diff --git a/include/cantera/thermo/IdealGasPhase.h b/include/cantera/thermo/IdealGasPhase.h
index cef7143f6..41b27e6f2 100644
--- a/include/cantera/thermo/IdealGasPhase.h
+++ b/include/cantera/thermo/IdealGasPhase.h
@@ -763,7 +763,7 @@ public:
 
 #ifdef H298MODIFY_CAPABILITY
 
-    virtual void modifyOneHf298SS(const int k, const doublereal Hf298New) {
+    virtual void modifyOneHf298SS(const size_t &k, const doublereal Hf298New) {
         m_spthermo->modifyOneHf298(k, Hf298New);
         m_tlast += 0.0001234;
     }
diff --git a/include/cantera/thermo/LatticePhase.h b/include/cantera/thermo/LatticePhase.h
index eae389309..5e827b577 100644
--- a/include/cantera/thermo/LatticePhase.h
+++ b/include/cantera/thermo/LatticePhase.h
@@ -768,7 +768,7 @@ public:
      *   @param  k           Species k
      *   @param  Hf298New    Specify the new value of the Heat of Formation at 298K and 1 bar
      */
-    virtual void modifyOneHf298SS(const int k, const doublereal Hf298New) {
+    virtual void modifyOneHf298SS(const size_t &k, const doublereal Hf298New) {
         m_spthermo->modifyOneHf298(k, Hf298New);
         m_tlast += 0.0001234;
     }
diff --git a/include/cantera/thermo/PDSS_HKFT.h b/include/cantera/thermo/PDSS_HKFT.h
index 003f6f40e..b55580847 100644
--- a/include/cantera/thermo/PDSS_HKFT.h
+++ b/include/cantera/thermo/PDSS_HKFT.h
@@ -421,7 +421,7 @@ public:
      *                   phase. If none is given, the first XML
      *                   phase element will be used.
      */
-    virtual void initThermoXML(const XML_Node& phaseNode, std::string& id);
+    virtual void initThermoXML(const XML_Node& phaseNode, const std::string& id);
 
     //! Initialize or Reinitialize all shallow pointers in the object
     /*!
diff --git a/include/cantera/thermo/PDSS_Water.h b/include/cantera/thermo/PDSS_Water.h
index 2a71ab99a..b4a3aaf82 100644
--- a/include/cantera/thermo/PDSS_Water.h
+++ b/include/cantera/thermo/PDSS_Water.h
@@ -482,7 +482,7 @@ public:
      *                   phase. If none is given, the first XML
      *                   phase element will be used.
      */
-    virtual void initThermoXML(const XML_Node& phaseNode, std::string& id);
+    virtual void initThermoXML(const XML_Node& phaseNode, const std::string& id);
 
     //@}
 
diff --git a/include/cantera/thermo/SingleSpeciesTP.h b/include/cantera/thermo/SingleSpeciesTP.h
index dc53012e6..41b2b2a93 100644
--- a/include/cantera/thermo/SingleSpeciesTP.h
+++ b/include/cantera/thermo/SingleSpeciesTP.h
@@ -402,7 +402,7 @@ public:
      *   @param  k           Species k
      *   @param  Hf298New    Specify the new value of the Heat of Formation at 298K and 1 bar
      */
-    virtual void modifyOneHf298SS(const int k, const doublereal Hf298New) {
+    virtual void modifyOneHf298SS(const size_t &k, const doublereal Hf298New) {
         m_spthermo->modifyOneHf298(k, Hf298New);
         m_tlast += 0.0001234;
     }
diff --git a/include/cantera/thermo/StoichSubstance.h b/include/cantera/thermo/StoichSubstance.h
index e33d10e64..a9ff97d8b 100644
--- a/include/cantera/thermo/StoichSubstance.h
+++ b/include/cantera/thermo/StoichSubstance.h
@@ -328,7 +328,7 @@ public:
 
 #ifdef H298MODIFY_CAPABILITY
 
-    virtual void modifyOneHf298SS(const int k, const doublereal Hf298New) {
+    virtual void modifyOneHf298SS(const size_t &k, const doublereal Hf298New) {
         m_spthermo->modifyOneHf298(k, Hf298New);
         m_tlast += 0.0001234;
     }
diff --git a/include/cantera/thermo/SurfPhase.h b/include/cantera/thermo/SurfPhase.h
index fd77d7f3b..a5ee4e1b0 100644
--- a/include/cantera/thermo/SurfPhase.h
+++ b/include/cantera/thermo/SurfPhase.h
@@ -536,7 +536,7 @@ public:
      *   @param  k           Species k
      *   @param  Hf298New    Specify the new value of the Heat of Formation at 298K and 1 bar
      */
-    virtual void modifyOneHf298SS(const int k, const doublereal Hf298New) {
+    virtual void modifyOneHf298SS(const size_t &k, const doublereal Hf298New) {
         m_spthermo->modifyOneHf298(k, Hf298New);
         m_tlast += 0.0001234;
     }
diff --git a/include/cantera/thermo/ThermoPhase.h b/include/cantera/thermo/ThermoPhase.h
index 63c4e37e2..b878f3bbd 100644
--- a/include/cantera/thermo/ThermoPhase.h
+++ b/include/cantera/thermo/ThermoPhase.h
@@ -204,7 +204,7 @@ public:
      *   @param  k           Species k
      *   @param  Hf298New    Specify the new value of the Heat of Formation at 298K and 1 bar
      */
-    virtual void modifyOneHf298SS(const int k, const doublereal Hf298New) {
+    virtual void modifyOneHf298SS(const size_t &k, const doublereal Hf298New) {
         m_spthermo->modifyOneHf298(k, Hf298New);
     }
 
diff --git a/include/cantera/thermo/VPStandardStateTP.h b/include/cantera/thermo/VPStandardStateTP.h
index b584ccec3..3574e2622 100644
--- a/include/cantera/thermo/VPStandardStateTP.h
+++ b/include/cantera/thermo/VPStandardStateTP.h
@@ -426,7 +426,7 @@ public:
      *   @param  Hf298New    Specify the new value of the Heat of Formation at 298K and 1 bar.
      *                       units = J/kmol.
      */
-    void modifyOneHf298SS(const int k, const doublereal Hf298New);
+    void modifyOneHf298SS(const size_t &k, const doublereal Hf298New);
 #endif
 
     //!  Returns the vector of nondimensional
diff --git a/include/cantera/transport/PecosTransport.h b/include/cantera/transport/PecosTransport.h
index 6b62843c5..f1e27a22c 100644
--- a/include/cantera/transport/PecosTransport.h
+++ b/include/cantera/transport/PecosTransport.h
@@ -87,7 +87,7 @@ public:
      */
     virtual doublereal thermalConductivity();
 
-    virtual void getBinaryDiffCoeffs(const int ld, doublereal* const d);
+    virtual void getBinaryDiffCoeffs(const size_t ld, doublereal* const d);
 
 
     //! Mixture-averaged diffusion coefficients [m^2/s].
@@ -146,11 +146,11 @@ public:
      *             Flat vector with the m_nsp in the inner loop.
      *             length = ldx * ndim
      */
-    virtual void getSpeciesFluxes(int ndim,
+    virtual void getSpeciesFluxes(size_t ndim,
                                   const doublereal* grad_T,
-                                  int ldx,
+                                  size_t ldx,
                                   const doublereal* grad_X,
-                                  int ldf, doublereal* fluxes);
+                                  size_t ldf, doublereal* fluxes);
 
     //! Initialize the transport object
     /*!
diff --git a/src/thermo/PDSS_HKFT.cpp b/src/thermo/PDSS_HKFT.cpp
index b9c1affe6..bc6f30e62 100644
--- a/src/thermo/PDSS_HKFT.cpp
+++ b/src/thermo/PDSS_HKFT.cpp
@@ -631,7 +631,7 @@ void PDSS_HKFT::initThermo()
 }
 
 
-void PDSS_HKFT::initThermoXML(const XML_Node& phaseNode, std::string& id)
+void PDSS_HKFT::initThermoXML(const XML_Node& phaseNode, const std::string& id)
 {
     PDSS::initThermoXML(phaseNode, id);
 }
diff --git a/src/thermo/PDSS_Water.cpp b/src/thermo/PDSS_Water.cpp
index 0ce2ccb95..d68250ec5 100644
--- a/src/thermo/PDSS_Water.cpp
+++ b/src/thermo/PDSS_Water.cpp
@@ -308,7 +308,7 @@ void PDSS_Water::initThermo()
     PDSS::initThermo();
 }
 
-void PDSS_Water::initThermoXML(const XML_Node& phaseNode, std::string& id)
+void PDSS_Water::initThermoXML(const XML_Node& phaseNode, const std::string& id)
 {
     PDSS::initThermoXML(phaseNode, id);
 }
diff --git a/src/thermo/VPStandardStateTP.cpp b/src/thermo/VPStandardStateTP.cpp
index 7605e85f1..f1fd58e0a 100644
--- a/src/thermo/VPStandardStateTP.cpp
+++ b/src/thermo/VPStandardStateTP.cpp
@@ -228,7 +228,7 @@ void VPStandardStateTP::getEnthalpy_RT(doublereal* hrt) const
  *   @param  k           Species k
  *   @param  Hf298New    Specify the new value of the Heat of Formation at 298K and 1 bar
  */
-void VPStandardStateTP::modifyOneHf298SS(const int k, const doublereal Hf298New)
+void VPStandardStateTP::modifyOneHf298SS(const size_t &k, const doublereal Hf298New)
 {
     m_spthermo->modifyOneHf298(k, Hf298New);
     m_Tlast_ss += 0.0001234;
diff --git a/src/transport/PecosTransport.cpp b/src/transport/PecosTransport.cpp
index 1fe20ede7..225e2da9b 100755
--- a/src/transport/PecosTransport.cpp
+++ b/src/transport/PecosTransport.cpp
@@ -171,7 +171,7 @@ doublereal PecosTransport::viscosity()
  *  Adding more doxygen would be good here
  */
 
-void PecosTransport::getBinaryDiffCoeffs(const int ld, doublereal* const d)
+void PecosTransport::getBinaryDiffCoeffs(const size_t ld, doublereal* const d)
 {
     int i,j;
 
@@ -272,9 +272,9 @@ void PecosTransport::getThermalDiffCoeffs(doublereal* const dt)
  * This is neglective pressure, forced and thermal diffusion.
  *
  */
-void PecosTransport::getSpeciesFluxes(int ndim,
-                                      const doublereal* grad_T, int ldx, const doublereal* grad_X,
-                                      int ldf, doublereal* fluxes)
+void PecosTransport::getSpeciesFluxes(size_t ndim,
+                                      const doublereal* grad_T, size_t ldx, const doublereal* grad_X,
+                                      size_t ldf, doublereal* fluxes)
 {
     int n=0, k;