diff --git a/Cantera/Makefile.in b/Cantera/Makefile.in
index 338cc8988..34b5e089f 100755
--- a/Cantera/Makefile.in
+++ b/Cantera/Makefile.in
@@ -26,7 +26,7 @@ endif
 
 clean:
 	cd src; @MAKE@ clean
-	cd cxx/src; @MAKE@ clean
+	cd cxx; @MAKE@ clean
 	cd clib/src; @MAKE@ clean
 	cd python; @MAKE@ clean
 ifeq ($(build_f90),1)
diff --git a/Cantera/clib/src/ct.cpp b/Cantera/clib/src/ct.cpp
index 59d15762f..471727fec 100755
--- a/Cantera/clib/src/ct.cpp
+++ b/Cantera/clib/src/ct.cpp
@@ -34,12 +34,17 @@ inline XML_Node* _xml(int i) {
 
 #ifdef INCL_PURE_FLUID
 static PureFluid* purefluid(int n) {
-    ThermoPhase* tp = th(n);
-    if (tp->eosType() == cPureFluid) {
-        return (PureFluid*)tp;
+    try {
+        ThermoPhase* tp = th(n);
+        if (tp->eosType() == cPureFluid) {
+            return (PureFluid*)tp;
+        }
+        else {
+            throw CanteraError("purefluid","object is not a PureFluid object");
+        }
     }
-    else {
-        throw CanteraError("purefluid","object is not a PureFluid object");
+    catch (CanteraError) {
+        return 0;
     }
 }
 #else
@@ -82,8 +87,7 @@ extern "C" {
     }
 
     int DLL_EXPORT phase_setDensity(int n, double rho) {
-        if (rho < 0.0) throw CanteraError("phase_setDensity",
-            "density cannot be negative");
+        if (rho < 0.0) return -1;
         ph(n)->setDensity(rho);
         return 0;
     }
diff --git a/Cantera/clib/src/ct.h b/Cantera/clib/src/ct.h
index fc305da1b..150f608e6 100755
--- a/Cantera/clib/src/ct.h
+++ b/Cantera/clib/src/ct.h
@@ -2,7 +2,7 @@
 #define CTC_CT_H
 
 #include "clib_defs.h"
-#include <cantera/Cantera.h>
+#include "../../../config.h"
 
 extern "C" {
 
diff --git a/Cantera/clib/src/ctreactor.cpp b/Cantera/clib/src/ctreactor.cpp
index f6769e8d4..f2ecd3772 100755
--- a/Cantera/clib/src/ctreactor.cpp
+++ b/Cantera/clib/src/ctreactor.cpp
@@ -94,10 +94,10 @@ extern "C" {
         return 0;
     }
 
-    //int DLL_EXPORT reactor_setInitialTime(int i, double t) {
-    //    _reactor(i)->setInitialTime(t);
-    //    return 0;
-    //}
+    int DLL_EXPORT reactor_setInitialTime(int i, double t) {
+       _reactor(i)->setInitialTime(t);
+       return 0;
+    }
 
     int DLL_EXPORT reactor_setThermoMgr(int i, int n) {
         _reactor(i)->setThermoMgr(*_th(n));
@@ -111,17 +111,17 @@ extern "C" {
         return 0;
     }
 
-    //int DLL_EXPORT reactor_advance(int i, double t) {
-    //    try {
-    //        _reactor(i)->advance(t);
-    //        return 0;
-    //    }
-    //    catch (CanteraError) {return -1;}
-    //}
+    int DLL_EXPORT reactor_advance(int i, double t) {
+       try {
+           _reactor(i)->advance(t);
+           return 0;
+       }
+       catch (CanteraError) {return -1;}
+    }
 
-    //    double DLL_EXPORT reactor_step(int i, double t) {
-    //    return _reactor(i)->step(t);
-    //}
+       double DLL_EXPORT reactor_step(int i, double t) {
+       return _reactor(i)->step(t);
+    }
 
     double DLL_EXPORT reactor_time(int i) {
         return _reactor(i)->time();
@@ -196,11 +196,26 @@ extern "C" {
         return 0;
     }
 
-    int DLL_EXPORT reactornet_addreactor(int i, int n) {
-        _reactornet(i)->addReactor(_reactor(n));
+    int DLL_EXPORT reactornet_setMaxTimeStep(int i, double maxstep) {
+        _reactornet(i)->setMaxTimeStep(maxstep);
         return 0;
     }
 
+    int DLL_EXPORT reactornet_setTolerances(int i, double rtol, double atol) {
+        _reactornet(i)->setTolerances(rtol, atol);
+        return 0;
+    }
+
+    int DLL_EXPORT reactornet_addreactor(int i, int n) {
+        try {
+            _reactornet(i)->addReactor(_reactor(n));
+            return 0;
+        }
+        catch (CanteraError) {
+            return -1;
+        }
+    }
+
     int DLL_EXPORT reactornet_advance(int i, double t) {
         try {
             _reactornet(i)->advance(t);
@@ -218,6 +233,19 @@ extern "C" {
         }
     }
 
+    double DLL_EXPORT reactornet_time(int i) {
+        return _reactornet(i)->time();
+    }
+
+    double DLL_EXPORT reactornet_rtol(int i) {
+        return _reactornet(i)->rtol();
+    }
+
+    double DLL_EXPORT reactornet_atol(int i) {
+        return _reactornet(i)->atol();
+    }
+
+
 
     // flow devices
 
diff --git a/Cantera/clib/src/ctreactor.h b/Cantera/clib/src/ctreactor.h
index 8fa53a5e6..5619a2878 100755
--- a/Cantera/clib/src/ctreactor.h
+++ b/Cantera/clib/src/ctreactor.h
@@ -10,12 +10,12 @@ extern "C" {
     int DLL_IMPORT reactor_copy(int i);
     int DLL_IMPORT reactor_assign(int i, int j);
     int DLL_IMPORT reactor_setInitialVolume(int i, double v);
-    //    int DLL_IMPORT reactor_setInitialTime(int i, double t);
+    int DLL_IMPORT reactor_setInitialTime(int i, double t);
     int DLL_IMPORT reactor_setEnergy(int i, int eflag);
     int DLL_IMPORT reactor_setThermoMgr(int i, int n);
     int DLL_IMPORT reactor_setKineticsMgr(int i, int n);
-    //int DLL_IMPORT reactor_advance(int i, double t);
-    //double DLL_IMPORT reactor_step(int i, double t);
+    int DLL_IMPORT reactor_advance(int i, double t);
+    double DLL_IMPORT reactor_step(int i, double t);
     double DLL_IMPORT reactor_time(int i);
     double DLL_IMPORT reactor_mass(int i);
     double DLL_IMPORT reactor_volume(int i);
@@ -31,9 +31,14 @@ extern "C" {
     int DLL_IMPORT reactornet_copy(int i);
     int DLL_IMPORT reactornet_assign(int i, int j);
     int DLL_IMPORT reactornet_setInitialTime(int i, double t);
+    int DLL_IMPORT reactornet_setMaxTimeStep(int i, double maxstep);
+    int DLL_IMPORT reactornet_setTolerances(int i, double rtol, double atol);
     int DLL_IMPORT reactornet_addreactor(int i, int n);
     int DLL_IMPORT reactornet_advance(int i, double t);
     double DLL_IMPORT reactornet_step(int i, double t);
+    double DLL_IMPORT reactornet_time(int i);
+    double DLL_IMPORT reactornet_rtol(int i);
+    double DLL_IMPORT reactornet_atol(int i);
 
     int DLL_IMPORT flowdev_new(int type);
     int DLL_IMPORT flowdev_del(int i);
diff --git a/Cantera/python/Cantera/Kinetics.py b/Cantera/python/Cantera/Kinetics.py
index a8afe475a..a6fcabfa8 100755
--- a/Cantera/python/Cantera/Kinetics.py
+++ b/Cantera/python/Cantera/Kinetics.py
@@ -100,11 +100,12 @@ class Kinetics:
         return _cantera.kin_speciesIndex(self.ckin, name, phase)
 
     def kineticsStart(self, n):
+        """The starting location of phase n in production rate arrays."""
         return _cantera.kin_start(self.ckin, n)
 
     def phase(self, n):
+        """Return an object representing the nth phase."""
         return ThermoPhase(index = _cantera.kin_phase(self.ckin, n))
-        #return self._ph[_cantera.kin_phase(self.ckin, n)]
     
     def nReactions(self):
         """Number of reactions."""
@@ -121,10 +122,9 @@ class Kinetics:
         """Type of reaction 'i'"""
         return _cantera.kin_rxntype(self.ckin,i)
 
-    #def reactionString(self,i):
-    #    return _cantera.kin_getstring(self.ckin,1,i)
-
     def reactionEqn(self,i):
+        """The equation for the specified reaction. If a list of equation numbers
+        is given, then a list of equation strings is returned."""
         try:
             eqs = []
             for rxn in i:
@@ -134,6 +134,7 @@ class Kinetics:
             return self.reactionString(i)
 
     def reactionString(self, i):
+        """Reaction string for reaction number 'i'"""
         s = ''
         nsp = _cantera.kin_nspecies(self.ckin)
         for k in range(nsp):
@@ -157,9 +158,13 @@ class Kinetics:
         return s
     
     def reactantStoichCoeff(self,k,i):
+        """The stoichiometric coefficient of species k as a reactant in reaction i."""
         return _cantera.kin_rstoichcoeff(self.ckin,k,i)
     
     def reactantStoichCoeffs(self):
+        """The array of reactant stoichiometric coefficients. Element
+        [k,i] of this array is the reactant stoichiometric
+        coefficient of species k in reaction i."""
         nsp = _cantera.kin_nspecies(self.ckin)
         nr = _cantera.kin_nreactions(self.ckin)
         nu = Numeric.zeros((nsp,nr),'d')
@@ -169,9 +174,13 @@ class Kinetics:
         return nu
 
     def productStoichCoeff(self,k,i):
+        """The stoichiometric coefficient of species k as a product in reaction i."""
         return _cantera.kin_pstoichcoeff(self.ckin,k,i)    
 
     def productStoichCoeffs(self):
+        """The array of product stoichiometric coefficients. Element
+        [k,i] of this array is the product stoichiometric
+        coefficient of species k in reaction i."""        
         nsp = _cantera.kin_nspecies(self.ckin)
         nr = _cantera.kin_nreactions(self.ckin)
         nu = Numeric.zeros((nsp,nr),'d')
@@ -181,12 +190,15 @@ class Kinetics:
         return nu
     
     def fwdRatesOfProgress(self):
+        """Forward rates of progress of the reactions."""
         return _cantera.kin_getarray(self.ckin,10)
 
     def revRatesOfProgress(self):
+        """Reverse rates of progress of the reactions."""
         return _cantera.kin_getarray(self.ckin,20)
 
     def netRatesOfProgress(self):
+        """Net rates of progress of the reactions."""
         return _cantera.kin_getarray(self.ckin,30)
 
     def equilibriumConstants(self):
@@ -198,9 +210,11 @@ class Kinetics:
         return _cantera.kin_getarray(self.ckin,32)
 
     def fwdRateConstants(self):
+        """Forward rate constants for all reactions."""
         return _cantera.kin_getarray(self.ckin,34)
 
     def revRateConstants(self, doIrreversible = 0):
+        """Reverse rate constants for all reactions."""
         if doIrreversible:
             return _cantera.kin_getarray(self.ckin,35)
         else:
diff --git a/Cantera/python/Cantera/Transport.py b/Cantera/python/Cantera/Transport.py
index 010896579..f6b0fe296 100755
--- a/Cantera/python/Cantera/Transport.py
+++ b/Cantera/python/Cantera/Transport.py
@@ -35,11 +35,12 @@ class Transport:
         self._models[self.model] = self.__tr_id
 
     def __del__(self):
-        for m in self._models.keys():
-            try:
-                _cantera.tran_delete(self._models[m])
-            except:
-                pass
+        if hasattr(self,'_models'):
+            for m in self._models.keys():
+                try:
+                    _cantera.tran_delete(self._models[m])
+                except:
+                    pass
 
     def addTransportModel(self, model, loglevel=1):
         new_id = _cantera.Transport(model,
diff --git a/Cantera/python/Cantera/constants.py b/Cantera/python/Cantera/constants.py
index 3dd496fbc..7534e9bfc 100755
--- a/Cantera/python/Cantera/constants.py
+++ b/Cantera/python/Cantera/constants.py
@@ -2,14 +2,31 @@
 Physical Constants
 """
 
+# One atmosphere in Pascals
 OneAtm = 101325.0
+
+# The ideal gas constant in J/kmo-K
 GasConstant = 8314.0
+
+# Avogadro's Number, /kmol
 Avogadro = 6.022136736e26
 
+# The ideal gas constant in cal/mol-K
 GasConst_cal_mol_K = 1.987
+
+# Boltzmann-s constant
 Boltzmann = GasConstant / Avogadro
+
+# The Stefan-Boltzmann constant, W/m^2K^4
 StefanBoltz = 5.67e-8
+
+# The charge on an electron
 ElectronCharge = 1.602e-19
+
 Pi = 3.1415926
+
+# Faraday's constant, C/kmol
 Faraday = ElectronCharge * Avogadro
+
+# Planck's constant
 Planck = 6.6262e-34
diff --git a/Cantera/python/Makefile.in b/Cantera/python/Makefile.in
index 42e652ec1..dba09737c 100755
--- a/Cantera/python/Makefile.in
+++ b/Cantera/python/Makefile.in
@@ -38,7 +38,7 @@ win: _winbuild
 
 _build: $(SRCS) $(LIB_DEPS)
 	touch src/pycantera.cpp 
-	(@PYTHON_CMD@ setup.py build)
+	(CXX=@CXX@; export CXX; CC=@CC@; export CC; @PYTHON_CMD@ setup.py build)
 	echo 'ok' > _build
 
 
diff --git a/Cantera/python/src/ctthermo_methods.cpp b/Cantera/python/src/ctthermo_methods.cpp
index 27daae7d4..3dbe8d1af 100644
--- a/Cantera/python/src/ctthermo_methods.cpp
+++ b/Cantera/python/src/ctthermo_methods.cpp
@@ -71,7 +71,7 @@ thermo_getfp(PyObject *self, PyObject *args)
     if (!PyArg_ParseTuple(args, "ii:thermo_getfp", &th, &job)) 
         return NULL;
 
-    try {
+    // try {
 
         // floating-point attributes
         switch (job) {
@@ -123,10 +123,10 @@ thermo_getfp(PyObject *self, PyObject *args)
             PyErr_SetString(ErrorObject,"Unknown floating-point attribute");
             return NULL;
         }
-    }
-    catch (CanteraError) {
-        return reportCanteraError();
-    }
+        //}
+        //catch (CanteraError) {
+        // return reportCanteraError();
+        //}
 }
 
 static PyObject*
diff --git a/Cantera/python/src/pycantera.cpp b/Cantera/python/src/pycantera.cpp
index 3dd882cd9..c52e854b3 100644
--- a/Cantera/python/src/pycantera.cpp
+++ b/Cantera/python/src/pycantera.cpp
@@ -11,6 +11,7 @@
 #pragma warning(disable:4503)
 #endif
 
+#include "../../../config.h"
 
 #include "Python.h"
 #include "Numeric/arrayobject.h"
diff --git a/Cantera/src/IdealGasPhase.h b/Cantera/src/IdealGasPhase.h
index f00df4451..53d93645e 100644
--- a/Cantera/src/IdealGasPhase.h
+++ b/Cantera/src/IdealGasPhase.h
@@ -178,6 +178,7 @@ namespace Cantera {
          */
         virtual void getActivityConcentrations(doublereal* c) const {
             getConcentrations(c);
+            //for (int k = 0; k < m_kk; k++) if (c[k] < 0.0) c[k] = 0.0;
         }
 
         /**
diff --git a/Cantera/src/converters/ck2ct.cpp b/Cantera/src/converters/ck2ct.cpp
index 946191eb1..1559972c5 100644
--- a/Cantera/src/converters/ck2ct.cpp
+++ b/Cantera/src/converters/ck2ct.cpp
@@ -12,14 +12,7 @@
 #include <iostream>
 #include <string>
 
-// on cygwin, #include <sstream> doesn't work
-#if defined(__CYGWIN__)
-#undef USE_STRINGSTREAM
-#else
-#define USE_STRINGSTREAM
-#endif
-
-#ifdef USE_STRINGSTREAM
+#ifdef HAS_SSTREAM
 #include <sstream>
 #endif
 using namespace std;
@@ -64,7 +57,7 @@ namespace pip {
 	   * somehow. Should probably default to the USE_STRINGSTREAM
 	   * option.
 	   */
-#ifdef USE_STRINGSTREAM
+#ifdef HAS_SSTREAM
 	  /*
 	   * Read a line from the file
 	   */
diff --git a/Cantera/src/zeroD/Reactor.h b/Cantera/src/zeroD/Reactor.h
index 5c9aba71e..b9fb5bae0 100644
--- a/Cantera/src/zeroD/Reactor.h
+++ b/Cantera/src/zeroD/Reactor.h
@@ -21,6 +21,8 @@
 #include "../CVode.h"
 #include "../Kinetics.h"
 
+#define INCL_REACTOR_INTEG
+
 namespace Cantera {
 
     /**
diff --git a/Cantera/src/zeroD/ReactorNet.cpp b/Cantera/src/zeroD/ReactorNet.cpp
index 3918cca74..fd1a8b771 100644
--- a/Cantera/src/zeroD/ReactorNet.cpp
+++ b/Cantera/src/zeroD/ReactorNet.cpp
@@ -5,9 +5,9 @@ namespace Cantera {
 
     ReactorNet::ReactorNet() : FuncEval(), m_nr(0), m_nreactors(0),
                                m_integ(0), m_time(0.0), m_init(false), 
-                               m_nv(0), m_rtol(1.0e-6), m_atols(1.0e-15),
+                               m_nv(0), m_rtol(1.0e-9), m_atols(1.0e-15),
                                m_maxstep(-1.0),
-                               m_verbose(false)
+                               m_verbose(true)
     {
         m_integ = new CVodeInt;
 
@@ -50,7 +50,7 @@ namespace Cantera {
         if (m_verbose) {
             sprintf(buf, "Number of equations: %d\n", neq());
             writelog(buf);
-            sprintf(buf, "Maximum time step:   %g14.6\n", m_maxstep);
+            sprintf(buf, "Maximum time step:   %14.6g\n", m_maxstep);
             writelog(buf);
         }
         m_integ->initialize(t0, *this);
@@ -59,8 +59,8 @@ namespace Cantera {
 
     void ReactorNet::advance(doublereal time) {
         if (!m_init) {
-            if (m_maxstep < 0.0)
-                m_maxstep = time - m_time;
+            //if (m_maxstep < 0.0)
+            m_maxstep = time;// - m_time;
             initialize();
         }
         m_integ->integrate(time);
@@ -70,8 +70,8 @@ namespace Cantera {
 
     double ReactorNet::step(doublereal time) {
         if (!m_init) {
-            if (m_maxstep < 0.0)
-                m_maxstep = time - m_time;
+            //if (m_maxstep < 0.0)
+            m_maxstep = time;// - m_time;
             initialize();
         }
         m_time = m_integ->step(time);
diff --git a/Cantera/src/zeroD/ReactorNet.h b/Cantera/src/zeroD/ReactorNet.h
index b8ef90346..33ee6dc01 100644
--- a/Cantera/src/zeroD/ReactorNet.h
+++ b/Cantera/src/zeroD/ReactorNet.h
@@ -54,8 +54,8 @@ namespace Cantera {
         }
             
         void setTolerances(doublereal rtol, doublereal atol) {
-            m_rtol = rtol;
-            m_atols = atol;
+            if (rtol >= 0.0) m_rtol = rtol;
+            if (atol >= 0.0) m_atols = atol;
             m_init = false;
         }
 
diff --git a/Makefile.in b/Makefile.in
index d6eb70a27..20104880f 100755
--- a/Makefile.in
+++ b/Makefile.in
@@ -245,7 +245,7 @@ depends:
 	endif
 
 changes: 
-	perl cvs2cl.pl --prune
+	cvs2cl.pl --prune
 
 export: changes
 	@INSTALL@ -d $(export_dir)
diff --git a/config.h.in b/config.h.in
index 3e06e669e..43b22a197 100755
--- a/config.h.in
+++ b/config.h.in
@@ -50,7 +50,7 @@ typedef  int          ftnlen;           // Fortran hidden string length type
 // OS X, This used to add some Mac-specific directories to the default
 // data file search path.
 #undef DARWIN
-
+#undef HAS_SSTREAM
 
 //--------- Fonts for reaction path diagrams ----------------------
 #undef RXNPATH_FONT
diff --git a/config/configure b/config/configure
index 044881677..03f80a9c7 100755
--- a/config/configure
+++ b/config/configure
@@ -3167,6 +3167,26 @@ fi
 echo "$as_me:$LINENO: result: ${precompile_headers}" >&5
 echo "${ECHO_T}${precompile_headers}" >&6
 
+has_sstream=no
+echo "$as_me:$LINENO: checking for sstream" >&5
+echo $ECHO_N "checking for sstream... $ECHO_C" >&6
+cat >> teststream.cpp << \EOF
+#include <sstream>
+main() {}
+EOF
+ msg=`$CXX -c testsstream &> /dev/null`
+ if test -f testsstream.o; then
+  has_sstream=yes
+  rm teststream.o
+  cat >>confdefs.h <<\_ACEOF
+#define HAS_SSTREAM 1
+_ACEOF
+
+ fi
+rm teststream.cpp
+echo "$as_me:$LINENO: result: ${has_sstream}" >&5
+echo "${ECHO_T}${has_sstream}" >&6
+
 
 #---------------------------------
 #     Fortran
@@ -3264,7 +3284,7 @@ fi
 
 
 # Provide some information about the compiler.
-echo "$as_me:3267:" \
+echo "$as_me:3287:" \
      "checking for Fortran 77 compiler version" >&5
 ac_compiler=`set X $ac_compile; echo $2`
 { (eval echo "$as_me:$LINENO: \"$ac_compiler --version </dev/null >&5\"") >&5
@@ -3441,7 +3461,7 @@ _ACEOF
 # flags.
 ac_save_FFLAGS=$FFLAGS
 FFLAGS="$FFLAGS $ac_verb"
-(eval echo $as_me:3444: \"$ac_link\") >&5
+(eval echo $as_me:3464: \"$ac_link\") >&5
 ac_f77_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'`
 echo "$ac_f77_v_output" >&5
 FFLAGS=$ac_save_FFLAGS
@@ -3521,7 +3541,7 @@ _ACEOF
 # flags.
 ac_save_FFLAGS=$FFLAGS
 FFLAGS="$FFLAGS $ac_cv_prog_f77_v"
-(eval echo $as_me:3524: \"$ac_link\") >&5
+(eval echo $as_me:3544: \"$ac_link\") >&5
 ac_f77_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'`
 echo "$ac_f77_v_output" >&5
 FFLAGS=$ac_save_FFLAGS
diff --git a/config/configure.in b/config/configure.in
index 3fcc200f3..76f8b2ec8 100755
--- a/config/configure.in
+++ b/config/configure.in
@@ -481,6 +481,21 @@ if test -n "$GCC"; then
 fi
 AC_MSG_RESULT(${precompile_headers})
 
+has_sstream=no
+AC_MSG_CHECKING(for sstream)
+cat >> teststream.cpp << \EOF
+#include <sstream>
+main() {}
+EOF
+ msg=`$CXX -c testsstream &> /dev/null`
+ if test -f testsstream.o; then 
+  has_sstream=yes
+  rm teststream.o
+  AC_DEFINE(HAS_SSTREAM)
+ fi
+rm teststream.cpp
+AC_MSG_RESULT(${has_sstream})
+
 
 #---------------------------------
 #     Fortran
diff --git a/tools/src/finish_install.py.in b/tools/src/finish_install.py.in
index bd5ec8a07..1b696cfc2 100644
--- a/tools/src/finish_install.py.in
+++ b/tools/src/finish_install.py.in
@@ -76,8 +76,8 @@ except:
     ctpath = "-"
 
 fm = open(ctdir+"/ctpath.m","w")
-fm.write("""path(path,'"""+prefix+"""/matlab/toolbox/cantera/cantera')\n""")
-fm.write("""path(path,'"""+prefix+"""/matlab/toolbox/cantera/cantera/1D')\n""")
+fm.write("""path('"""+prefix+"""/matlab/toolbox/cantera/cantera',path)\n""")
+fm.write("""path('"""+prefix+"""/matlab/toolbox/cantera/cantera/1D',path)\n""")
 fm.close()
 
 print """