From 1ff7c2386079aa54a8c072e5276c2b1a5e00a793 Mon Sep 17 00:00:00 2001
From: Ray Speth <speth@mit.edu>
Date: Tue, 17 Jan 2012 23:58:48 +0000
Subject: [PATCH] Fixed signed/unsigned equality comparisons

---
 Cantera/clib/src/Storage.cpp                  |  6 +--
 Cantera/src/base/ct_defs.h                    |  2 +
 Cantera/src/base/ctml.cpp                     |  4 +-
 Cantera/src/equil/ChemEquil.cpp               | 10 ++---
 Cantera/src/equil/MultiPhase.cpp              | 10 ++---
 Cantera/src/equil/MultiPhaseEquil.cpp         |  4 +-
 Cantera/src/equil/vcs_Gibbs.cpp               |  2 +-
 Cantera/src/equil/vcs_MultiPhaseEquil.cpp     |  2 +-
 Cantera/src/equil/vcs_VolPhase.cpp            | 12 ++---
 Cantera/src/equil/vcs_elem.cpp                |  2 +-
 Cantera/src/equil/vcs_internal.h              |  1 +
 Cantera/src/equil/vcs_prob.cpp                |  2 +-
 Cantera/src/equil/vcs_solve.h                 |  4 +-
 Cantera/src/equil/vcs_solve_TP.cpp            | 24 +++++-----
 Cantera/src/kinetics/AqueousKinetics.cpp      |  2 +-
 Cantera/src/kinetics/GasKinetics.cpp          |  2 +-
 Cantera/src/kinetics/InterfaceKinetics.cpp    | 10 ++---
 Cantera/src/kinetics/Kinetics.cpp             | 14 +++---
 Cantera/src/kinetics/ReactionPath.cpp         |  6 +--
 Cantera/src/kinetics/importKinetics.cpp       |  4 +-
 Cantera/src/oneD/Domain1D.cpp                 |  6 +--
 Cantera/src/oneD/MultiJac.cpp                 |  2 +-
 Cantera/src/oneD/MultiNewton.cpp              |  4 +-
 Cantera/src/oneD/OneDim.cpp                   |  4 +-
 Cantera/src/oneD/StFlow.cpp                   | 16 +++----
 Cantera/src/oneD/StFlow.h                     | 12 ++---
 Cantera/src/oneD/boundaries1D.cpp             | 14 +++---
 Cantera/src/thermo/ConstDensityThermo.h       |  3 +-
 Cantera/src/thermo/Constituents.cpp           |  2 +-
 Cantera/src/thermo/DebyeHuckel.cpp            |  4 +-
 Cantera/src/thermo/GeneralSpeciesThermo.cpp   |  6 +--
 Cantera/src/thermo/HMWSoln_input.cpp          | 44 +++++++++----------
 Cantera/src/thermo/IdealGasPhase.h            |  3 +-
 Cantera/src/thermo/IdealMolalSoln.cpp         |  2 +-
 Cantera/src/thermo/IdealSolidSolnPhase.cpp    | 13 +++---
 Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp  |  2 +-
 Cantera/src/thermo/MargulesVPSSTP.cpp         |  8 ++--
 Cantera/src/thermo/MineralEQ3.cpp             |  2 +-
 Cantera/src/thermo/MolalityVPSSTP.cpp         | 10 ++---
 Cantera/src/thermo/MolalityVPSSTP.h           |  2 +-
 Cantera/src/thermo/Mu0Poly.cpp                |  8 ++--
 Cantera/src/thermo/NasaThermo.h               | 12 ++---
 Cantera/src/thermo/PDSS_HKFT.cpp              |  2 +-
 Cantera/src/thermo/Phase.cpp                  |  6 +--
 Cantera/src/thermo/PseudoBinaryVPSSTP.cpp     |  2 +-
 Cantera/src/thermo/ShomateThermo.h            | 12 ++---
 Cantera/src/thermo/SimpleThermo.h             | 14 +++---
 Cantera/src/thermo/SpeciesThermoFactory.cpp   |  2 +-
 .../src/thermo/SpeciesThermoInterpType.cpp    |  2 +-
 Cantera/src/thermo/SpeciesThermoInterpType.h  |  2 +-
 Cantera/src/thermo/SpeciesThermoMgr.h         |  4 +-
 Cantera/src/thermo/State.cpp                  |  5 +--
 Cantera/src/thermo/VPSSMgr.cpp                |  6 +--
 Cantera/src/thermo/VPSSMgr_IdealGas.cpp       |  2 +-
 Cantera/src/thermo/VPSSMgr_Water_ConstVol.cpp |  2 +-
 Cantera/src/thermo/WaterSSTP.cpp              |  4 +-
 Cantera/src/transport/TransportFactory.cpp    |  2 +-
 Cantera/src/zeroD/ConstPressureReactor.cpp    |  4 +-
 Cantera/src/zeroD/FlowReactor.cpp             |  2 +-
 Cantera/src/zeroD/Reactor.cpp                 |  4 +-
 Cantera/src/zeroD/Wall.cpp                    |  6 +--
 tools/testtools/tok_input_util.cpp            |  2 +-
 62 files changed, 192 insertions(+), 195 deletions(-)

diff --git a/Cantera/clib/src/Storage.cpp b/Cantera/clib/src/Storage.cpp
index 741598f5d..f6c4db931 100755
--- a/Cantera/clib/src/Storage.cpp
+++ b/Cantera/clib/src/Storage.cpp
@@ -20,7 +20,7 @@ Storage::Storage() {
 Storage::~Storage() { clear(); }
 
 size_t Storage::addThermo(thermo_t* th) {
-    if (th->index() != -1)
+    if (th->index() != npos)
         return th->index();
     __thtable.push_back(th);
     size_t n = __thtable.size() - 1;
@@ -42,7 +42,7 @@ size_t Storage::nThermo() {
 }
 
 size_t Storage::addKinetics(Kinetics* kin) {
-    if (kin->index() != -1)
+    if (kin->index() != npos)
         return kin->index();
     __ktable.push_back(kin);
     size_t n = __ktable.size() - 1;
@@ -51,7 +51,7 @@ size_t Storage::addKinetics(Kinetics* kin) {
 }
 
 size_t Storage::addTransport(Transport* tr) {
-    if (tr->index() != -1)
+    if (tr->index() != npos)
         return tr->index();
     __trtable.push_back(tr);
     size_t n = __trtable.size() - 1;
diff --git a/Cantera/src/base/ct_defs.h b/Cantera/src/base/ct_defs.h
index 08c360b53..a71e6182f 100644
--- a/Cantera/src/base/ct_defs.h
+++ b/Cantera/src/base/ct_defs.h
@@ -225,6 +225,8 @@ namespace Cantera {
   //! typedef for a pointer to temporary work storage which is treated as constant
     typedef const doublereal* const_workPtr;
 
+  //! index returned by functions to indicate "no position"
+  const size_t npos = -1;
 
 }  // namespace
 
diff --git a/Cantera/src/base/ctml.cpp b/Cantera/src/base/ctml.cpp
index 9a3c5411d..12b93347c 100644
--- a/Cantera/src/base/ctml.cpp
+++ b/Cantera/src/base/ctml.cpp
@@ -1149,7 +1149,7 @@ namespace ctml {
 	  break;
 	}
       }
-      if (irow == -1) {
+      if (irow == npos) {
 	throw CanteraError("getMatrixValues","Row not matched by string: "
 			   + key1);		
       }
@@ -1159,7 +1159,7 @@ namespace ctml {
 	  break;
 	}
       }
-      if (icol == -1) {
+      if (icol == npos) {
 	throw CanteraError("getMatrixValues","Col not matched by string: "
 			   + key2);	
       }
diff --git a/Cantera/src/equil/ChemEquil.cpp b/Cantera/src/equil/ChemEquil.cpp
index fbd9b4ff8..005dfcf12 100755
--- a/Cantera/src/equil/ChemEquil.cpp
+++ b/Cantera/src/equil/ChemEquil.cpp
@@ -148,7 +148,7 @@ namespace Cantera {
 	  // if negative atom numbers have already been specified
 	  // for some element other than this one, throw
 	  // an exception
-	  if (mneg != -1 && mneg != m)
+	  if (mneg != npos && mneg != m)
 	    throw CanteraError("ChemEquil::initialize",
 			       "negative atom numbers allowed for only one element"); 
 	  mneg = m;
@@ -1573,7 +1573,7 @@ namespace Cantera {
 	  if (n_i_calc[k] > nCutoff) {
 	    if (fabs(nAtoms(k,m)) > 0.001) {
 	      nSpeciesWithElem++;
-	      if (kMSp != -1) {
+	      if (kMSp != npos) {
 		kMSp2 = k;
 		double factor = fabs(nAtoms(kMSp,m) / nAtoms(kMSp2,m));
 		for (n = 0; n < m_mm; n++) {
@@ -1763,7 +1763,7 @@ namespace Cantera {
        */
       modifiedMatrix = false;
       for (m = 0; m < m_mm; m++) {
-	size_t sameAsRow = -1;
+	size_t sameAsRow = npos;
 	for (size_t im = 0; im < m; im++) {
 	  bool theSame = true;
 	  for (n = 0; n < m_mm; n++) {
@@ -1776,7 +1776,7 @@ namespace Cantera {
 	    sameAsRow = im;
 	  }
 	}
-	if (sameAsRow != -1 || lumpSum[m]) {
+	if (sameAsRow != npos || lumpSum[m]) {
 #ifdef DEBUG_MODE
 	  if (ChemEquil_print_lvl > 0) {
 	    if (lumpSum[m]) {
@@ -1897,7 +1897,7 @@ namespace Cantera {
    *
    */
   void ChemEquil::adjustEloc(thermo_t &s, vector_fp & elMolesGoal) {
-    if (m_eloc == -1) return;
+    if (m_eloc == npos) return;
     if (fabs(elMolesGoal[m_eloc]) > 1.0E-20) return; 
     s.getMoleFractions(DATA_PTR(m_molefractions));
     size_t k;
diff --git a/Cantera/src/equil/MultiPhase.cpp b/Cantera/src/equil/MultiPhase.cpp
index 8edba916c..1d8fe19ec 100644
--- a/Cantera/src/equil/MultiPhase.cpp
+++ b/Cantera/src/equil/MultiPhase.cpp
@@ -144,7 +144,7 @@ namespace Cantera {
 	nsp = p->nSpecies();
 	mlocal = p->elementIndex(sym);    
 	for (kp = 0; kp < nsp; kp++) {
-	  if (mlocal != -1) {
+	  if (mlocal != npos) {
 	    m_atoms(m, k) = p->nAtoms(kp, mlocal);
 	  }
 	  if (m == 0) {
@@ -159,12 +159,12 @@ namespace Cantera {
       }
     }
 
-    if (m_eloc >= 0) {
+    if (m_eloc != npos) {
       doublereal esum;
       for (k = 0; k < m_nsp; k++) {
 	esum = 0.0;
 	for (m = 0; m < m_nel; m++) {
-	  if (int(m) != m_eloc)
+	  if (m != m_eloc)
 	    esum += m_atoms(m,k) * m_atomicNumber[m];
 	}
 	//m_atoms(m_eloc, k) += esum;
@@ -226,11 +226,11 @@ namespace Cantera {
 
   size_t MultiPhase::speciesIndex(std::string speciesName, std::string phaseName) {
     size_t p = phaseIndex(phaseName);
-    if (p == -1) {
+    if (p == npos) {
       throw CanteraError("MultiPhase::speciesIndex", "phase not found: " + phaseName);
     }
     size_t k = m_phase[p]->speciesIndex(speciesName);
-    if (k == -1) {
+    if (k == npos) {
       throw CanteraError("MultiPhase::speciesIndex", "species not found: " + speciesName);
     }
     return m_spstart[p] + k;
diff --git a/Cantera/src/equil/MultiPhaseEquil.cpp b/Cantera/src/equil/MultiPhaseEquil.cpp
index 6c6f5775d..0393fc4bf 100644
--- a/Cantera/src/equil/MultiPhaseEquil.cpp
+++ b/Cantera/src/equil/MultiPhaseEquil.cpp
@@ -460,7 +460,7 @@ namespace Cantera {
         // The left m_nel columns of A are now upper-diagonal.  Now
         // reduce the m_nel columns to diagonal form by back-solving
         for (m = nRows-1; m > 0; m--) {
-            for (size_t n = m-1; n != -1; n--) {
+            for (size_t n = m-1; n != npos; n--) {
                 if (m_A(n,m) != 0.0) {
                     fctr = m_A(n,m);
                     for (k = m; k < m_nsp; k++) {
@@ -828,7 +828,7 @@ namespace Cantera {
             }
             ok = false;
             for (ij = 0; ij < m_nel; ij++) {
-                if (int(k) == m_order[ij]) ok = true;
+                if (k == m_order[ij]) ok = true;
             }
             if (!ok || m_force) {
                 getComponents(m_sortindex);
diff --git a/Cantera/src/equil/vcs_Gibbs.cpp b/Cantera/src/equil/vcs_Gibbs.cpp
index 8d2a36c18..c3e184442 100644
--- a/Cantera/src/equil/vcs_Gibbs.cpp
+++ b/Cantera/src/equil/vcs_Gibbs.cpp
@@ -64,7 +64,7 @@ namespace VCSnonideal {
    * @param w        Species mole number vector
    * @param fe       vector of partial molar free energies of the species.
    */
-  double VCS_SOLVE::vcs_GibbsPhase(int iphase, const double * const w,
+  double VCS_SOLVE::vcs_GibbsPhase(size_t iphase, const double * const w,
 				   const double * const fe) {
 	double g = 0.0;
     double phaseMols = 0.0;
diff --git a/Cantera/src/equil/vcs_MultiPhaseEquil.cpp b/Cantera/src/equil/vcs_MultiPhaseEquil.cpp
index 1377a3054..56a4e0af7 100644
--- a/Cantera/src/equil/vcs_MultiPhaseEquil.cpp
+++ b/Cantera/src/equil/vcs_MultiPhaseEquil.cpp
@@ -1334,7 +1334,7 @@ namespace VCSnonideal {
 
 	kT++;
       }
-      if (volPhase->phiVarIndex() != -1) {
+      if (volPhase->phiVarIndex() != npos) {
 	size_t kphi = volPhase->phiVarIndex();
 	size_t kglob = volPhase->spGlobalIndexVCS(kphi);
 	vprob->w[kglob] = tPhase->electricPotential();
diff --git a/Cantera/src/equil/vcs_VolPhase.cpp b/Cantera/src/equil/vcs_VolPhase.cpp
index 35727d9a3..0dd3fa0c3 100644
--- a/Cantera/src/equil/vcs_VolPhase.cpp
+++ b/Cantera/src/equil/vcs_VolPhase.cpp
@@ -291,7 +291,7 @@ namespace VCSnonideal {
 
     IndSpecies.resize(nspecies, -1);
 
-    if ((int) ListSpeciesPtr.size() >= m_numSpecies) {
+    if (ListSpeciesPtr.size() >= m_numSpecies) {
       for (size_t i = 0; i < m_numSpecies; i++) {
 	if (ListSpeciesPtr[i]) {
 	  delete ListSpeciesPtr[i]; 
@@ -646,7 +646,7 @@ namespace VCSnonideal {
      * Update the electric potential if it is a solution variable
      * in the equation system
      */
-    if (m_phiVarIndex != -1) {
+    if (m_phiVarIndex != npos) {
       kglob = IndSpecies[m_phiVarIndex];
       if (m_numSpecies == 1) {
 	Xmol[m_phiVarIndex] = 1.0;
@@ -1468,7 +1468,7 @@ namespace VCSnonideal {
   size_t vcs_VolPhase::transferElementsFM(const Cantera::ThermoPhase * const tPhase) {
     size_t e, k, eT;
     std::string ename; 
-    size_t eFound = -2;
+    size_t eFound = npos;
     /*
      *
      */
@@ -1492,7 +1492,7 @@ namespace VCSnonideal {
     elemResize(ne);
 
 
-    if (ChargeNeutralityElement != -1) {
+    if (ChargeNeutralityElement != npos) {
       m_elementType[ChargeNeutralityElement] = VCS_ELEM_TYPE_CHARGENEUTRALITY;
     }
 
@@ -1524,7 +1524,7 @@ namespace VCSnonideal {
 	  }
 	}
       }
-      if (eFound == -2) {
+      if (eFound == npos) {
 	eFound = ne;
 	m_elementType[ne] = VCS_ELEM_TYPE_ELECTRONCHARGE;
 	m_elementActive[ne] = 0;
@@ -1568,7 +1568,7 @@ namespace VCSnonideal {
 	fm[e][k] = tPhase->nAtoms(k, eT);
 	e++;
       }
-      if (eFound != -2) {
+      if (eFound != npos) {
 	fm[eFound][k] = - tPhase->charge(k);
       }
     }
diff --git a/Cantera/src/equil/vcs_elem.cpp b/Cantera/src/equil/vcs_elem.cpp
index d880c3b68..b0453d67d 100644
--- a/Cantera/src/equil/vcs_elem.cpp
+++ b/Cantera/src/equil/vcs_elem.cpp
@@ -127,7 +127,7 @@ namespace VCSnonideal {
   /*****************************************************************************/
   /*****************************************************************************/
 
-  void VCS_SOLVE::vcs_elabPhase(int iphase, double * const elemAbundPhase)
+  void VCS_SOLVE::vcs_elabPhase(size_t iphase, double * const elemAbundPhase)
    
     /*************************************************************************
      *
diff --git a/Cantera/src/equil/vcs_internal.h b/Cantera/src/equil/vcs_internal.h
index 33d9e5e59..cc8e12cfb 100644
--- a/Cantera/src/equil/vcs_internal.h
+++ b/Cantera/src/equil/vcs_internal.h
@@ -20,6 +20,7 @@
 #include "global.h"
 
 namespace VCSnonideal {
+  using Cantera::npos;
 
   //! Points to the data in a std::vector<> object
 #define VCS_DATA_PTR(vvv) (&(vvv[0]))
diff --git a/Cantera/src/equil/vcs_prob.cpp b/Cantera/src/equil/vcs_prob.cpp
index 6110b6138..2178e91ef 100644
--- a/Cantera/src/equil/vcs_prob.cpp
+++ b/Cantera/src/equil/vcs_prob.cpp
@@ -376,7 +376,7 @@ namespace VCSnonideal {
 	  foundPos = e;
 	}
       }
-      if (foundPos == -1) {
+      if (foundPos == npos) {
 	int elType = volPhase->elementType(eVP);
 	int elactive = volPhase->elementActive(eVP);
 	e = addElement(enVP.c_str(), elType, elactive);
diff --git a/Cantera/src/equil/vcs_solve.h b/Cantera/src/equil/vcs_solve.h
index 79ec859d0..7f2ce49f3 100644
--- a/Cantera/src/equil/vcs_solve.h
+++ b/Cantera/src/equil/vcs_solve.h
@@ -1012,7 +1012,7 @@ public:
   void vcs_elab();
 
   int vcs_elabcheck(int ibound);
-  void vcs_elabPhase(int iphase, double * const elemAbundPhase);
+  void vcs_elabPhase(size_t iphase, double * const elemAbundPhase);
   int vcs_elcorr(double aa[], double x[]);
 
   
@@ -1054,7 +1054,7 @@ public:
    * @param fe       vector of partial molar free energies of all of the
    *                 species
    */
-  double vcs_GibbsPhase(int iphase, const double * const w,
+  double vcs_GibbsPhase(size_t iphase, const double * const w,
 			const double * const fe);
 
   //! Transfer the results of the equilibrium calculation back to VCS_PROB
diff --git a/Cantera/src/equil/vcs_solve_TP.cpp b/Cantera/src/equil/vcs_solve_TP.cpp
index 09bb1ef28..b1889e929 100644
--- a/Cantera/src/equil/vcs_solve_TP.cpp
+++ b/Cantera/src/equil/vcs_solve_TP.cpp
@@ -107,8 +107,8 @@ namespace VCSnonideal {
     bool justDeletedMultiPhase = false;
     size_t usedZeroedSpecies; /* return flag from basopt indicating that
 			      one of the components had a zero concentration */
-    size_t doPhaseDeleteIph = -1;
-    size_t doPhaseDeleteKspec = -1;
+    size_t doPhaseDeleteIph = npos;
+    size_t doPhaseDeleteKspec = npos;
     vcs_VolPhase *Vphase;
     double     *sc_irxn = NULL;  /* Stoichiometric coefficients for cur rxn  */
     double *dnPhase_irxn;
@@ -395,10 +395,10 @@ namespace VCSnonideal {
      *
      */
     soldel = -1;
-    if (iphasePop != -1) {
+    if (iphasePop != npos) {
       soldel = vcs_popPhaseRxnStepSizes(iphasePop);
       if (soldel == 3) {
-	iphasePop = -1;
+	iphasePop = npos;
 #ifdef DEBUG_MODE
 	if (m_debug_print_lvl >= 2) {
 	  plogf("   --- vcs_popPhaseRxnStepSizes() was called but stoich "
@@ -407,7 +407,7 @@ namespace VCSnonideal {
 #endif
       }
     }
-    if (iphasePop == -1) {
+    if (iphasePop == npos) {
       /*
        * Figure out the new reaction step sizes
        * for the major species (do minor species in the future too)  
@@ -429,8 +429,8 @@ namespace VCSnonideal {
     }
 #endif
     lec = FALSE;
-    doPhaseDeleteIph = -1;
-    doPhaseDeleteKspec = -1;
+    doPhaseDeleteIph = npos;
+    doPhaseDeleteKspec = npos;
     /*
      *    Zero out the net change in moles of multispecies phases 
      */
@@ -486,7 +486,7 @@ namespace VCSnonideal {
 #ifdef DEBUG_MODE
       ANOTE[0] = '\0';	 
 #endif
-      if (iphasePop != -1) {
+      if (iphasePop != npos) {
 	if (iph == iphasePop) {
 	  dx =  m_deltaMolNumSpecies[kspec];
 	  m_molNumSpecies_new[kspec] = m_molNumSpecies_old[kspec] +  m_deltaMolNumSpecies[kspec];
@@ -865,7 +865,7 @@ namespace VCSnonideal {
 	   */
 	  if ((dx != 0.0) && 
 	      (m_molNumSpecies_old[kspec] > 0.0) && 
-	      (doPhaseDeleteIph == -1) && 
+	      (doPhaseDeleteIph == npos) &&
 	      (m_speciesUnknownType[kspec] != VCS_SPECIES_TYPE_INTERFACIALVOLTAGE)) {
 	    double dx_old = dx;
 
@@ -935,7 +935,7 @@ namespace VCSnonideal {
       }
     L_MAIN_LOOP_END_NO_PRINT: ;
 #endif
-      if (doPhaseDeleteIph != -1) {
+      if (doPhaseDeleteIph != npos) {
 	if (DEBUG_MODE_ENABLED && m_debug_print_lvl >= 2) {
 	  plogf("   --- "); 
 	  plogf("%-12.12s Main Loop Special Case deleting phase with species: ",
@@ -1335,7 +1335,7 @@ namespace VCSnonideal {
       for (i = 0; i < m_numRxnRdc; ++i) {
 	l = m_indexRxnToSpecies[i];
 	if (m_speciesUnknownType[l] != VCS_SPECIES_TYPE_INTERFACIALVOLTAGE) {
-	  for (j = m_numComponents - 1; j != -1; j--) {
+	  for (j = m_numComponents - 1; j != npos; j--) {
 	    bool doSwap = false;
 	    if (m_SSPhase[j]) {
 	      doSwap = (m_molNumSpecies_old[l] * m_spSize[l]) > 
@@ -3198,7 +3198,7 @@ namespace VCSnonideal {
 	      }
 	    }
 	  }
-	  if (kfound == -1) {
+	  if (kfound == npos) {
 	    double gmin = 0.0;
 	    kfound = k;
 	    for (kspec = ncTrial; kspec < m_numSpeciesTot; kspec++) {
diff --git a/Cantera/src/kinetics/AqueousKinetics.cpp b/Cantera/src/kinetics/AqueousKinetics.cpp
index 799d90043..e46c6163e 100644
--- a/Cantera/src/kinetics/AqueousKinetics.cpp
+++ b/Cantera/src/kinetics/AqueousKinetics.cpp
@@ -331,7 +331,7 @@ namespace Cantera {
     m_rxnstoich->multiplyRevProducts(&m_conc[0], &ropr[0]); 
     //m_revProductStoich.multiply(m_conc.begin(), ropr.begin());
 
-    for (int j = 0; j != m_ii; ++j) {
+    for (size_t j = 0; j != m_ii; ++j) {
       ropnet[j] = ropf[j] - ropr[j];
     }
 
diff --git a/Cantera/src/kinetics/GasKinetics.cpp b/Cantera/src/kinetics/GasKinetics.cpp
index e707ef212..3feaa7ba2 100644
--- a/Cantera/src/kinetics/GasKinetics.cpp
+++ b/Cantera/src/kinetics/GasKinetics.cpp
@@ -370,7 +370,7 @@ namespace Cantera {
         m_rxnstoich->multiplyRevProducts(&m_conc[0], &ropr[0]); 
         //m_revProductStoich.multiply(m_conc.begin(), ropr.begin());
 
-        for (int j = 0; j != m_ii; ++j) {
+        for (size_t j = 0; j != m_ii; ++j) {
             ropnet[j] = ropf[j] - ropr[j];
         }
 
diff --git a/Cantera/src/kinetics/InterfaceKinetics.cpp b/Cantera/src/kinetics/InterfaceKinetics.cpp
index 5112fd5ef..f51c66fc7 100644
--- a/Cantera/src/kinetics/InterfaceKinetics.cpp
+++ b/Cantera/src/kinetics/InterfaceKinetics.cpp
@@ -318,7 +318,7 @@ namespace Cantera {
 
       for (size_t i = 0; i < m_nrev; i++) {
 	size_t irxn = m_revindex[i];
-	if (irxn == -1 || irxn >= nReactions()) {
+	if (irxn == npos || irxn >= nReactions()) {
 	  throw CanteraError("InterfaceKinetics",
 			     "illegal value: irxn = "+int2str(int(irxn)));
 	}
@@ -1129,8 +1129,8 @@ namespace Cantera {
     Kinetics::finalize();
     m_rwork.resize(nReactions());
     size_t ks = reactionPhaseIndex();
-    if (ks == -1) throw CanteraError("InterfaceKinetics::finalize",
-				     "no surface phase is present.");
+    if (ks == npos) throw CanteraError("InterfaceKinetics::finalize",
+				       "no surface phase is present.");
     m_surf = (SurfPhase*)&thermo(ks);
     if (m_surf->nDim() != 2) 
       throw CanteraError("InterfaceKinetics::finalize",
@@ -1231,8 +1231,8 @@ namespace Cantera {
   void EdgeKinetics::finalize() {
     m_rwork.resize(nReactions());
     size_t ks = reactionPhaseIndex();
-    if (ks == -1) throw CanteraError("EdgeKinetics::finalize",
-				     "no edge phase is present.");
+    if (ks == npos) throw CanteraError("EdgeKinetics::finalize",
+				       "no edge phase is present.");
     m_surf = (SurfPhase*)&thermo(ks);
     if (m_surf->nDim() != 1) 
       throw CanteraError("EdgeKinetics::finalize",
diff --git a/Cantera/src/kinetics/Kinetics.cpp b/Cantera/src/kinetics/Kinetics.cpp
index 3fdd84e32..bb6c512f1 100644
--- a/Cantera/src/kinetics/Kinetics.cpp
+++ b/Cantera/src/kinetics/Kinetics.cpp
@@ -173,9 +173,7 @@ namespace Cantera {
    *  return
    *   - If a match is found, the position in the species list
    *   is returned. 
-   *   - If a specific phase is specified and no match is found,
-   *   the value -1 is returned.
-   *   - If no match is found in any phase, the value -2 is returned.
+   *   - If no match is found, the value -1 (npos) is returned.
    */
   size_t Kinetics::kineticsSpeciesIndex(std::string nm, std::string ph) const {
     size_t np = m_thermo.size();
@@ -185,7 +183,7 @@ namespace Cantera {
       id = thermo(n).id();
       if (ph == id) {
 	k = thermo(n).speciesIndex(nm);
-	if (k == -1) return -1;
+	if (k == npos) return npos;
 	return k + m_start[n];
       }
       else if (ph == "<any>") {
@@ -194,10 +192,10 @@ namespace Cantera {
 	 * ThermoPhase object to find a match.
 	 */
 	k = thermo(n).speciesIndex(nm);
-	if (k != -1) return k + m_start[n];
+	if (k != npos) return k + m_start[n];
       }                    
     }
-    return -2;
+    return npos;
   }
 
   /**
@@ -212,7 +210,7 @@ namespace Cantera {
     string id;
     for (size_t n = 0; n < np; n++) {
       k = thermo(n).speciesIndex(nm);
-      if (k != -1) return thermo(n);
+      if (k != npos) return thermo(n);
     }
     throw CanteraError("speciesPhase", "unknown species "+nm);
     return thermo(0);
@@ -226,7 +224,7 @@ namespace Cantera {
    * species.
    */
   size_t Kinetics::speciesPhaseIndex(size_t k) {
-    for (size_t n = m_start.size()-1; n != -1; n--) {
+    for (size_t n = m_start.size()-1; n != npos; n--) {
       if (k >= m_start[n]) {
 	return n;
       }
diff --git a/Cantera/src/kinetics/ReactionPath.cpp b/Cantera/src/kinetics/ReactionPath.cpp
index a2922ab92..cc8450a67 100644
--- a/Cantera/src/kinetics/ReactionPath.cpp
+++ b/Cantera/src/kinetics/ReactionPath.cpp
@@ -296,7 +296,7 @@ namespace Cantera {
                 {
                     k2 = m_speciesNumber[i2];
                     flx = netFlow(k1, k2);
-                    if (m_local != -1) {
+                    if (m_local != npos) {
                         if (k1 != m_local && k2 != m_local) flx = 0.0;
                     }
                     if (flx != 0.0) 
@@ -383,7 +383,7 @@ namespace Cantera {
             for (size_t i = 0; i < nPaths(); i++) {
                 p = path(i);
                 flxratio = p->flow()/flmax;
-                if (m_local != -1) {
+                if (m_local != npos) {
                     if (p->begin()->number != m_local 
                         && p->end()->number != m_local) flxratio = 0.0;
                 }
@@ -678,7 +678,7 @@ namespace Cantera {
                 size_t nsp = p->nSpecies();
                 size_t mlocal = p->elementIndex(sym);
                 for (size_t kp = 0; kp < nsp; kp++) {
-                    if (mlocal != -1) {
+                    if (mlocal != npos) {
                         m_atoms(k, m) = p->nAtoms(kp, mlocal);
                     }
                     k++;
diff --git a/Cantera/src/kinetics/importKinetics.cpp b/Cantera/src/kinetics/importKinetics.cpp
index 8b5f5e179..986b0b3ac 100644
--- a/Cantera/src/kinetics/importKinetics.cpp
+++ b/Cantera/src/kinetics/importKinetics.cpp
@@ -213,7 +213,7 @@ namespace Cantera {
        * for the species in all phases defined in the kinetics operator. 
        */
       size_t isp = kin.kineticsSpeciesIndex(sp,"<any>");
-      if (isp == -2) {
+      if (isp == npos) {
 	if (rule == 1) 
 	  return false;
 	else {
@@ -1105,7 +1105,7 @@ namespace Cantera {
 
 	  // if no phase with this id has been added to 
 	  //the kinetics manager yet, then add this one
-	  if (kin.phaseIndex(phase_id) == -1) {
+	  if (kin.phaseIndex(phase_id) == npos) {
 	    kin.addPhase(*th[m]);
 	  }
 	}
diff --git a/Cantera/src/oneD/Domain1D.cpp b/Cantera/src/oneD/Domain1D.cpp
index a17fe4abd..c5745d21c 100644
--- a/Cantera/src/oneD/Domain1D.cpp
+++ b/Cantera/src/oneD/Domain1D.cpp
@@ -72,10 +72,10 @@ namespace Cantera {
     eval(size_t jg, doublereal* xg, doublereal* rg,
         integer* mask, doublereal rdt) {
 
-        if (jg != -1 && (jg + 1 < firstPoint() || jg > lastPoint() + 1)) return;
+        if (jg != npos && (jg + 1 < firstPoint() || jg > lastPoint() + 1)) return;
 
         // if evaluating a Jacobian, compute the steady-state residual
-        if (jg != -1) rdt = 0.0;
+        if (jg != npos) rdt = 0.0;
 
         // start of local part of global arrays
         doublereal* x = xg + loc();
@@ -85,7 +85,7 @@ namespace Cantera {
         size_t jmin, jmax, jpt,  j, i;
         jpt = jg - firstPoint();
         
-        if (jg == -1) {      // evaluate all points
+        if (jg == npos) {      // evaluate all points
             jmin = 0;
             jmax = m_points - 1;
         }
diff --git a/Cantera/src/oneD/MultiJac.cpp b/Cantera/src/oneD/MultiJac.cpp
index 3eee1c255..e1824b5f9 100644
--- a/Cantera/src/oneD/MultiJac.cpp
+++ b/Cantera/src/oneD/MultiJac.cpp
@@ -73,7 +73,7 @@ namespace Cantera {
 
                 // compute nth column of Jacobian
                 for (i = j - 1; i <= j+1; i++) {
-                    if (i != -1 && i < m_points) {
+                    if (i != npos && i < m_points) {
                         mv = m_resid->nVars(i);
                         iloc = m_resid->loc(i);
                         for (m = 0; m < mv; m++) {
diff --git a/Cantera/src/oneD/MultiNewton.cpp b/Cantera/src/oneD/MultiNewton.cpp
index ae0e85e50..584b2555d 100644
--- a/Cantera/src/oneD/MultiNewton.cpp
+++ b/Cantera/src/oneD/MultiNewton.cpp
@@ -45,7 +45,7 @@ namespace Cantera {
     "-----------------------------------------------------------------";
 
     const doublereal DampFactor = sqrt(2.0);
-    const int NDAMP = 7;
+    const size_t NDAMP = 7;
 
 
 
@@ -124,7 +124,7 @@ namespace Cantera {
 	    iok--;
 	    size_t nd = r.nDomains();
 	    size_t n;
-	    for (n = nd-1; n != -1; n--)
+	    for (n = nd-1; n != npos; n--)
                 if (iok >= r.start(n)) { break; }
 	    Domain1D& dom = r.domain(n);
 	    size_t offset = iok - r.start(n);
diff --git a/Cantera/src/oneD/OneDim.cpp b/Cantera/src/oneD/OneDim.cpp
index c2b2656d4..bd8de714f 100644
--- a/Cantera/src/oneD/OneDim.cpp
+++ b/Cantera/src/oneD/OneDim.cpp
@@ -165,14 +165,14 @@ namespace Cantera {
 
             // bandwidth of the local block
             bw1 = d->bandwidth();
-            if (bw1 == -1)
+            if (bw1 == npos)
                 bw1 = 2*d->nComponents() - 1;
 
             // bandwidth of the block coupling the first point of this
             // domain to the last point of the previous domain
             if (i > 0) {
                 bw2 = m_dom[i-1]->bandwidth();
-                if (bw2 == -1)
+                if (bw2 == npos)
                     bw2 = m_dom[i-1]->nComponents();
                 bw2 += d->nComponents() - 1;
             }
diff --git a/Cantera/src/oneD/StFlow.cpp b/Cantera/src/oneD/StFlow.cpp
index 87a79bc11..791aca5bc 100644
--- a/Cantera/src/oneD/StFlow.cpp
+++ b/Cantera/src/oneD/StFlow.cpp
@@ -328,10 +328,10 @@ namespace Cantera {
         // if evaluating a Jacobian, and the global point is outside
         // the domain of influence for this domain, then skip
         // evaluating the residual
-        if (jg != -1 && (jg + 1 < firstPoint() || jg > lastPoint() + 1)) return;
+        if (jg != npos && (jg + 1 < firstPoint() || jg > lastPoint() + 1)) return;
 
         // if evaluating a Jacobian, compute the steady-state residual
-        if (jg != -1) rdt = 0.0;
+        if (jg != npos) rdt = 0.0;
 
         // start of local part of global arrays
         doublereal* x = xg + loc();
@@ -341,7 +341,7 @@ namespace Cantera {
         size_t jmin, jmax, jpt;
         jpt = jg - firstPoint();
 
-        if (jg == -1) {      // evaluate all points
+        if (jg == npos) {      // evaluate all points
             jmin = 0;
             jmax = m_points - 1;
         }
@@ -632,10 +632,10 @@ namespace Cantera {
         // if evaluating a Jacobian, and the global point is outside
         // the domain of influence for this domain, then skip
         // evaluating the residual
-        if (jg != -1 && (jg + 1 < firstPoint() || jg > lastPoint() + 1)) return;
+        if (jg != npos && (jg + 1 < firstPoint() || jg > lastPoint() + 1)) return;
 
         // if evaluating a Jacobian, compute the steady-state residual
-        if (jg != -1) rdt = 0.0;
+        if (jg != npos) rdt = 0.0;
 
         // start of local part of global arrays
         doublereal* x = xg + loc();
@@ -645,7 +645,7 @@ namespace Cantera {
         size_t jmin, jmax, jpt;
         jpt = jg - firstPoint();
 
-        if (jg == -1) {      // evaluate all points
+        if (jg == npos) {      // evaluate all points
             jmin = 0;
             jmax = m_points - 1;
         }
@@ -1051,7 +1051,7 @@ namespace Cantera {
             getFloatArray(fa,x,false);
             if (nm == "u") {
                 writelog("axial velocity   ");
-                if ((int) x.size() == np) {
+                if (x.size() == np) {
                     for (j = 0; j < np; j++) {
                         soln[index(0,j)] = x[j];
                     }
@@ -1065,7 +1065,7 @@ namespace Cantera {
             }
             else if (nm == "V") {
                 writelog("radial velocity   ");
-                if ((int) x.size() == np) {
+                if (x.size() == np) {
                     for (j = 0; j < np; j++)
                         soln[index(1,j)] = x[j];
                 }
diff --git a/Cantera/src/oneD/StFlow.h b/Cantera/src/oneD/StFlow.h
index 0a6d239a8..9a205c728 100644
--- a/Cantera/src/oneD/StFlow.h
+++ b/Cantera/src/oneD/StFlow.h
@@ -192,8 +192,8 @@ namespace Cantera {
             needJacUpdate();
         }
 
-        void fixTemperature(int j=-1) {
-            if (j < 0)
+        void fixTemperature(size_t j=npos) {
+            if (j == npos)
                 for (size_t i = 0; i < m_points; i++) {
                     m_do_energy[i] = false;
                 }
@@ -207,8 +207,8 @@ namespace Cantera {
         bool doSpecies(size_t k) { return m_do_species[k]; }
         bool doEnergy(size_t j) { return m_do_energy[j]; }
 
-        void solveSpecies(int k=-1) {
-            if (k == -1) {
+        void solveSpecies(size_t k=npos) {
+            if (k == npos) {
                 for (size_t i = 0; i < m_nsp; i++)
                     m_do_species[i] = true;
             }
@@ -216,8 +216,8 @@ namespace Cantera {
             needJacUpdate();
         }
 
-        void fixSpecies(int k=-1) {
-            if (k == -1) {
+        void fixSpecies(size_t k=npos) {
+            if (k == npos) {
                 for (size_t i = 0; i < m_nsp; i++)
                     m_do_species[i] = false;
             }
diff --git a/Cantera/src/oneD/boundaries1D.cpp b/Cantera/src/oneD/boundaries1D.cpp
index 3651eed44..b18b85c51 100644
--- a/Cantera/src/oneD/boundaries1D.cpp
+++ b/Cantera/src/oneD/boundaries1D.cpp
@@ -158,7 +158,7 @@ namespace Cantera {
     void Inlet1D::
     eval(size_t jg, doublereal* xg, doublereal* rg,
         integer* diagg, doublereal rdt) {
-        if (jg != -1 && (jg + 2 < firstPoint() || jg > lastPoint() + 2)) return;
+        if (jg != npos && (jg + 2 < firstPoint() || jg > lastPoint() + 2)) return;
 
         // start of local part of global arrays
         doublereal* x = xg + loc();
@@ -285,7 +285,7 @@ namespace Cantera {
     void Empty1D::
     eval(size_t jg, doublereal* xg, doublereal* rg,
         integer* diagg, doublereal rdt) {
-        if (jg != -1 && (jg + 2 < firstPoint() || jg > lastPoint() + 2)) return;
+        if (jg != npos && (jg + 2 < firstPoint() || jg > lastPoint() + 2)) return;
 
         // start of local part of global arrays
         doublereal* x = xg + loc();
@@ -343,7 +343,7 @@ namespace Cantera {
     void Symm1D::
     eval(size_t jg, doublereal* xg, doublereal* rg,
         integer* diagg, doublereal rdt) {
-        if (jg != -1 && (jg + 2< firstPoint() || jg > lastPoint() + 2)) return;
+        if (jg != npos && (jg + 2< firstPoint() || jg > lastPoint() + 2)) return;
 
         // start of local part of global arrays
         doublereal* x = xg + loc();
@@ -429,7 +429,7 @@ namespace Cantera {
     void Outlet1D::
     eval(size_t jg, doublereal* xg, doublereal* rg,
         integer* diagg, doublereal rdt) {
-        if (jg != -1 && (jg + 2 < firstPoint() || jg > lastPoint() + 2)) return;
+        if (jg != npos && (jg + 2 < firstPoint() || jg > lastPoint() + 2)) return;
 
         // start of local part of global arrays
         doublereal* x = xg + loc();
@@ -565,7 +565,7 @@ namespace Cantera {
     eval(size_t jg, doublereal* xg, doublereal* rg,
         integer* diagg, doublereal rdt) {
 
-        if (jg != -1 && (jg + 2 < firstPoint() || jg > lastPoint() + 2)) return;
+        if (jg != npos && (jg + 2 < firstPoint() || jg > lastPoint() + 2)) return;
 
         // start of local part of global arrays
         doublereal* x = xg + loc();
@@ -669,7 +669,7 @@ namespace Cantera {
     void Surf1D::
     eval(size_t jg, doublereal* xg, doublereal* rg,
         integer* diagg, doublereal rdt) {
-        if (jg != -1 && (jg + 2 < firstPoint() || jg > lastPoint() + 2)) return;
+        if (jg != npos && (jg + 2 < firstPoint() || jg > lastPoint() + 2)) return;
 
         // start of local part of global arrays
         doublereal* x = xg + loc();
@@ -766,7 +766,7 @@ namespace Cantera {
     void ReactingSurf1D::
     eval(size_t jg, doublereal* xg, doublereal* rg,
         integer* diagg, doublereal rdt) {
-        if (jg != -1 && (jg + 2 < firstPoint() || jg > lastPoint() + 2)) return;
+        if (jg != npos && (jg + 2 < firstPoint() || jg > lastPoint() + 2)) return;
 
         // start of local part of global arrays
         doublereal* x = xg + loc();
diff --git a/Cantera/src/thermo/ConstDensityThermo.h b/Cantera/src/thermo/ConstDensityThermo.h
index 544108fb0..ec9d4ec31 100644
--- a/Cantera/src/thermo/ConstDensityThermo.h
+++ b/Cantera/src/thermo/ConstDensityThermo.h
@@ -285,8 +285,7 @@ namespace Cantera {
     //!  of the solution and the reference pressure for the species.
     const array_fp& expGibbs_RT() const {
       _updateThermo();
-      int k;
-      for (k = 0; k != m_kk; k++) m_expg0_RT[k] = std::exp(m_g0_RT[k]);
+      for (size_t k = 0; k != m_kk; k++) m_expg0_RT[k] = std::exp(m_g0_RT[k]);
       return m_expg0_RT;
     }
 
diff --git a/Cantera/src/thermo/Constituents.cpp b/Cantera/src/thermo/Constituents.cpp
index ec2619643..c906cd44c 100644
--- a/Cantera/src/thermo/Constituents.cpp
+++ b/Cantera/src/thermo/Constituents.cpp
@@ -286,7 +286,7 @@ namespace Cantera {
     const vector_fp &aw = m_Elements->atomicWeights();
     if (charge != 0.0) {
       size_t eindex = m_Elements->elementIndex("E");
-      if (eindex != -1) {
+      if (eindex != npos) {
 	doublereal ecomp = compNew[eindex];
 	if (fabs (charge + ecomp) > 0.001) {
 	  if (ecomp != 0.0) {
diff --git a/Cantera/src/thermo/DebyeHuckel.cpp b/Cantera/src/thermo/DebyeHuckel.cpp
index 899af3d5d..a5c764be3 100644
--- a/Cantera/src/thermo/DebyeHuckel.cpp
+++ b/Cantera/src/thermo/DebyeHuckel.cpp
@@ -1152,7 +1152,7 @@ namespace Cantera {
 	break;
       }
     }
-    if (m_indexSolvent == -1) {
+    if (m_indexSolvent == npos) {
       cout << "DebyeHuckel::initThermoXML: Solvent Name not found" 
 	   << endl;
       throw CanteraError("DebyeHuckel::initThermoXML",
@@ -1484,7 +1484,7 @@ namespace Cantera {
 	    break;
 	  }
 	}
-	if (jmap != -1) {
+	if (jmap != npos) {
 	  const XML_Node& sp = *xspecies[jmap];
 	  if (sp.hasChild("stoichIsMods")) {
 	    double val = getFloat(sp, "stoichIsMods");
diff --git a/Cantera/src/thermo/GeneralSpeciesThermo.cpp b/Cantera/src/thermo/GeneralSpeciesThermo.cpp
index c94a7687f..4457c773c 100644
--- a/Cantera/src/thermo/GeneralSpeciesThermo.cpp
+++ b/Cantera/src/thermo/GeneralSpeciesThermo.cpp
@@ -309,7 +309,7 @@ namespace Cantera {
    * value applies only to the species with that index.
    */
   doublereal GeneralSpeciesThermo::minTemp(size_t k) const {
-    if (k == -1)
+    if (k == npos)
       return m_tlow_max;
     else {
       SpeciesThermoInterpType *sp = m_sp[k];
@@ -321,7 +321,7 @@ namespace Cantera {
   }
 
   doublereal GeneralSpeciesThermo::maxTemp(size_t k) const {
-    if (k == -1) {
+    if (k == npos) {
       return m_thigh_min;
     } else {
       SpeciesThermoInterpType *sp = m_sp[k];
@@ -333,7 +333,7 @@ namespace Cantera {
   }
 
   doublereal GeneralSpeciesThermo::refPressure(size_t k) const {
-    if (k == -1) {
+    if (k == npos) {
       return m_p0;
     } else {
       SpeciesThermoInterpType *sp = m_sp[k];
diff --git a/Cantera/src/thermo/HMWSoln_input.cpp b/Cantera/src/thermo/HMWSoln_input.cpp
index 982fbf557..28f0d213d 100644
--- a/Cantera/src/thermo/HMWSoln_input.cpp
+++ b/Cantera/src/thermo/HMWSoln_input.cpp
@@ -83,7 +83,7 @@ namespace Cantera {
      * an error to not find the species
      */
     size_t iSpecies = speciesIndex(iName);
-    if (iSpecies == -1) {
+    if (iSpecies == npos) {
       return;
     }
     string ispName = speciesName(iSpecies);
@@ -91,7 +91,7 @@ namespace Cantera {
       throw CanteraError("HMWSoln::readXMLBinarySalt", "cation charge problem");
     }
     size_t jSpecies = speciesIndex(jName);
-    if (jSpecies == -1) {
+    if (jSpecies == npos) {
       return;
     }
     string jspName = speciesName(jSpecies);
@@ -289,14 +289,14 @@ namespace Cantera {
      * an error to not find the species
      */
     size_t iSpecies = speciesIndex(ispName);
-    if (iSpecies == -1) {
+    if (iSpecies == npos) {
       return;
     }
     if (charge[iSpecies] >= 0) {
       throw CanteraError("HMWSoln::readXMLThetaAnion", "anion1 charge problem");
     }
     size_t jSpecies = speciesIndex(jspName);
-    if (jSpecies == -1) {
+    if (jSpecies == npos) {
       return;
     }
     if (charge[jSpecies] >= 0) {
@@ -376,14 +376,14 @@ namespace Cantera {
      * an error to not find the species
      */
     size_t iSpecies = speciesIndex(ispName);
-    if (iSpecies == -1) {
+    if (iSpecies == npos) {
       return;
     }
     if (charge[iSpecies] <= 0) {
       throw CanteraError("HMWSoln::readXMLThetaCation", "cation1 charge problem");
     }
     size_t jSpecies = speciesIndex(jspName);
-    if (jSpecies == -1) {
+    if (jSpecies == npos) {
       return;
     }
     if (charge[jSpecies] <= 0) {
@@ -467,7 +467,7 @@ namespace Cantera {
      * an error to not find the species
      */
     size_t kSpecies = speciesIndex(kName);
-    if (kSpecies == -1) {
+    if (kSpecies == npos) {
       return;
     }
     if (charge[kSpecies] <= 0) {
@@ -475,7 +475,7 @@ namespace Cantera {
 			 "cation charge problem");
     }
     size_t iSpecies = speciesIndex(iName);
-    if (iSpecies == -1) {
+    if (iSpecies == npos) {
       return;
     }
     if (charge[iSpecies] >= 0) {
@@ -483,7 +483,7 @@ namespace Cantera {
 			 "anion1 charge problem");
     }
     size_t jSpecies = speciesIndex(jName);
-    if (jSpecies == -1) {
+    if (jSpecies == npos) {
       return;
     }
     if (charge[jSpecies] >= 0) {
@@ -613,14 +613,14 @@ namespace Cantera {
      * an error to not find the species
      */
     size_t kSpecies = speciesIndex(kName);
-    if (kSpecies == -1) {
+    if (kSpecies == npos) {
       return;
     }
     if (charge[kSpecies] >= 0) {
       throw CanteraError("HMWSoln::readXMLPsiCommonAnion", "anion charge problem");
     }
     size_t iSpecies = speciesIndex(iName);
-    if (iSpecies == -1) {
+    if (iSpecies == npos) {
       return;
     }
     if (charge[iSpecies] <= 0) {
@@ -628,7 +628,7 @@ namespace Cantera {
 			 "cation1 charge problem");
     }
     size_t jSpecies = speciesIndex(jName);
-    if (jSpecies == -1) {
+    if (jSpecies == npos) {
       return;
     }
     if (charge[jSpecies] <= 0) {
@@ -759,7 +759,7 @@ namespace Cantera {
      * an error to not find the species
      */
     size_t iSpecies = speciesIndex(iName);
-    if (iSpecies == -1) {
+    if (iSpecies == npos) {
       return;
     }
     if (charge[iSpecies] != 0) {
@@ -767,7 +767,7 @@ namespace Cantera {
 			 "neutral charge problem");
     }
     size_t jSpecies = speciesIndex(jName);
-    if (jSpecies == -1) {
+    if (jSpecies == npos) {
       return;
     }
 	
@@ -842,7 +842,7 @@ namespace Cantera {
      * an error to not find the species
      */
     size_t iSpecies = speciesIndex(iName);
-    if (iSpecies == -1) {
+    if (iSpecies == npos) {
       return;
     }
     if (charge[iSpecies] != 0) {
@@ -928,7 +928,7 @@ namespace Cantera {
      * an error to not find the species
      */
     size_t iSpecies = speciesIndex(iName);
-    if (iSpecies == -1) {
+    if (iSpecies == npos) {
       return;
     }
     if (charge[iSpecies] != 0.0) {
@@ -936,7 +936,7 @@ namespace Cantera {
     }
  
     size_t jSpecies = speciesIndex(jName);
-    if (jSpecies == -1) {
+    if (jSpecies == npos) {
       return;
     }
     if (charge[jSpecies] <= 0.0) {
@@ -944,7 +944,7 @@ namespace Cantera {
     }
 
     size_t kSpecies = speciesIndex(kName);
-    if (kSpecies == -1) {
+    if (kSpecies == npos) {
       return;
     }
     if (charge[kSpecies] >= 0.0) {
@@ -1307,7 +1307,7 @@ namespace Cantera {
 	break;
       }
     }
-    if (m_indexSolvent == -1) {
+    if (m_indexSolvent == npos) {
       std::cout << "HMWSoln::initThermo: Solvent Name not found" 
 		<< std::endl;
       throw CanteraError("HMWSoln::initThermoXML",
@@ -1503,7 +1503,7 @@ namespace Cantera {
 	    break;
 	  }
 	}
-	if (jmap != -1) {
+	if (jmap != npos) {
 	  const XML_Node& sp = *xspecies[jmap];
 	  getOptionalFloat(sp, "stoichIsMods",  m_speciesCharge_Stoich[k]);
 	  // if (sp.hasChild("stoichIsMods")) {
@@ -1525,7 +1525,7 @@ namespace Cantera {
 	  map<string,string>::const_iterator _b = msIs.begin();
 	  for (; _b != msIs.end(); ++_b) {
 	    size_t kk = speciesIndex(_b->first);
-	    if (kk != -1) {
+	    if (kk != npos) {
 	      double val = fpValue(_b->second);
 	      m_speciesCharge_Stoich[kk] = val;
 	    }
@@ -1625,7 +1625,7 @@ namespace Cantera {
 	map<string,string>::const_iterator _b = msEST.begin();
 	for (; _b != msEST.end(); ++_b) {
 	  size_t kk = speciesIndex(_b->first);
-	  if (kk != -1) {
+	  if (kk != npos) {
 	    string est = _b->second;
 	    if ((m_electrolyteSpeciesType[kk] = interp_est(est))  == -1) {
 	      throw CanteraError("HMWSoln::initThermoXML",
diff --git a/Cantera/src/thermo/IdealGasPhase.h b/Cantera/src/thermo/IdealGasPhase.h
index 4e5c350a0..5eab5089f 100644
--- a/Cantera/src/thermo/IdealGasPhase.h
+++ b/Cantera/src/thermo/IdealGasPhase.h
@@ -806,8 +806,7 @@ namespace Cantera {
      */
     const array_fp& expGibbs_RT_ref() const {
       _updateThermo();
-      int k;
-      for (k = 0; k != m_kk; k++) m_expg0_RT[k] = std::exp(m_g0_RT[k]);
+      for (size_t k = 0; k != m_kk; k++) m_expg0_RT[k] = std::exp(m_g0_RT[k]);
       return m_expg0_RT;
     }
 
diff --git a/Cantera/src/thermo/IdealMolalSoln.cpp b/Cantera/src/thermo/IdealMolalSoln.cpp
index d268c2659..ee2d4a975 100644
--- a/Cantera/src/thermo/IdealMolalSoln.cpp
+++ b/Cantera/src/thermo/IdealMolalSoln.cpp
@@ -1023,7 +1023,7 @@ namespace Cantera {
 	break;
       }
     }
-    if (m_indexSolvent == -1) {
+    if (m_indexSolvent == npos) {
       std::cout << "IdealMolalSoln::initThermo: Solvent Name not found" 
 	   << std::endl;
       throw CanteraError("IdealMolalSoln::initThermo",
diff --git a/Cantera/src/thermo/IdealSolidSolnPhase.cpp b/Cantera/src/thermo/IdealSolidSolnPhase.cpp
index b17a07a92..bdcdb0b03 100644
--- a/Cantera/src/thermo/IdealSolidSolnPhase.cpp
+++ b/Cantera/src/thermo/IdealSolidSolnPhase.cpp
@@ -906,7 +906,7 @@ namespace Cantera {
    */
   void IdealSolidSolnPhase::getEnthalpy_RT_ref(doublereal *hrt) const {
     _updateThermo();
-    for (int k = 0; k != m_kk; k++) {
+    for (size_t k = 0; k != m_kk; k++) {
       hrt[k] = m_h0_RT[k];
     }
   }
@@ -919,7 +919,7 @@ namespace Cantera {
    */
   void IdealSolidSolnPhase::getGibbs_RT_ref(doublereal *grt) const {
     _updateThermo();
-    for (int k = 0; k != m_kk; k++) {
+    for (size_t k = 0; k != m_kk; k++) {
       grt[k] = m_g0_RT[k];
     }
   }
@@ -933,7 +933,7 @@ namespace Cantera {
   void IdealSolidSolnPhase::getGibbs_ref(doublereal *g) const {
     _updateThermo();
     double tmp = GasConstant * temperature();
-    for (int k = 0; k != m_kk; k++) {
+    for (size_t k = 0; k != m_kk; k++) {
       g[k] = tmp * m_g0_RT[k];
     }
   }
@@ -960,7 +960,7 @@ namespace Cantera {
    */
   void IdealSolidSolnPhase::getEntropy_R_ref(doublereal *er) const {
     _updateThermo();
-    for (int k = 0; k != m_kk; k++) {
+    for (size_t k = 0; k != m_kk; k++) {
       er[k] = m_s0_R[k];
     }
   }
@@ -973,7 +973,7 @@ namespace Cantera {
    */
   void IdealSolidSolnPhase::getCp_R_ref(doublereal *cpr) const {
     _updateThermo();
-    for (int k = 0; k != m_kk; k++) {
+    for (size_t k = 0; k != m_kk; k++) {
       cpr[k] = m_cp0_R[k];
     }
   }
@@ -999,8 +999,7 @@ namespace Cantera {
    */
   const array_fp& IdealSolidSolnPhase::expGibbs_RT_ref() const {
     _updateThermo();
-    int k;
-    for (k = 0; k != m_kk; k++) m_expg0_RT[k] = exp(m_g0_RT[k]);
+    for (size_t k = 0; k != m_kk; k++) m_expg0_RT[k] = exp(m_g0_RT[k]);
     return m_expg0_RT;
   }
 
diff --git a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp
index b9dffbd4a..2bf665842 100644
--- a/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp
+++ b/Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp
@@ -881,7 +881,7 @@ namespace Cantera {
       break;
 
     case cIonSolnType_SINGLEANION:
-      for (size_t k = 0; k < (int) cationList_.size(); k++) {
+      for (size_t k = 0; k < cationList_.size(); k++) {
 	//! Get the id for the next cation
         icat = cationList_[k];
 	jNeut = fm_invert_ionForNeutral[icat];
diff --git a/Cantera/src/thermo/MargulesVPSSTP.cpp b/Cantera/src/thermo/MargulesVPSSTP.cpp
index b62619e5d..a5ac704fe 100644
--- a/Cantera/src/thermo/MargulesVPSSTP.cpp
+++ b/Cantera/src/thermo/MargulesVPSSTP.cpp
@@ -178,7 +178,7 @@ namespace Cantera {
     
 
     size_t iLiCl = speciesIndex("LiCl(L)");
-    if (iLiCl == -1) {
+    if (iLiCl == npos) {
       throw CanteraError("MargulesVPSSTP test1 constructor",
 			 "Unable to find LiCl(L)");
     }
@@ -186,7 +186,7 @@ namespace Cantera {
 
 
     size_t iKCl = speciesIndex("KCl(L)");
-    if (iKCl == -1) {
+    if (iKCl == npos) {
       throw CanteraError("MargulesVPSSTP test1 constructor",
 			 "Unable to find KCl(L)");
     }
@@ -974,7 +974,7 @@ namespace Cantera {
      * an error to not find the species
      */
     size_t iSpecies = speciesIndex(iName);
-    if (iSpecies == -1) {
+    if (iSpecies == npos) {
       return;
     }
     string ispName = speciesName(iSpecies);
@@ -982,7 +982,7 @@ namespace Cantera {
       throw CanteraError("MargulesVPSSTP::readXMLBinarySpecies", "speciesA charge problem");
     }
     size_t jSpecies = speciesIndex(jName);
-    if (jSpecies == -1) {
+    if (jSpecies == npos) {
       return;
     }
     string jspName = speciesName(jSpecies);
diff --git a/Cantera/src/thermo/MineralEQ3.cpp b/Cantera/src/thermo/MineralEQ3.cpp
index 859ca948b..bfb3aaec7 100644
--- a/Cantera/src/thermo/MineralEQ3.cpp
+++ b/Cantera/src/thermo/MineralEQ3.cpp
@@ -540,7 +540,7 @@ namespace Cantera {
     return -1.0;
 #else
     size_t iE = elementIndex(elemName);
-    if (iE == -1) {
+    if (iE == npos) {
       throw CanteraError("PDSS_HKFT::LookupGe", "element " + elemName + " not found");
     }
     doublereal geValue = entropyElement298(iE);
diff --git a/Cantera/src/thermo/MolalityVPSSTP.cpp b/Cantera/src/thermo/MolalityVPSSTP.cpp
index d44ac1220..0243aec0c 100644
--- a/Cantera/src/thermo/MolalityVPSSTP.cpp
+++ b/Cantera/src/thermo/MolalityVPSSTP.cpp
@@ -700,7 +700,7 @@ namespace Cantera {
       }
     }
     // We have failed if we can't find the Cl element index
-    if (eCl == -1) {
+    if (eCl == npos) {
       return -1;
     }
     for (size_t e = 0; e < ne; e++) {
@@ -711,8 +711,8 @@ namespace Cantera {
       }
     }
     // We have failed if we can't find the E element index
-    if (eE == -1) {
-      return -1;
+    if (eE == npos) {
+      return npos;
     }
     for (size_t k = 1; k < m_kk; k++) {
       doublereal nCl = nAtoms(k, eCl);
@@ -816,7 +816,7 @@ namespace Cantera {
       getActivities(&actMolal[0]);
  
       size_t iHp = speciesIndex("H+");
-      if (iHp != -1) {
+      if (iHp != npos) {
 	double pH = -log(actMolal[iHp]) / log(10.0);
 	sprintf(p, "                pH    %12.4g  \n", pH);
 	s += p;
@@ -964,7 +964,7 @@ namespace Cantera {
 	pNames.push_back("Molal Activity");
 	data.push_back(temp);
 	size_t iHp = speciesIndex("H+");
-	if (iHp != -1) {
+	if (iHp != npos) {
 	  double pH = -log(temp[iHp]) / log(10.0);
 	  csvFile << setw(tabL) << "pH = " << setw(tabS) << pH << endl;
 	}
diff --git a/Cantera/src/thermo/MolalityVPSSTP.h b/Cantera/src/thermo/MolalityVPSSTP.h
index 699187573..63e60eb89 100644
--- a/Cantera/src/thermo/MolalityVPSSTP.h
+++ b/Cantera/src/thermo/MolalityVPSSTP.h
@@ -855,7 +855,7 @@ namespace Cantera {
     /*!
      * Currently the index of the solvent is hard-coded to the value 0
      */
-    int        m_indexSolvent;
+    size_t m_indexSolvent;
 
     //! Scaling to be used for output of single-ion species activity
     //! coefficients.
diff --git a/Cantera/src/thermo/Mu0Poly.cpp b/Cantera/src/thermo/Mu0Poly.cpp
index a44b6f45f..9bf738e9d 100644
--- a/Cantera/src/thermo/Mu0Poly.cpp
+++ b/Cantera/src/thermo/Mu0Poly.cpp
@@ -198,7 +198,7 @@ namespace Cantera {
       h298 = getFloat(Mu0Node, "H298", "actEnergy");
     }
 
-    int numPoints = 1;
+    size_t numPoints = 1;
     if (Mu0Node.hasChild("numPoints")) {
       numPoints = getInteger(Mu0Node, "numPoints");
     }
@@ -248,7 +248,7 @@ namespace Cantera {
      * Fix up dimensionless Mu0 values if input
      */
     if (dimensionlessMu0Values) {
-      for (int i = 0; i < numPoints; i++) {
+      for (size_t i = 0; i < numPoints; i++) {
 	cValues[i] *= cTemperatures[i] / 273.15;
       }
     }
@@ -258,7 +258,7 @@ namespace Cantera {
      
     c[0] = numPoints;
     c[1] = h298;
-    for (int i = 0; i < numPoints; i++) {
+    for (size_t i = 0; i < numPoints; i++) {
       c[2+i*2]   = cTemperatures[i];
       c[2+i*2+1] = cValues[i];
     }
@@ -365,7 +365,7 @@ namespace Cantera {
       mu2 = m_mu0_R_int[iT298];
       m_h0_R_int[iT298] = m_H298;
       m_s0_R_int[iT298] = - (mu2 - m_h0_R_int[iT298]) / T2;
-      for (i = iT298 - 1; i != -1; i--) {
+      for (i = iT298 - 1; i != npos; i--) {
 	T1      = m_t0_int[i];
 	mu1     = m_mu0_R_int[i];
 	T2      = m_t0_int[i+1];
diff --git a/Cantera/src/thermo/NasaThermo.h b/Cantera/src/thermo/NasaThermo.h
index 79a2581b9..7df61a86b 100644
--- a/Cantera/src/thermo/NasaThermo.h
+++ b/Cantera/src/thermo/NasaThermo.h
@@ -194,7 +194,7 @@ namespace Cantera {
 
       if (tlow > m_tlow_max)    m_tlow_max = tlow;
       if (thigh < m_thigh_min)  m_thigh_min = thigh;
-      if ((int) m_tlow.size() < index + 1) {
+      if (m_tlow.size() < index + 1) {
 	m_tlow.resize(index + 1,  tlow);
 	m_thigh.resize(index + 1, thigh);
       }
@@ -313,8 +313,8 @@ namespace Cantera {
      *
      * @param k    Species index
      */ 
-    virtual doublereal minTemp(size_t k=-1) const {
-      if (k == -1)
+    virtual doublereal minTemp(size_t k=npos) const {
+      if (k == npos)
 	return m_tlow_max;
       else
 	return m_tlow[k];
@@ -330,8 +330,8 @@ namespace Cantera {
      *
      * @param k Species index
      */
-    virtual doublereal maxTemp(size_t k=-1) const {
-      if (k == -1)
+    virtual doublereal maxTemp(size_t k=npos) const {
+      if (k == npos)
 	return m_thigh_min;
       else
 	return m_thigh[k];
@@ -350,7 +350,7 @@ namespace Cantera {
      *
      * @param k Species index
      */
-    virtual doublereal refPressure(size_t k = -1) const {
+    virtual doublereal refPressure(size_t k=npos) const {
       return m_p0;
     }
 
diff --git a/Cantera/src/thermo/PDSS_HKFT.cpp b/Cantera/src/thermo/PDSS_HKFT.cpp
index d4bb8081a..5fb2ba722 100644
--- a/Cantera/src/thermo/PDSS_HKFT.cpp
+++ b/Cantera/src/thermo/PDSS_HKFT.cpp
@@ -1215,7 +1215,7 @@ namespace Cantera {
     return -1.0;
 #else
     size_t iE = m_tp->elementIndex(elemName);
-    if (iE == -1) {
+    if (iE == npos) {
       throw CanteraError("PDSS_HKFT::LookupGe", "element " + elemName + " not found");
     }
     doublereal geValue = m_tp->entropyElement298(iE);
diff --git a/Cantera/src/thermo/Phase.cpp b/Cantera/src/thermo/Phase.cpp
index 0c4534693..1503a73c3 100644
--- a/Cantera/src/thermo/Phase.cpp
+++ b/Cantera/src/thermo/Phase.cpp
@@ -147,7 +147,7 @@ namespace Cantera {
   }
 
   void Phase::restoreState(size_t lenstate, const doublereal* state) {
-    if (int(lenstate) >= nSpecies() + 2) {
+    if (lenstate >= nSpecies() + 2) {
       setMassFractions_NoNorm(state + 2);
       setTemperature(state[0]);
       setDensity(state[1]);
@@ -312,7 +312,7 @@ namespace Cantera {
 
   doublereal Phase::moleFraction(std::string name) const {
     size_t iloc = speciesIndex(name);
-    if (iloc != -1) return State::moleFraction(iloc);
+    if (iloc != npos) return State::moleFraction(iloc);
     else return 0.0;
   }
 
@@ -322,7 +322,7 @@ namespace Cantera {
 
   doublereal Phase::massFraction(std::string name) const {
     size_t iloc = speciesIndex(name);
-    if (iloc != -1) return massFractions()[iloc];
+    if (iloc != npos) return massFractions()[iloc];
     else return 0.0;
   }
 
diff --git a/Cantera/src/thermo/PseudoBinaryVPSSTP.cpp b/Cantera/src/thermo/PseudoBinaryVPSSTP.cpp
index dec1be676..7927e26b5 100644
--- a/Cantera/src/thermo/PseudoBinaryVPSSTP.cpp
+++ b/Cantera/src/thermo/PseudoBinaryVPSSTP.cpp
@@ -179,7 +179,7 @@ namespace Cantera {
       for (k = 0; k < m_kk; k++) {
 	moleFractionsTmp_[k] = moleFractions_[k];
       }
-      for (k = 0; k < (int) cationList_.size(); k++) {
+      for (k = 0; k < cationList_.size(); k++) {
 	sumCat += moleFractions_[cationList_[k]];
       }
       sumAnion =  moleFractions_[anionList_[k]];
diff --git a/Cantera/src/thermo/ShomateThermo.h b/Cantera/src/thermo/ShomateThermo.h
index d959af4f6..8f529d2b3 100644
--- a/Cantera/src/thermo/ShomateThermo.h
+++ b/Cantera/src/thermo/ShomateThermo.h
@@ -188,7 +188,7 @@ namespace Cantera {
       if (tlow > m_tlow_max)    m_tlow_max = tlow;
       if (thigh < m_thigh_min)  m_thigh_min = thigh;
 
-      if ((int) m_tlow.size() < index + 1) {
+      if (m_tlow.size() < index + 1) {
 	m_tlow.resize(index + 1,  tlow);
 	m_thigh.resize(index + 1, thigh);
       }
@@ -311,8 +311,8 @@ namespace Cantera {
      *
      * @param k    Species index
      */ 
-    virtual doublereal minTemp(size_t k=-1) const {
-      if (k == -1)
+    virtual doublereal minTemp(size_t k=npos) const {
+      if (k == npos)
 	return m_tlow_max;
       else
 	return m_tlow[k];
@@ -328,8 +328,8 @@ namespace Cantera {
      *
      * @param k  species index
      */
-    virtual doublereal maxTemp(size_t k=-1) const {
-      if (k == -1)
+    virtual doublereal maxTemp(size_t k=npos) const {
+      if (k == npos)
 	return m_thigh_min;
       else
 	return m_thigh[k];
@@ -348,7 +348,7 @@ namespace Cantera {
      *
      * @param k species index
      */
-    virtual doublereal refPressure(size_t k=-1) const {
+    virtual doublereal refPressure(size_t k=npos) const {
       return m_p0;
     }
 
diff --git a/Cantera/src/thermo/SimpleThermo.h b/Cantera/src/thermo/SimpleThermo.h
index 14c4b8648..c67455fe5 100644
--- a/Cantera/src/thermo/SimpleThermo.h
+++ b/Cantera/src/thermo/SimpleThermo.h
@@ -164,7 +164,7 @@ namespace Cantera {
       if (tlow > m_tlow_max)    m_tlow_max = tlow;
       if (thigh < m_thigh_min)  m_thigh_min = thigh;
      
-      if ((int) m_tlow.size() < index + 1) {
+      if (m_tlow.size() < index + 1) {
 	m_tlow.resize(index + 1,  tlow);
 	m_thigh.resize(index + 1, thigh);
       }
@@ -253,8 +253,8 @@ namespace Cantera {
      *
      * @param k    Species index
      */ 
-    virtual doublereal minTemp(size_t k=-1) const {
-      if (k == -1)
+    virtual doublereal minTemp(size_t k=npos) const {
+      if (k == npos)
 	return m_tlow_max;
       else
 	return m_tlow[m_loc[k]];
@@ -270,8 +270,8 @@ namespace Cantera {
      *
      * @param k  Species Index
      */
-    virtual doublereal maxTemp(size_t k=-1) const {
-      if (k == -1)
+    virtual doublereal maxTemp(size_t k=npos) const {
+      if (k == npos)
 	return m_thigh_min;
       else
 	return m_thigh[m_loc[k]];
@@ -290,7 +290,7 @@ namespace Cantera {
      *
      * @param k Species Index
      */
-    virtual doublereal refPressure(size_t k=-1) const {return m_p0;}
+    virtual doublereal refPressure(size_t k=npos) const {return m_p0;}
 
     //! This utility function reports the type of parameterization
     //! used for the species with index number index.
@@ -344,7 +344,7 @@ namespace Cantera {
      */
     virtual void modifyParams(size_t index, doublereal *c) {
       size_t loc = m_loc[index];
-      if (loc == -1) {
+      if (loc == npos) {
 	throw CanteraError("SimpleThermo::modifyParams",
 			   "modifying parameters for species which hasn't been set yet");
       }
diff --git a/Cantera/src/thermo/SpeciesThermoFactory.cpp b/Cantera/src/thermo/SpeciesThermoFactory.cpp
index 410dceef5..57a0ae7ca 100644
--- a/Cantera/src/thermo/SpeciesThermoFactory.cpp
+++ b/Cantera/src/thermo/SpeciesThermoFactory.cpp
@@ -445,7 +445,7 @@ namespace Cantera {
     return -1.0;
 #else
     size_t iE = th_ptr->elementIndex(elemName);
-    if (iE == -1) {
+    if (iE == npos) {
       throw CanteraError("PDSS_HKFT::LookupGe", "element " + elemName + " not found");
     }
     doublereal geValue = th_ptr->entropyElement298(iE);
diff --git a/Cantera/src/thermo/SpeciesThermoInterpType.cpp b/Cantera/src/thermo/SpeciesThermoInterpType.cpp
index c7adc6d51..0e98a949d 100644
--- a/Cantera/src/thermo/SpeciesThermoInterpType.cpp
+++ b/Cantera/src/thermo/SpeciesThermoInterpType.cpp
@@ -72,7 +72,7 @@ namespace Cantera {
   }
 
 
-  void STITbyPDSS::initAllPtrs(int speciesIndex, VPSSMgr *vpssmgr_ptr, PDSS *PDSS_ptr) {
+  void STITbyPDSS::initAllPtrs(size_t speciesIndex, VPSSMgr *vpssmgr_ptr, PDSS *PDSS_ptr) {
     AssertThrow(speciesIndex == m_speciesIndex, "STITbyPDSS::initAllPtrs internal confusion");
     m_vpssmgr_ptr = vpssmgr_ptr;
     m_PDSS_ptr = PDSS_ptr;
diff --git a/Cantera/src/thermo/SpeciesThermoInterpType.h b/Cantera/src/thermo/SpeciesThermoInterpType.h
index 30be1b764..e0858e577 100644
--- a/Cantera/src/thermo/SpeciesThermoInterpType.h
+++ b/Cantera/src/thermo/SpeciesThermoInterpType.h
@@ -347,7 +347,7 @@ namespace Cantera {
      *  @param PDSS_ptr     Pointer to the PDSS object that handles calls for this object
      *
      */
-    void initAllPtrs(int speciesIndex, VPSSMgr *vpssmgr_ptr, PDSS *PDSS_ptr);
+    void initAllPtrs(size_t speciesIndex, VPSSMgr *vpssmgr_ptr, PDSS *PDSS_ptr);
 
     //! Returns the minimum temperature that the thermo
     //! parameterization is valid
diff --git a/Cantera/src/thermo/SpeciesThermoMgr.h b/Cantera/src/thermo/SpeciesThermoMgr.h
index 38a4bffc5..0c94dc6f3 100644
--- a/Cantera/src/thermo/SpeciesThermoMgr.h
+++ b/Cantera/src/thermo/SpeciesThermoMgr.h
@@ -715,7 +715,7 @@ namespace Cantera {
   template<class SPM>
   doublereal 
   SpeciesThermo1<SPM>::minTemp(size_t k) const {
-    if (k == -1)
+    if (k == npos)
       return _minTemp(m_thermo.begin(), m_thermo.end());
     else
       return m_thermo[k].minTemp();
@@ -724,7 +724,7 @@ namespace Cantera {
   template<class SPM>
   doublereal 
   SpeciesThermo1<SPM>::maxTemp(size_t k) const {
-    if (k == -1)
+    if (k == npos)
       return _maxTemp(m_thermo.begin(), m_thermo.end());
     else
       return m_thermo[k].maxTemp();
diff --git a/Cantera/src/thermo/State.cpp b/Cantera/src/thermo/State.cpp
index 47cdda2bd..acde8ec2e 100644
--- a/Cantera/src/thermo/State.cpp
+++ b/Cantera/src/thermo/State.cpp
@@ -193,16 +193,15 @@ namespace Cantera {
   }
 
   void State::setConcentrations(const doublereal* const conc) {
-    int k;
     doublereal sum = 0.0, norm = 0.0;
-    for (k = 0; k != m_kk; ++k) {
+    for (size_t k = 0; k != m_kk; ++k) {
       sum += conc[k]*m_molwts[k];
       norm += conc[k];
     }
     m_mmw = sum/norm;
     setDensity(sum);
     doublereal rsum = 1.0/sum;
-    for (k = 0; k != m_kk; ++k) {
+    for (size_t k = 0; k != m_kk; ++k) {
       m_ym[k] = conc[k] * rsum;
       m_y[k] =  m_ym[k] * m_molwts[k];
     }
diff --git a/Cantera/src/thermo/VPSSMgr.cpp b/Cantera/src/thermo/VPSSMgr.cpp
index a90f0d7ba..6bd985829 100644
--- a/Cantera/src/thermo/VPSSMgr.cpp
+++ b/Cantera/src/thermo/VPSSMgr.cpp
@@ -429,7 +429,7 @@ namespace Cantera {
 
  /*****************************************************************/
   doublereal VPSSMgr::minTemp(size_t k) const {
-    if (k != -1) {
+    if (k != npos) {
       const PDSS *kPDSS = m_vptp_ptr->providePDSS(k);
       return kPDSS->minTemp();
     }
@@ -437,7 +437,7 @@ namespace Cantera {
   }
 
  doublereal VPSSMgr::maxTemp(size_t k) const {
-    if (k != -1) {
+    if (k != npos) {
       const PDSS *kPDSS = m_vptp_ptr->providePDSS(k);
       return kPDSS->maxTemp();
     }
@@ -445,7 +445,7 @@ namespace Cantera {
   }
 
   doublereal VPSSMgr::refPressure(size_t k) const {
-    if (k != -1) {
+    if (k != npos) {
       const PDSS *kPDSS = m_vptp_ptr->providePDSS(k);
       return kPDSS->refPressure();
     }
diff --git a/Cantera/src/thermo/VPSSMgr_IdealGas.cpp b/Cantera/src/thermo/VPSSMgr_IdealGas.cpp
index 409af3ee0..75622b2fa 100644
--- a/Cantera/src/thermo/VPSSMgr_IdealGas.cpp
+++ b/Cantera/src/thermo/VPSSMgr_IdealGas.cpp
@@ -101,7 +101,7 @@ namespace Cantera {
 			   "ideal_gas: " + speciesNode.name());
       }
     }
-    if ((int) m_Vss.size() < k+1) {
+    if (m_Vss.size() < k+1) {
       m_Vss.resize(k+1, 0.0);
     }
 
diff --git a/Cantera/src/thermo/VPSSMgr_Water_ConstVol.cpp b/Cantera/src/thermo/VPSSMgr_Water_ConstVol.cpp
index bb0f0bedf..1a0f661ea 100644
--- a/Cantera/src/thermo/VPSSMgr_Water_ConstVol.cpp
+++ b/Cantera/src/thermo/VPSSMgr_Water_ConstVol.cpp
@@ -286,7 +286,7 @@ namespace Cantera {
 			   "standardState model for species isn't "
 			   "constant_incompressible: " + speciesNode.name());
       }
-      if ((int) m_Vss.size() < k+1) {
+      if (m_Vss.size() < k+1) {
 	m_Vss.resize(k+1, 0.0);
       }
       m_Vss[k] = getFloat(*ss, "molarVolume", "toSI");
diff --git a/Cantera/src/thermo/WaterSSTP.cpp b/Cantera/src/thermo/WaterSSTP.cpp
index e99bd74a6..bdd596e19 100644
--- a/Cantera/src/thermo/WaterSSTP.cpp
+++ b/Cantera/src/thermo/WaterSSTP.cpp
@@ -213,13 +213,13 @@ namespace Cantera {
      * a consistent H2O molecular weight based on that.
      */
     size_t nH = elementIndex("H");
-    if (nH == -1) {
+    if (nH == npos) {
       throw CanteraError("WaterSSTP::initThermo",
 			 "H not an element");
     }
     double mw_H = atomicWeight(nH);
     size_t nO = elementIndex("O");
-    if (nO == -1) {
+    if (nO == npos) {
       throw CanteraError("WaterSSTP::initThermo",
 			 "O not an element");
     }
diff --git a/Cantera/src/transport/TransportFactory.cpp b/Cantera/src/transport/TransportFactory.cpp
index 21d303587..7bca50e46 100644
--- a/Cantera/src/transport/TransportFactory.cpp
+++ b/Cantera/src/transport/TransportFactory.cpp
@@ -1116,7 +1116,7 @@ namespace Cantera {
     char s[100];
 #endif
     // number of points to use in generating fit data
-    const int np = 50;
+    const size_t np = 50;
 
     int mode = tr.mode_;
     int degree = (mode == CK_Mode ? 3 : 4);
diff --git a/Cantera/src/zeroD/ConstPressureReactor.cpp b/Cantera/src/zeroD/ConstPressureReactor.cpp
index 4ca0b984b..098ab4619 100644
--- a/Cantera/src/zeroD/ConstPressureReactor.cpp
+++ b/Cantera/src/zeroD/ConstPressureReactor.cpp
@@ -281,7 +281,7 @@ namespace CanteraZeroD {
         if (nm == "V") return 1;
         // check for a gas species name
         size_t k = m_thermo->speciesIndex(nm);
-        if (k != -1) return k + 2;
+        if (k != npos) return k + 2;
 
         // check for a wall species
         size_t walloffset = 0, kp = 0;
@@ -291,7 +291,7 @@ namespace CanteraZeroD {
                 kp = m_wall[m]->kinetics(m_lr[m])->reactionPhaseIndex();
                 th = &m_wall[m]->kinetics(m_lr[m])->thermo(kp);
                 k = th->speciesIndex(nm);
-                if (k != -1) {
+                if (k != npos) {
                     return k + 2 + m_nsp + walloffset;
                 }
                 else {
diff --git a/Cantera/src/zeroD/FlowReactor.cpp b/Cantera/src/zeroD/FlowReactor.cpp
index 5b46dd01f..322a1628d 100644
--- a/Cantera/src/zeroD/FlowReactor.cpp
+++ b/Cantera/src/zeroD/FlowReactor.cpp
@@ -132,7 +132,7 @@ namespace CanteraZeroD {
         if (nm == "U") return 1;
         // check for a gas species name
         size_t k = m_thermo->speciesIndex(nm);
-        if (k != -1) return k + 2;
+        if (k != npos) return k + 2;
         else return -1;
     }
 
diff --git a/Cantera/src/zeroD/Reactor.cpp b/Cantera/src/zeroD/Reactor.cpp
index 1d57c4337..10961e0a3 100644
--- a/Cantera/src/zeroD/Reactor.cpp
+++ b/Cantera/src/zeroD/Reactor.cpp
@@ -107,7 +107,7 @@ namespace CanteraZeroD {
     }
     
     size_t Reactor::nSensParams() {
-        if (m_nsens == -1) {
+        if (m_nsens == npos) {
             // determine the number of sensitivity parameters
             size_t m, ns;
             m_nsens = m_pnum.size();
@@ -347,7 +347,7 @@ namespace CanteraZeroD {
         if (nm == "V") return 1;
         // check for a gas species name
         size_t k = m_thermo->speciesIndex(nm);
-        if (k != -1) return k + 2;
+        if (k != npos) return k + 2;
 
         // check for a wall species
         size_t walloffset = 0, kp = 0;
diff --git a/Cantera/src/zeroD/Wall.cpp b/Cantera/src/zeroD/Wall.cpp
index 476f43fa1..f80cd42a0 100644
--- a/Cantera/src/zeroD/Wall.cpp
+++ b/Cantera/src/zeroD/Wall.cpp
@@ -43,7 +43,7 @@ namespace CanteraZeroD {
         size_t ileft = 0, iright = 0;
         if (left) {
             ileft = left->surfacePhaseIndex();
-            if (ileft != -1) {
+            if (ileft != npos) {
                 m_surf[0] = (SurfPhase*)&left->thermo(ileft);
                 m_nsp[0] = m_surf[0]->nSpecies();
                 m_leftcov.resize(m_nsp[0]);
@@ -52,14 +52,14 @@ namespace CanteraZeroD {
         }
         if (right) {
             iright = right->surfacePhaseIndex();
-            if (iright != -1) {
+            if (iright != npos) {
                 m_surf[1] = (SurfPhase*)&right->thermo(iright);
                 m_nsp[1] = m_surf[1]->nSpecies();
                 m_rightcov.resize(m_nsp[1]);
                 m_surf[1]->getCoverages(DATA_PTR(m_rightcov));
             }
         }
-        if (ileft == -1 || iright == -1) {
+        if (ileft == npos || iright == npos) {
             throw CanteraError("Wall::setKinetics",
                 "specified surface kinetics manager does not "
                 "represent a surface reaction mechanism.");
diff --git a/tools/testtools/tok_input_util.cpp b/tools/testtools/tok_input_util.cpp
index c9dbb721b..9c358165b 100644
--- a/tools/testtools/tok_input_util.cpp
+++ b/tools/testtools/tok_input_util.cpp
@@ -1539,7 +1539,7 @@ void strip_item_from_token(int iword, TOKEN *tok)
   size_t i = ioffset;
   size_t j = ioffset + ilength;
 #endif
-  if (j <= (int) strlen(tok->orig_str)) {
+  if (j <= strlen(tok->orig_str)) {
     while(tok->orig_str[j] != '\0') {
       tok->orig_str[i] = tok->orig_str[j];
       i++;