERS="$CONFIG_HEADERS ../config.h" ;;
-  *) { { echo "$as_me:3282: error: invalid argument: $ac_config_target" >&5
+  *) { { echo "$as_me:3290: error: invalid argument: $ac_config_target" >&5
 echo "$as_me: error: invalid argument: $ac_config_target" >&2;}
    { (exit 1); exit 1; }; };;
   esac
@@ -3383,6 +3391,8 @@ s,@SHARED@,$SHARED,;t t
 s,@PIC@,$PIC,;t t
 s,@LCXX_FLAGS@,$LCXX_FLAGS,;t t
 s,@LCXX_END_LIBS@,$LCXX_END_LIBS,;t t
+s,@USERDIR@,$USERDIR,;t t
+s,@INCL_USER_CODE@,$INCL_USER_CODE,;t t
 s,@KERNEL@,$KERNEL,;t t
 s,@BUILD_CK@,$BUILD_CK,;t t
 s,@LIB_DIR@,$LIB_DIR,;t t
@@ -3549,7 +3559,7 @@ done; }
   esac
 
   if test x"$ac_file" != x-; then
-    { echo "$as_me:3552: creating $ac_file" >&5
+    { echo "$as_me:3562: creating $ac_file" >&5
 echo "$as_me: creating $ac_file" >&6;}
     rm -f "$ac_file"
   fi
@@ -3567,7 +3577,7 @@ echo "$as_me: creating $ac_file" >&6;}
       -) echo $tmp/stdin ;;
       [\\/$]*)
          # Absolute (can't be DOS-style, as IFS=:)
-         test -f "$f" || { { echo "$as_me:3570: error: cannot find input file: $f" >&5
+         test -f "$f" || { { echo "$as_me:3580: error: cannot find input file: $f" >&5
 echo "$as_me: error: cannot find input file: $f" >&2;}
    { (exit 1); exit 1; }; }
          echo $f;;
@@ -3580,7 +3590,7 @@ echo "$as_me: error: cannot find input file: $f" >&2;}
            echo $srcdir/$f
          else
            # /dev/null tree
-           { { echo "$as_me:3583: error: cannot find input file: $f" >&5
+           { { echo "$as_me:3593: error: cannot find input file: $f" >&5
 echo "$as_me: error: cannot find input file: $f" >&2;}
    { (exit 1); exit 1; }; }
          fi;;
@@ -3641,7 +3651,7 @@ for ac_file in : $CONFIG_HEADERS; do test "x$ac_file" = x: && continue
   * )   ac_file_in=$ac_file.in ;;
   esac
 
-  test x"$ac_file" != x- && { echo "$as_me:3644: creating $ac_file" >&5
+  test x"$ac_file" != x- && { echo "$as_me:3654: creating $ac_file" >&5
 echo "$as_me: creating $ac_file" >&6;}
 
   # First look for the input files in the build tree, otherwise in the
@@ -3652,7 +3662,7 @@ echo "$as_me: creating $ac_file" >&6;}
       -) echo $tmp/stdin ;;
       [\\/$]*)
          # Absolute (can't be DOS-style, as IFS=:)
-         test -f "$f" || { { echo "$as_me:3655: error: cannot find input file: $f" >&5
+         test -f "$f" || { { echo "$as_me:3665: error: cannot find input file: $f" >&5
 echo "$as_me: error: cannot find input file: $f" >&2;}
    { (exit 1); exit 1; }; }
          echo $f;;
@@ -3665,7 +3675,7 @@ echo "$as_me: error: cannot find input file: $f" >&2;}
            echo $srcdir/$f
          else
            # /dev/null tree
-           { { echo "$as_me:3668: error: cannot find input file: $f" >&5
+           { { echo "$as_me:3678: error: cannot find input file: $f" >&5
 echo "$as_me: error: cannot find input file: $f" >&2;}
    { (exit 1); exit 1; }; }
          fi;;
@@ -3782,7 +3792,7 @@ cat >>$CONFIG_STATUS <<\EOF
   rm -f $tmp/in
   if test x"$ac_file" != x-; then
     if cmp -s $ac_file $tmp/config.h 2>/dev/null; then
-      { echo "$as_me:3785: $ac_file is unchanged" >&5
+      { echo "$as_me:3795: $ac_file is unchanged" >&5
 echo "$as_me: $ac_file is unchanged" >&6;}
     else
       ac_dir=`$as_expr X"$ac_file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
diff --git a/config/configure.in b/config/configure.in
index 33d7e3da6..041862eb1 100755
--- a/config/configure.in
+++ b/config/configure.in
@@ -75,6 +75,15 @@ AC_SUBST(LCXX_FLAGS)
 #if test -z "$LCXX_END_LIBS"; then LCXX_END_LIBS='-lm'; fi
 AC_SUBST(LCXX_END_LIBS)
 
+#########################################################
+#  User Code
+#########################################################
+USERDIR=""
+INCL_USER_CODE=0
+if test -n "$USER_SRC_DIR"; then USERDIR=$USER_SRC_DIR; INCL_USER_CODE=1; fi
+AC_SUBST(USERDIR)
+AC_SUBST(INCL_USER_CODE)
+
 #########################################################
 #  The Cantera Kernel
 #########################################################
@@ -407,6 +416,7 @@ AC_OUTPUT(../Cantera/Makefile \
 	  ../Cantera/python/Makefile \
           ../Cantera/python/setup.py \
 	  ../Cantera/cxx/Makefile \
+	  ../Cantera/user/Makefile \
 	  ../Cantera/python/src/Makefile \
           ../ext/lapack/Makefile \
 	  ../ext/blas/Makefile \
diff --git a/configure b/configure
index 46d9b32c8..8c0a1029a 100755
--- a/configure
+++ b/configure
@@ -61,6 +61,17 @@ BUILD_PYTHON_INTERFACE=${BUILD_PYTHON_INTERFACE:="y"}
 PYTHON_CMD=${PYTHON_CMD:="python"}
 BUILD_MATLAB_TOOLBOX=${BUILD_MATLAB_TOOLBOX:="y"}
 
+
+#----------------------------------------------------------------------
+#         Customizations / Extensions
+#
+# You can build your own libraries as part of the Cantera build process.
+# This allows you to derive your own classes from those provided by 
+# Cantera and build them automatically along with the rest of Cantera.
+# All you need to do is specify the directory where your source code is
+# located.
+USER_SRC_DIR="Cantera/user"
+
 #----------------------------------------------------------------------
 #         Kernel Configuration
 #----------------------------------------------------------------------
@@ -146,7 +157,7 @@ LAPACK_FTN_STRING_LEN_AT_END='y'
 CXX=${CXX:=g++}
 
 # C++ compiler flags
-CXXFLAGS=${CXXFLAGS:="-O2 -Wall"}
+CXXFLAGS=${CXXFLAGS:="-O2 -g -Wall"}
 
 # the C++ flags required for linking
 #LCXX_FLAGS=
@@ -217,6 +228,7 @@ CT_SHARED_LIB=${CT_SHARED_LIB:=clib}
 #------------------- don't change anything below!! ---------------------
 #-----------------------------------------------------------------------
 
+export USER_SRC_DIR
 export ARCHIVE
 export BLAS_LIBRARY
 export BUILD_F90
diff --git a/tools/doc/Cantera.cfg b/tools/doc/Cantera.cfg
index 78bea1f18..27dcc307f 100755
--- a/tools/doc/Cantera.cfg
+++ b/tools/doc/Cantera.cfg
@@ -1,4 +1,4 @@
-# Doxyfile 1.2.14
+# Doxyfile 1.3.4
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project
@@ -11,7 +11,7 @@
 # Values that contain spaces should be placed between quotes (" ")
 
 #---------------------------------------------------------------------------
-# General configuration options
+# Project related configuration options
 #---------------------------------------------------------------------------
 
 # The PROJECT_NAME tag is a single word (or a sequence of words surrounded 
@@ -29,21 +29,152 @@ PROJECT_NUMBER         = 1.5
 # base path where the generated documentation will be put. 
 # If a relative path is entered, it will be relative to the location 
 # where doxygen was started. If left blank the current directory will be used.
-#
-# HKM -> use current directory
-#
+
 OUTPUT_DIRECTORY       = 
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all 
 # documentation generated by doxygen is written. Doxygen will use this 
 # information to generate all constant output in the proper language. 
 # The default language is English, other supported languages are: 
-# Brazilian, Chinese, Croatian, Czech, Danish, Dutch, Finnish, French, 
-# German, Greek, Hungarian, Italian, Japanese, Korean, Norwegian, Polish, 
-# Portuguese, Romanian, Russian, Slovak, Slovene, Spanish and Swedish.
+# Brazilian, Catalan, Chinese, Chinese-Traditional, Croatian, Czech, Danish, Dutch, 
+# Finnish, French, German, Greek, Hungarian, Italian, Japanese, Japanese-en 
+# (Japanese with English messages), Korean, Norwegian, Polish, Portuguese, 
+# Romanian, Russian, Serbian, Slovak, Slovene, Spanish, Swedish, and Ukrainian.
 
 OUTPUT_LANGUAGE        = English
 
+# This tag can be used to specify the encoding used in the generated output. 
+# The encoding is not always determined by the language that is chosen, 
+# but also whether or not the output is meant for Windows or non-Windows users. 
+# In case there is a difference, setting the USE_WINDOWS_ENCODING tag to YES 
+# forces the Windows encoding (this is the default for the Windows binary), 
+# whereas setting the tag to NO uses a Unix-style encoding (the default for 
+# all platforms other than Windows).
+
+USE_WINDOWS_ENCODING   = NO
+
+# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will 
+# include brief member descriptions after the members that are listed in 
+# the file and class documentation (similar to JavaDoc). 
+# Set to NO to disable this.
+
+BRIEF_MEMBER_DESC      = YES
+
+# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend 
+# the brief description of a member or function before the detailed description. 
+# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the 
+# brief descriptions will be completely suppressed.
+
+REPEAT_BRIEF           = YES
+
+# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then 
+# Doxygen will generate a detailed section even if there is only a brief 
+# description.
+
+ALWAYS_DETAILED_SEC    = YES
+
+# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all inherited 
+# members of a class in the documentation of that class as if those members were 
+# ordinary class members. Constructors, destructors and assignment operators of 
+# the base classes will not be shown.
+
+INLINE_INHERITED_MEMB  = NO
+
+# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full 
+# path before files name in the file list and in the header files. If set 
+# to NO the shortest path that makes the file name unique will be used.
+
+FULL_PATH_NAMES        = NO
+
+# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag 
+# can be used to strip a user-defined part of the path. Stripping is 
+# only done if one of the specified strings matches the left-hand part of 
+# the path. It is allowed to use relative paths in the argument list.
+
+STRIP_FROM_PATH        = 
+
+# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter 
+# (but less readable) file names. This can be useful is your file systems 
+# doesn't support long names like on DOS, Mac, or CD-ROM.
+
+SHORT_NAMES            = NO
+
+# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen 
+# will interpret the first line (until the first dot) of a JavaDoc-style 
+# comment as the brief description. If set to NO, the JavaDoc 
+# comments will behave just like the Qt-style comments (thus requiring an 
+# explict @brief command for a brief description.
+
+JAVADOC_AUTOBRIEF      = YES
+
+# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen 
+# treat a multi-line C++ special comment block (i.e. a block of //! or /// 
+# comments) as a brief description. This used to be the default behaviour. 
+# The new default is to treat a multi-line C++ comment block as a detailed 
+# description. Set this tag to YES if you prefer the old behaviour instead.
+
+MULTILINE_CPP_IS_BRIEF = NO
+
+# If the DETAILS_AT_TOP tag is set to YES then Doxygen 
+# will output the detailed description near the top, like JavaDoc.
+# If set to NO, the detailed description appears after the member 
+# documentation.
+
+DETAILS_AT_TOP         = NO
+
+# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented 
+# member inherits the documentation from any documented member that it 
+# reimplements.
+
+INHERIT_DOCS           = YES
+
+# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC 
+# tag is set to YES, then doxygen will reuse the documentation of the first 
+# member in the group (if any) for the other members of the group. By default 
+# all members of a group must be documented explicitly.
+
+DISTRIBUTE_GROUP_DOC   = NO
+
+# The TAB_SIZE tag can be used to set the number of spaces in a tab. 
+# Doxygen uses this value to replace tabs by spaces in code fragments.
+
+TAB_SIZE               = 8
+
+# This tag can be used to specify a number of aliases that acts 
+# as commands in the documentation. An alias has the form "name=value". 
+# For example adding "sideeffect=\par Side Effects:\n" will allow you to 
+# put the command \sideeffect (or @sideeffect) in the documentation, which 
+# will result in a user-defined paragraph with heading "Side Effects:". 
+# You can put \n's in the value part of an alias to insert newlines.
+
+ALIASES                = 
+
+# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources 
+# only. Doxygen will then generate output that is more tailored for C. 
+# For instance, some of the names that are used will be different. The list 
+# of all members will be omitted, etc.
+
+OPTIMIZE_OUTPUT_FOR_C  = NO
+
+# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java sources 
+# only. Doxygen will then generate output that is more tailored for Java. 
+# For instance, namespaces will be presented as packages, qualified scopes 
+# will look different, etc.
+
+OPTIMIZE_OUTPUT_JAVA   = NO
+
+# Set the SUBGROUPING tag to YES (the default) to allow class member groups of 
+# the same type (for instance a group of public functions) to be put as a 
+# subgroup of that type (e.g. under the Public Functions section). Set it to 
+# NO to prevent subgrouping. Alternatively, this can be done per class using 
+# the \nosubgrouping command.
+
+SUBGROUPING            = YES
+
+#---------------------------------------------------------------------------
+# Build related configuration options
+#---------------------------------------------------------------------------
+
 # If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in 
 # documentation are documented, even if no documentation was available. 
 # Private class members and static file members will be hidden unless 
@@ -53,10 +184,7 @@ EXTRACT_ALL            = NO
 
 # If the EXTRACT_PRIVATE tag is set to YES all private members of a class 
 # will be included in the documentation.
-#
-# HKM -> Changed this to yes, as I want to use documentation as 
-#        a development tool, and thus need private info as well
-#
+
 EXTRACT_PRIVATE        = YES
 
 # If the EXTRACT_STATIC tag is set to YES all static members of a file 
@@ -80,53 +208,24 @@ HIDE_UNDOC_MEMBERS     = YES
 
 # If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all 
 # undocumented classes that are normally visible in the class hierarchy. 
-# If set to NO (the default) these class will be included in the various 
+# If set to NO (the default) these classes will be included in the various 
 # overviews. This option has no effect if EXTRACT_ALL is enabled.
 
 HIDE_UNDOC_CLASSES     = YES
 
-# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will 
-# include brief member descriptions after the members that are listed in 
-# the file and class documentation (similar to JavaDoc). 
-# Set to NO to disable this.
+# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all 
+# friend (class|struct|union) declarations. 
+# If set to NO (the default) these declarations will be included in the 
+# documentation.
 
-BRIEF_MEMBER_DESC      = YES
+HIDE_FRIEND_COMPOUNDS  = NO
 
-# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend 
-# the brief description of a member or function before the detailed description. 
-# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the 
-# brief descriptions will be completely suppressed.
+# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any 
+# documentation blocks found inside the body of a function. 
+# If set to NO (the default) these blocks will be appended to the 
+# function's detailed documentation block.
 
-REPEAT_BRIEF           = YES
-
-# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then 
-# Doxygen will generate a detailed section even if there is only a brief 
-# description.
-#
-# HKM turned to true -> was getting confused at not seeing the presence
-#                       of some members in the detailed members section
-#
-ALWAYS_DETAILED_SEC    = YES
-
-# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all inherited 
-# members of a class in the documentation of that class as if those members were 
-# ordinary class members. Constructors, destructors and assignment operators of 
-# the base classes will not be shown.
-
-INLINE_INHERITED_MEMB  = NO
-
-# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full 
-# path before files name in the file list and in the header files. If set 
-# to NO the shortest path that makes the file name unique will be used.
-
-FULL_PATH_NAMES        = NO
-
-# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag 
-# can be used to strip a user defined part of the path. Stripping is 
-# only done if one of the specified strings matches the left-hand part of 
-# the path. It is allowed to use relative paths in the argument list.
-
-STRIP_FROM_PATH        = 
+HIDE_IN_BODY_DOCS      = NO
 
 # The INTERNAL_DOCS tag determines if documentation 
 # that is typed after a \internal command is included. If the tag is set 
@@ -135,60 +234,26 @@ STRIP_FROM_PATH        =
 
 INTERNAL_DOCS          = NO
 
-# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct 
-# doxygen to hide any special comment blocks from generated source code 
-# fragments. Normal C and C++ comments will always remain visible.
-#
-# HKM turned this off -> that way the files will look the same in doxygen
-#
-STRIP_CODE_COMMENTS    = NO
-
 # If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate 
-# file names in lower case letters. If set to YES upper case letters are also 
+# file names in lower-case letters. If set to YES upper-case letters are also 
 # allowed. This is useful if you have classes or files whose names only differ 
 # in case and if your file system supports case sensitive file names. Windows 
-# users are adviced to set this option to NO.
+# users are advised to set this option to NO.
 
 CASE_SENSE_NAMES       = YES
 
-# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter 
-# (but less readable) file names. This can be useful is your file systems 
-# doesn't support long names like on DOS, Mac, or CD-ROM.
-
-SHORT_NAMES            = NO
-
 # If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen 
 # will show members with their full class and namespace scopes in the 
 # documentation. If set to YES the scope will be hidden.
 
 HIDE_SCOPE_NAMES       = YES
 
-# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen 
-# will generate a verbatim copy of the header file for each class for 
-# which an include is specified. Set to NO to disable this.
-
-VERBATIM_HEADERS       = YES
-
 # If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen 
-# will put list of the files that are included by a file in the documentation 
+# will put a list of the files that are included by a file in the documentation 
 # of that file.
 
 SHOW_INCLUDE_FILES     = YES
 
-# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen 
-# will interpret the first line (until the first dot) of a JavaDoc-style 
-# comment as the brief description. If set to NO, the JavaDoc 
-# comments  will behave just like the Qt-style comments (thus requiring an 
-# explict @brief command for a brief description.
-
-JAVADOC_AUTOBRIEF      = YES
-
-# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented 
-# member inherits the documentation from any documented member that it 
-# reimplements.
-
-INHERIT_DOCS           = YES
-
 # If the INLINE_INFO tag is set to YES (the default) then a tag [inline] 
 # is inserted in the documentation for inline members.
 
@@ -201,18 +266,6 @@ INLINE_INFO            = YES
 
 SORT_MEMBER_DOCS       = YES
 
-# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC 
-# tag is set to YES, then doxygen will reuse the documentation of the first 
-# member in the group (if any) for the other members of the group. By default 
-# all members of a group must be documented explicitly.
-
-DISTRIBUTE_GROUP_DOC   = NO
-
-# The TAB_SIZE tag can be used to set the number of spaces in a tab. 
-# Doxygen uses this value to replace tabs by spaces in code fragments.
-
-TAB_SIZE               = 8
-
 # The GENERATE_TODOLIST tag can be used to enable (YES) or 
 # disable (NO) the todo list. This list is created by putting \todo 
 # commands in the documentation.
@@ -231,14 +284,11 @@ GENERATE_TESTLIST      = YES
 
 GENERATE_BUGLIST       = YES
 
-# This tag can be used to specify a number of aliases that acts 
-# as commands in the documentation. An alias has the form "name=value". 
-# For example adding "sideeffect=\par Side Effects:\n" will allow you to 
-# put the command \sideeffect (or @sideeffect) in the documentation, which 
-# will result in a user defined paragraph with heading "Side Effects:". 
-# You can put \n's in the value part of an alias to insert newlines.
+# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or 
+# disable (NO) the deprecated list. This list is created by putting 
+# \deprecated commands in the documentation.
 
-ALIASES                = 
+GENERATE_DEPRECATEDLIST= YES
 
 # The ENABLED_SECTIONS tag can be used to enable conditional 
 # documentation sections, marked by \if sectionname ... \endif.
@@ -246,7 +296,7 @@ ALIASES                =
 ENABLED_SECTIONS       = 
 
 # The MAX_INITIALIZER_LINES tag determines the maximum number of lines 
-# the initial value of a variable or define consist of for it to appear in 
+# the initial value of a variable or define consists of for it to appear in 
 # the documentation. If the initializer consists of more lines than specified 
 # here it will be hidden. Use a value of 0 to hide initializers completely. 
 # The appearance of the initializer of individual variables and defines in the 
@@ -255,13 +305,6 @@ ENABLED_SECTIONS       =
 
 MAX_INITIALIZER_LINES  = 30
 
-# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources 
-# only. Doxygen will then generate output that is more tailored for C. 
-# For instance some of the names that are used will be different. The list 
-# of all members will be omitted, etc.
-
-OPTIMIZE_OUTPUT_FOR_C  = NO
-
 # Set the SHOW_USED_FILES tag to NO to disable the list of files generated 
 # at the bottom of the documentation of classes and structs. If set to YES the 
 # list will mention the files that were used to generate the documentation.
@@ -289,6 +332,13 @@ WARNINGS               = YES
 
 WARN_IF_UNDOCUMENTED   = NO
 
+# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for 
+# potential errors in the documentation, such as not documenting some 
+# parameters in a documented function, or documenting parameters that 
+# don't exist or using markup commands wrongly.
+
+WARN_IF_DOC_ERROR      = YES
+
 # The WARN_FORMAT tag determines the format of the warning messages that 
 # doxygen can produce. The string should contain the $file, $line, and $text 
 # tags, which will be replaced by the file and line number from which the 
@@ -318,10 +368,12 @@ INPUT                  = ../../Cantera/src
 # and *.h) to filter out the source-files in the directories. If left 
 # blank the following patterns are tested: 
 # *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx *.hpp 
-# *.h++ *.idl *.odl
-
-FILE_PATTERNS          = *.h *.cpp *.c *.txt
+# *.h++ *.idl *.odl *.cs *.php *.php3 *.inc
 
+FILE_PATTERNS          = *.h \
+                         *.cpp \
+                         *.c \
+                         *.txt
 
 # The RECURSIVE tag can be used to turn specify whether or not subdirectories 
 # should be searched for input files as well. Possible values are YES and NO. 
@@ -334,7 +386,7 @@ RECURSIVE              = YES
 # subdirectory from a directory tree whose root is specified with the INPUT tag.
 
 EXCLUDE                = CVS \
-                         examples
+                         examples converters
 
 # The EXCLUDE_SYMLINKS tag can be used select whether or not files or directories 
 # that are symbolic links (a Unix filesystem feature) are excluded from the input.
@@ -351,7 +403,7 @@ EXCLUDE_PATTERNS       = *old/* \
                          *CVS/* \
                          *examples/* \
                          *test/* \
-                         *tests/*
+                         *tests/* 
 
 # The EXAMPLE_PATH tag can be used to specify one or more files or 
 # directories that contain example code fragments that are included (see 
@@ -391,7 +443,7 @@ INPUT_FILTER           =
 
 # If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using 
 # INPUT_FILTER) will be used to filter the input files when producing source 
-# files to browse.
+# files to browse (i.e. when SOURCE_BROWSER is set to YES).
 
 FILTER_SOURCE_FILES    = NO
 
@@ -409,6 +461,12 @@ SOURCE_BROWSER         = YES
 
 INLINE_SOURCES         = NO
 
+# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct 
+# doxygen to hide any special comment blocks from generated source code 
+# fragments. Normal C and C++ comments will always remain visible.
+
+STRIP_CODE_COMMENTS    = NO
+
 # If the REFERENCED_BY_RELATION tag is set to YES (the default) 
 # then for each documented function all documented 
 # functions referencing it will be listed.
@@ -421,6 +479,12 @@ REFERENCED_BY_RELATION = YES
 
 REFERENCES_RELATION    = YES
 
+# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen 
+# will generate a verbatim copy of the header file for each class for 
+# which an include is specified. Set to NO to disable this.
+
+VERBATIM_HEADERS       = YES
+
 #---------------------------------------------------------------------------
 # configuration options related to the alphabetical class index
 #---------------------------------------------------------------------------
@@ -477,7 +541,7 @@ HTML_HEADER            = header.html
 
 HTML_FOOTER            = footer.html
 
-# The HTML_STYLESHEET tag can be used to specify a user defined cascading 
+# The HTML_STYLESHEET tag can be used to specify a user-defined cascading 
 # style sheet that is used by each HTML page. It can be used to 
 # fine-tune the look of the HTML output. If the tag is left blank doxygen 
 # will generate a default style sheet
@@ -497,6 +561,20 @@ HTML_ALIGN_MEMBERS     = YES
 
 GENERATE_HTMLHELP      = YES
 
+# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can 
+# be used to specify the file name of the resulting .chm file. You 
+# can add a path in front of the file if the result should not be 
+# written to the html output dir.
+
+CHM_FILE               = 
+
+# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can 
+# be used to specify the location (absolute path including file name) of 
+# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run 
+# the HTML help compiler on the generated index.hhp.
+
+HHC_LOCATION           = 
+
 # If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag 
 # controls if a separate .chi index file is generated (YES) or that 
 # it should be included in the master .chm file (NO).
@@ -510,7 +588,7 @@ GENERATE_CHI           = NO
 BINARY_TOC             = NO
 
 # The TOC_EXPAND flag can be set to YES to add extra items for group members 
-# to the contents of the Html help documentation and to the tree view.
+# to the contents of the HTML help documentation and to the tree view.
 
 TOC_EXPAND             = NO
 
@@ -528,10 +606,9 @@ ENUM_VALUES_PER_LINE   = 4
 # If the GENERATE_TREEVIEW tag is set to YES, a side panel will be
 # generated containing a tree-like index structure (just like the one that 
 # is generated for HTML Help). For this to work a browser that supports 
-# JavaScript and frames is required (for instance Mozilla, Netscape 4.0+, 
-# or Internet explorer 4.0+). Note that for large projects the tree generation 
-# can take a very long time. In such cases it is better to disable this feature. 
-# Windows users are probably better off using the HTML help feature.
+# JavaScript, DHTML, CSS and frames is required (for instance Mozilla 1.0+, 
+# Netscape 6.0+, Internet explorer 5.0+, or Konqueror). Windows users are 
+# probably better off using the HTML help feature.
 
 GENERATE_TREEVIEW      = YES
 
@@ -556,6 +633,17 @@ GENERATE_LATEX         = YES
 
 LATEX_OUTPUT           = latex
 
+# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be 
+# invoked. If left blank `latex' will be used as the default command name.
+
+LATEX_CMD_NAME         = latex
+
+# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to 
+# generate index for LaTeX. If left blank `makeindex' will be used as the 
+# default command name.
+
+MAKEINDEX_CMD_NAME     = makeindex
+
 # If the COMPACT_LATEX tag is set to YES Doxygen generates more compact 
 # LaTeX documents. This may be useful for small projects and may help to 
 # save some trees in general.
@@ -600,6 +688,12 @@ USE_PDFLATEX           = NO
 
 LATEX_BATCHMODE        = NO
 
+# If LATEX_HIDE_INDICES is set to YES then doxygen will not 
+# include the index chapters (such as File Index, Compound Index, etc.) 
+# in the output.
+
+LATEX_HIDE_INDICES     = NO
+
 #---------------------------------------------------------------------------
 # configuration options related to the RTF output
 #---------------------------------------------------------------------------
@@ -682,6 +776,24 @@ MAN_LINKS              = NO
 
 GENERATE_XML           = NO
 
+# The XML_OUTPUT tag is used to specify where the XML pages will be put. 
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
+# put in front of it. If left blank `xml' will be used as the default path.
+
+XML_OUTPUT             = xml
+
+# The XML_SCHEMA tag can be used to specify an XML schema, 
+# which can be used by a validating XML parser to check the 
+# syntax of the XML files.
+
+XML_SCHEMA             = 
+
+# The XML_DTD tag can be used to specify an XML DTD, 
+# which can be used by a validating XML parser to check the 
+# syntax of the XML files.
+
+XML_DTD                = 
+
 #---------------------------------------------------------------------------
 # configuration options for the AutoGen Definitions output
 #---------------------------------------------------------------------------
@@ -694,6 +806,39 @@ GENERATE_XML           = NO
 
 GENERATE_AUTOGEN_DEF   = NO
 
+#---------------------------------------------------------------------------
+# configuration options related to the Perl module output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_PERLMOD tag is set to YES Doxygen will 
+# generate a Perl module file that captures the structure of 
+# the code including all documentation. Note that this 
+# feature is still experimental and incomplete at the 
+# moment.
+
+GENERATE_PERLMOD       = NO
+
+# If the PERLMOD_LATEX tag is set to YES Doxygen will generate 
+# the necessary Makefile rules, Perl scripts and LaTeX code to be able 
+# to generate PDF and DVI output from the Perl module output.
+
+PERLMOD_LATEX          = NO
+
+# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be 
+# nicely formatted so it can be parsed by a human reader.  This is useful 
+# if you want to understand what is going on.  On the other hand, if this 
+# tag is set to NO the size of the Perl module output will be much smaller 
+# and Perl will parse it just the same.
+
+PERLMOD_PRETTY         = YES
+
+# The names of the make variables in the generated doxyrules.make file 
+# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. 
+# This is useful so different doxyrules.make files included by the same 
+# Makefile don't overwrite each other's variables.
+
+PERLMOD_MAKEVAR_PREFIX = 
+
 #---------------------------------------------------------------------------
 # Configuration options related to the preprocessor   
 #---------------------------------------------------------------------------
@@ -743,7 +888,7 @@ INCLUDE_FILE_PATTERNS  =
 
 PREDEFINED             = 
 
-# If the MACRO_EXPANSION and EXPAND_PREDEF_ONLY tags are set to YES then 
+# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then 
 # this tag can be used to specify a list of macro names that should be expanded. 
 # The macro definition that is found in the sources will be used. 
 # Use the PREDEFINED tag if you want to use a different macro definition.
@@ -752,8 +897,9 @@ EXPAND_AS_DEFINED      = YES
 
 # If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then 
 # doxygen's preprocessor will remove all function-like macros that are alone 
-# on a line and do not end with a semicolon. Such function macros are typically 
-# used for boiler-plate code, and will confuse the parser if not removed.
+# on a line, have an all uppercase name, and do not end with a semicolon. Such 
+# function macros are typically used for boiler-plate code, and will confuse the 
+# parser if not removed.
 
 SKIP_FUNCTION_MACROS   = YES
 
@@ -761,7 +907,20 @@ SKIP_FUNCTION_MACROS   = YES
 # Configuration::addtions related to external references   
 #---------------------------------------------------------------------------
 
-# The TAGFILES tag can be used to specify one or more tagfiles.
+# The TAGFILES option can be used to specify one or more tagfiles. 
+# Optionally an initial location of the external documentation 
+# can be added for each tagfile. The format of a tag file without 
+# this location is as follows: 
+#   TAGFILES = file1 file2 ... 
+# Adding location for the tag files is done as follows: 
+#   TAGFILES = file1=loc1 "file2 = loc2" ... 
+# where "loc1" and "loc2" can be relative or absolute paths or 
+# URLs. If a location is present for each tag, the installdox tool 
+# does not have to be run to correct the links.
+# Note that each tag file must have a unique name
+# (where the name does NOT include the path)
+# If a tag file is not located in the directory in which doxygen 
+# is run, you must also specify the path to the tagfile here.
 
 TAGFILES               = 
 
@@ -792,13 +951,19 @@ PERL_PATH              = /usr/bin/perl
 #---------------------------------------------------------------------------
 
 # If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will 
-# generate a inheritance diagram (in Html, RTF and LaTeX) for classes with base or 
+# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base or 
 # super classes. Setting the tag to NO turns the diagrams off. Note that this 
 # option is superceded by the HAVE_DOT option below. This is only a fallback. It is 
-# recommended to install and use dot, since it yield more powerful graphs.
+# recommended to install and use dot, since it yields more powerful graphs.
 
 CLASS_DIAGRAMS         = YES
 
+# If set to YES, the inheritance and collaboration graphs will hide 
+# inheritance and usage relations if the target is undocumented 
+# or is not a class.
+
+HIDE_UNDOC_RELATIONS   = YES
+
 # If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is 
 # available from the path. This tool is part of Graphviz, a graph visualization 
 # toolkit from AT&T and Lucent Bell Labs. The other options in this section 
@@ -820,17 +985,17 @@ CLASS_GRAPH            = YES
 
 COLLABORATION_GRAPH    = YES
 
+# If the UML_LOOK tag is set to YES doxygen will generate inheritance and 
+# collaboration diagrams in a style similiar to the OMG's Unified Modeling 
+# Language.
+
+UML_LOOK               = NO
+
 # If set to YES, the inheritance and collaboration graphs will show the 
 # relations between templates and their instances.
 
 TEMPLATE_RELATIONS     = YES
 
-# If set to YES, the inheritance and collaboration graphs will hide 
-# inheritance and usage relations if the target is undocumented 
-# or is not a class.
-
-HIDE_UNDOC_RELATIONS   = YES
-
 # If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT 
 # tags are set to YES then doxygen will generate a graph for each documented 
 # file showing the direct and indirect include dependencies of the file with 
@@ -845,14 +1010,22 @@ INCLUDE_GRAPH          = YES
 
 INCLUDED_BY_GRAPH      = YES
 
+# If the CALL_GRAPH and HAVE_DOT tags are set to YES then doxygen will 
+# generate a call dependency graph for every global function or class method. 
+# Note that enabling this option will significantly increase the time of a run. 
+# So in most cases it will be better to enable call graphs for selected 
+# functions only using the \callgraph command.
+
+CALL_GRAPH             = NO
+
 # If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen 
 # will graphical hierarchy of all classes instead of a textual one.
 
 GRAPHICAL_HIERARCHY    = YES
 
 # The DOT_IMAGE_FORMAT tag can be used to set the image format of the images 
-# generated by dot. Possible values are gif, jpg, and png
-# If left blank gif will be used.
+# generated by dot. Possible values are png, jpg, or gif
+# If left blank png will be used.
 
 DOT_IMAGE_FORMAT       = gif
 
@@ -883,6 +1056,17 @@ MAX_DOT_GRAPH_WIDTH    = 1024
 
 MAX_DOT_GRAPH_HEIGHT   = 1024
 
+# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the 
+# graphs generated by dot. A depth value of 3 means that only nodes reachable 
+# from the root by following a path via at most 3 edges will be shown. Nodes that 
+# lay further from the root node will be omitted. Note that setting this option to 
+# 1 or 2 may greatly reduce the computation time needed for large code bases. Also 
+# note that a graph may be further truncated if the graph's image dimensions are 
+# not sufficient to fit the graph (see MAX_DOT_GRAPH_WIDTH and MAX_DOT_GRAPH_HEIGHT). 
+# If 0 is used for the depth value (the default), the graph is not depth-constrained.
+
+MAX_DOT_GRAPH_DEPTH    = 0
+
 # If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will 
 # generate a legend page explaining the meaning of the various boxes and 
 # arrows in the dot generated graphs.
@@ -890,7 +1074,7 @@ MAX_DOT_GRAPH_HEIGHT   = 1024
 GENERATE_LEGEND        = YES
 
 # If the DOT_CLEANUP tag is set to YES (the default) Doxygen will 
-# remove the intermedate dot files that are used to generate 
+# remove the intermediate dot files that are used to generate 
 # the various graphs.
 
 DOT_CLEANUP            = YES
@@ -903,38 +1087,3 @@ DOT_CLEANUP            = YES
 # used. If set to NO the values of all tags below this one will be ignored.
 
 SEARCHENGINE           = NO
-
-# The CGI_NAME tag should be the name of the CGI script that 
-# starts the search engine (doxysearch) with the correct parameters. 
-# A script with this name will be generated by doxygen.
-
-CGI_NAME               = search.cgi
-
-# The CGI_URL tag should be the absolute URL to the directory where the 
-# cgi binaries are located. See the documentation of your http daemon for 
-# details.
-
-CGI_URL                = http://blue.caltech.edu/cgi-bin
-
-# The DOC_URL tag should be the absolute URL to the directory where the 
-# documentation is located. If left blank the absolute path to the 
-# documentation, with file:// prepended to it, will be used.
-
-DOC_URL                = http://blue.caltech.edu/cantera/ref/
-
-# The DOC_ABSPATH tag should be the absolute path to the directory where the 
-# documentation is located. If left blank the directory on the local machine 
-# will be used.
-
-DOC_ABSPATH            = 
-
-# The BIN_ABSPATH tag must point to the directory where the doxysearch binary 
-# is installed.
-
-BIN_ABSPATH            = /usr/bin
-
-# The EXT_DOC_PATHS tag can be used to specify one or more paths to 
-# documentation generated for other projects. This allows doxysearch to search 
-# the documentation for these projects as well.
-
-EXT_DOC_PATHS          = 
diff --git a/tools/doc/footer.html b/tools/doc/footer.html
index 4f184ddda..fd594b115 100755
--- a/tools/doc/footer.html
+++ b/tools/doc/footer.html
@@ -3,7 +3,7 @@
 <table cellspacing="0" cellpadding="0" border="0" bgcolor="#ffffff" width=100%>
    <tr>
       <td><div align="center"><i><font face="Arial, Helvetica, sans-serif" color="#66333" size=-1>created by <a href="mailto:dgoodwin@caltech.edu">Prof. David G. Goodwin</a></font> </i></div></td></tr>
-      <td><div align="center"><i><font face="Arial, Helvetica, sans-serif" color="#66333" size=-1>Copyright (c) 2001 California Institute of Technology</font> </i></div></td></tr></table>
+      <td><div align="center"><i><font face="Arial, Helvetica, sans-serif" color="#66333" size=-1>Copyright (c) 2003 California Institute of Technology</font> </i></div></td></tr></table>