Fixed erroneous inequality comparisons between size_t and 0

Cantera/src/equil/ChemEquil.cpp

@@ -999,7 +999,7 @@ namespace Cantera {
 	  addLogEntry("element "+ s.elementName(m), fp2str(x[m]));
       }
 
-      if (m_eloc >= 0) {
+      if (m_eloc != npos) {
 	adjustEloc(s, elMolesGoal);
       }
       /*
@@ -1780,7 +1780,7 @@ namespace Cantera {
 	  if (ChemEquil_print_lvl > 0) {
 	    if (lumpSum[m]) {
 	      writelogf("Lump summing row %d, due to rank deficiency analysis\n", m);
-	    } else if (sameAsRow >= 0) {
+	    } else if (sameAsRow != npos) {
 	      writelogf("Identified that rows %d and %d are the same\n", m, sameAsRow);
 	    }
 	  }

Cantera/src/equil/vcs_prob.cpp

@@ -440,7 +440,7 @@ namespace VCSnonideal {
     for (eVP = 0; eVP < volPhase->nElemConstraints(); eVP++) {
       e = volPhase->elemGlobalIndex(eVP);
 #ifdef DEBUG_MODE
-      if (e < 0) {
+      if (e == npos) {
 	exit(EXIT_FAILURE);
       }
 #endif

Cantera/src/equil/vcs_solve.cpp

@@ -318,7 +318,7 @@ namespace VCSnonideal {
       iprintTime = m_timing_print_lvl ;
     }
     
-    if (ifunc < 0 || ifunc > 2) {
+    if (ifunc > 2) {
       plogf("vcs: Unrecognized value of ifunc, %d: bailing!\n",
 	    ifunc);
       return VCS_PUB_BAD;
@@ -649,7 +649,7 @@ namespace VCSnonideal {
       std::vector<size_t> numPhSp(nph, 0);
       for (size_t kspec = 0; kspec < nspecies; kspec++) {
 	size_t iph = pub->PhaseID[kspec];
-	if (iph < 0 || iph >= nph) {
+	if (iph >= nph) {
 	  plogf("%sSpecies to Phase Mapping, PhaseID, has a bad value\n",
 		ser);
 	  plogf("\tPhaseID[%d] = %d\n", kspec, iph);

Cantera/src/equil/vcs_solve_TP.cpp

@@ -2062,7 +2062,7 @@ namespace VCSnonideal {
     double tmp;
     double delta = *delta_ptr;
 #ifdef DEBUG_MODE
-    if (irxn < 0) {
+    if (kspec < m_numComponents) {
 	plogf("  --- delete_species() ERROR: called for a component %d", kspec);
 	plogendl();
 	exit(EXIT_FAILURE);
@@ -3173,7 +3173,7 @@ namespace VCSnonideal {
 		}
 		if ((maxConcPossKspec >= maxConcPoss) || (maxConcPossKspec > 1.0E-5)) {
 		  if (nonZeroesKspec <= minNonZeroes) {
-		    if (kfound < 0 || nonZeroesKspec < minNonZeroes) {
+		    if (kfound == npos || nonZeroesKspec < minNonZeroes) {
 		      kfound = kspec;
 		    } else {
 		      // ok we are sitting pretty equal here decide on the raw ss Gibbs energy
@@ -5073,8 +5073,8 @@ namespace VCSnonideal {
     VCS_SPECIES_THERMO *st_tmp;
     if (k1 == k2) return;
 #ifdef DEBUG_MODE
-    if (k1 < 0 || k1 > (m_numSpeciesTot - 1) ||
+    if (k1 > (m_numSpeciesTot - 1) ||
-	k2 < 0 || k2 > (m_numSpeciesTot - 1)    ) {
+	k2 > (m_numSpeciesTot - 1)    ) {
       plogf("vcs_switch_pos: ifunc = 0: inappropriate args: %d %d\n",
 	    k1, k2);
     }
@@ -5143,8 +5143,8 @@ namespace VCSnonideal {
       i1 = k1 - m_numComponents;
       i2 = k2 - m_numComponents;
 #ifdef DEBUG_MODE
-      if (i1 < 0 || i1 > (m_numRxnTot - 1) ||
+      if (i1 > (m_numRxnTot - 1) ||
-	  i2 < 0 || i2 > (m_numRxnTot - 1)    ) {
+	  i2 > (m_numRxnTot - 1)    ) {
 	plogf("switch_pos: ifunc = 1: inappropriate noncomp values: %d %d\n",
 	      i1 , i2);
       }

Cantera/src/kinetics/ImplicitSurfChem.cpp

@@ -42,7 +42,7 @@ namespace Cantera {
       InterfaceKinetics *kinPtr = k[n];
       m_vecKinPtrs.push_back(kinPtr);
       ns = k[n]->surfacePhaseIndex();
-      if (ns < 0) 
+      if (ns == npos)
 	throw CanteraError("ImplicitSurfChem",
 			   "kinetics manager contains no surface phase");
       m_surfindex.push_back(ns);

Cantera/src/kinetics/InterfaceKinetics.cpp

@@ -1212,7 +1212,7 @@ namespace Cantera {
   //================================================================================================
 
   void InterfaceKinetics::setPhaseExistence(const size_t iphase, const bool exists) {
-    if (iphase < 0 || iphase >= m_thermo.size()) {
+    if (iphase >= m_thermo.size()) {
       throw CanteraError("InterfaceKinetics:setPhaseExistence", "out of bounds");
     }
     if (exists) {

Cantera/src/kinetics/Kinetics.cpp

@@ -153,7 +153,7 @@ namespace Cantera {
    * "<unknown>" is returned. 
    */
   string Kinetics::kineticsSpeciesName(size_t k) const {
-    for (size_t n = m_start.size()-1; n >= 0; n--) {
+    for (size_t n = m_start.size()-1; n != npos; n--) {
       if (k >= m_start[n]) {
 	return thermo(n).speciesName(k - m_start[n]);
       }

Cantera/src/kinetics/ReactionPath.cpp

@@ -845,7 +845,7 @@ namespace Cantera {
         size_t m = m_enamemap[element]-1; //ph.elementIndex(element);
 
         r.element = element;
-        if (m < 0) return -1;
+        if (m == npos) return -1;
 
         s.getFwdRatesOfProgress(DATA_PTR(m_ropf));
         s.getRevRatesOfProgress(DATA_PTR(m_ropr));

Cantera/src/kinetics/solveSP.cpp

@@ -77,7 +77,7 @@ namespace Cantera {
         for (size_t n = 0; n < numPossibleSurfPhases; n++) {
             InterfaceKinetics *m_kin = m_objects[n];
             size_t surfPhaseIndex = m_kin->surfacePhaseIndex();
-            if (surfPhaseIndex >= 0) {
+            if (surfPhaseIndex != npos) {
                 m_numSurfPhases++;
                 m_indexKinObjSurfPhase.push_back(n);
                 m_kinObjPhaseIDSurfPhase.push_back(surfPhaseIndex);

Cantera/src/numerics/BandMatrix.cpp

@@ -87,7 +87,7 @@ namespace Cantera {
         for (m = 0; m < nr; m++) {
             sum = 0.0;
             for (j = m - m_kl; j <= m + m_ku; j++) {
-                if (j >= 0 && j < m_n)
+                if (j < m_n)
                     sum += _value(m,j)*b[j];
             }
             prod[m] = sum;
@@ -105,7 +105,7 @@ namespace Cantera {
         for (n = 0; n < nc; n++) {
             sum = 0.0;
             for (i = n - m_ku; i <= n + m_kl; i++) {
-                if (i >= 0 && i < m_n)
+                if (i < m_n)
                     sum += _value(i,n)*b[i];
             }
             prod[n] = sum;

Cantera/src/oneD/StFlow.cpp

@@ -62,7 +62,7 @@ namespace Cantera {
             knew = newmech.speciesIndex(nm); 
 
             // copy this species from the old to the new solution vectors
-            if (knew >= 0) {
+            if (knew != npos) {
                 for (j = 0; j < points; j++) {
                     newSoln[nv_new*j + 4 + knew] = oldSoln[nv_old*j + 4 + k];
                 }
@@ -364,7 +364,7 @@ namespace Cantera {
 
         // update thermodynamic properties only if a Jacobian is not
         // being evaluated
-        if (jpt < 0) { //if (jpt < 0 || (m_transport_option == c_Multi_Transport)) {
+        if (jpt == npos) { //if (jpt < 0 || (m_transport_option == c_Multi_Transport)) {
             updateThermo(x, j0, j1);
 
             // update transport properties only if a Jacobian is not being
@@ -668,7 +668,7 @@ namespace Cantera {
 
         // update thermodynamic properties only if a Jacobian is not
         // being evaluated
-        if (jpt < 0) {
+        if (jpt == npos) {
             updateThermo(x, j0, j1);
             updateTransport(x, j0, j1);
         }
@@ -1097,7 +1097,7 @@ namespace Cantera {
                 }
                 else goto error;
             }
-            else if (m_thermo->speciesIndex(nm) >= 0) {
+            else if (m_thermo->speciesIndex(nm) != npos) {
                 writelog(nm+"   ");
                 if (x.size() == np) {
                     k = m_thermo->speciesIndex(nm);

Cantera/src/oneD/boundaries1D.cpp

@@ -24,7 +24,7 @@ namespace Cantera {
 
     void Bdry1D::
     _init(size_t n) {
-        if (m_index < 0) {
+        if (m_index == npos) {
             throw CanteraError("Bdry1D", 
                 "install in container before calling init.");
         }

Cantera/src/thermo/Constituents.cpp

@@ -417,7 +417,7 @@ namespace Cantera {
    *      Name of the species with index k
    */
   string Constituents::speciesName(size_t k) const {
-    if (k < 0 || k >= nSpecies()) 
+    if (k >= nSpecies())
       throw SpeciesRangeError("Constituents::speciesName",
 			      k, nSpecies());
     return m_speciesNames[k];

Cantera/src/thermo/Elements.cpp

@@ -318,7 +318,7 @@ namespace Cantera {
     AssertThrowMsg(m_entropy298[m] != ENTROPY298_UNKNOWN,
 		   "Elements::entropy298",
 		   "Entropy at 298 K of element is unknown");
-    AssertTrace(m >= 0 && m < m_mm);
+    AssertTrace(m < m_mm);
     return (m_entropy298[m]);
   }
   

Cantera/src/thermo/IonsFromNeutralVPSSTP.cpp

@@ -772,7 +772,7 @@ namespace Cantera {
 	//! Get the id for the next cation
         icat = cationList_[k];
 	jNeut = fm_invert_ionForNeutral[icat];
-	if (jNeut >= 0) {
+	if (jNeut != npos) {
 	  fmij =  fm_neutralMolec_ions_[icat + jNeut * m_kk];
 	  AssertTrace(fmij != 0.0);
 	  NeutralMolecMoleFractions_[jNeut] += moleFractions_[icat] / fmij;
@@ -885,7 +885,7 @@ namespace Cantera {
 	//! Get the id for the next cation
         icat = cationList_[k];
 	jNeut = fm_invert_ionForNeutral[icat];
-	if (jNeut >= 0) {
+	if (jNeut != npos) {
 	  fmij =  fm_neutralMolec_ions_[icat + jNeut * m_kk];
 	  AssertTrace(fmij != 0.0);
 	  dy[jNeut] += dx[icat] / fmij;

Cantera/src/thermo/SpeciesThermoInterpType.cpp

@@ -153,7 +153,7 @@ namespace Cantera {
 					 doublereal* s_R) const {
     //m_vpssmgr_ptr->setState_T(temp);
     m_PDSS_ptr->setTemperature(temp);
-    AssertThrowMsg(m_speciesIndex >= 0, "STITbyPDSS::updatePropertiesTemp", 
+    AssertThrowMsg(m_speciesIndex != npos, "STITbyPDSS::updatePropertiesTemp",
 		   "object was probably not installed correctly");
     h_RT[m_speciesIndex] = m_PDSS_ptr->enthalpy_RT_ref();
     cp_R[m_speciesIndex] = m_PDSS_ptr->cp_R_ref();

Cantera/src/thermo/ThermoFactory.cpp

@@ -680,7 +680,7 @@ namespace Cantera {
     // otherwise, throw an exception
     map<string,string>::const_iterator _b = comp.begin();
     for (; _b != comp.end(); ++_b) {
-      if (th.elementIndex(_b->first) < 0) {
+      if (th.elementIndex(_b->first) == npos) {
 	if (rule == 0) {
 	  throw CanteraError("installSpecies", 
 			     "Species " + s["name"] + 

Cantera/src/zeroD/FlowDevice.cpp

@@ -46,9 +46,9 @@ namespace CanteraZeroD {
      * species is not present in the upstream mixture.
      */
     doublereal FlowDevice::outletSpeciesMassFlowRate(size_t k) {
-        if (k < 0 || k >= m_nspout) return 0.0;
+        if (k >= m_nspout) return 0.0;
         size_t ki = m_out2in[k];
-        if (ki < 0) return 0.0;
+        if (ki == npos) return 0.0;
         return m_mdot * m_in->massFraction(ki);
     }
 

Cantera/src/zeroD/Reactor.cpp

@@ -357,7 +357,7 @@ 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 >= 0) {
+                if (k != npos) {
                     return k + 2 + m_nsp + walloffset;
                 }
                 else {

apps/bvp/stagnation.cpp

@@ -1043,7 +1043,7 @@ AxiStagnBVP::AxiStagnBVP(igthermo_t* ph, int nsp, int points) :
                 }
                 else goto error;
             }
-            else if (m_thermo->speciesIndex(nm) >= 0) {
+            else if (m_thermo->speciesIndex(nm) != npos) {
                 writelog(nm+"   ");
                 if ((int) x.size() == np) {
                     k = m_thermo->speciesIndex(nm);

tools/testtools/mdp_allo.cpp

@@ -315,11 +315,7 @@ static double *smalloc(size_t n)
   FILE *file;
 #endif
   double *pntr; 
-  if (n < 0) {
+  if (n == 0) pntr = NULL;
-      Fprintf(stderr, "smalloc ERROR: Non-positive argument. (%d)\n", int(n));
-    return NULL;
-  }
-  else if (n == 0) pntr = NULL;
   else {
     n = ((n - 1) / 8);
     n = (n + 1) * 8;