STYLE: Code clean-up

src/thermophysicalModels/chemistryModel/chemistryModel/TDACChemistryModel/TDACChemistryModel.C

@@ -405,13 +405,15 @@ void Foam::TDACChemistryModel<CompType, ThermoType>::jacobian
     // but according to the informations of the complete set
     // (i.e. for the third-body efficiencies)
 
-    const scalar T = c[this->nSpecie_];
-    const scalar p = c[this->nSpecie_ + 1];
+    const label nSpecie = this->nSpecie_;
+
+    const scalar T = c[nSpecie];
+    const scalar p = c[nSpecie + 1];
 
     if (reduced)
     {
         this->c_ = completeC_;
-        for (label i=0; i<NsDAC_; i++)
+        for (label i=0; i<NsDAC_; ++i)
         {
             this->c_[simplifiedToCompleteIndex_[i]] = max(0.0, c[i]);
         }
@@ -557,20 +559,19 @@ void Foam::TDACChemistryModel<CompType, ThermoType>::jacobian
     const scalar delta = 1e-3;
 
     omega(this->c_, T + delta, p, this->dcdt_);
-    for (label i=0; i<this->nSpecie_; i++)
+    for (label i=0; i<nSpecie; ++i)
     {
-        dfdc(i, this->nSpecie_) = this->dcdt_[i];
+        dfdc(i, nSpecie) = this->dcdt_[i];
     }
 
     omega(this->c_, T - delta, p, this->dcdt_);
-    for (label i=0; i<this->nSpecie_; i++)
+    for (label i=0; i<nSpecie; ++i)
     {
-        dfdc(i, this->nSpecie_) =
-            0.5*(dfdc(i, this->nSpecie_) - this->dcdt_[i])/delta;
+        dfdc(i, nSpecie) = 0.5*(dfdc(i, nSpecie) - this->dcdt_[i])/delta;
     }
 
-    dfdc(this->nSpecie_, this->nSpecie_) = 0;
-    dfdc(this->nSpecie_ + 1, this->nSpecie_) = 0;
+    dfdc(nSpecie, nSpecie) = 0;
+    dfdc(nSpecie + 1, nSpecie) = 0;
 }
 
 
@@ -666,12 +667,13 @@ Foam::scalar Foam::TDACChemistryModel<CompType, ThermoType>::solve
 
         for (label i=0; i<this->nSpecie_; i++)
         {
-            c[i] = rhoi*this->Y_[i][celli]/this->specieThermo_[i].W();
+            const volScalarField& Yi = this->Y_[i];
+            c[i] = rhoi*Yi[celli]/this->specieThermo_[i].W();
             c0[i] = c[i];
-            phiq[i] = this->Y()[i][celli];
+            phiq[i] = Yi[celli];
         }
-        phiq[this->nSpecie()]=Ti;
-        phiq[this->nSpecie() + 1]=pi;
+        phiq[this->nSpecie()] = Ti;
+        phiq[this->nSpecie() + 1] = pi;
         if (tabulation_->variableTimeStep())
         {
             phiq[this->nSpecie() + 2] = deltaT[celli];
@@ -692,7 +694,7 @@ Foam::scalar Foam::TDACChemistryModel<CompType, ThermoType>::solve
         if (tabulation_->active() && tabulation_->retrieve(phiq, Rphiq))
         {
             // Retrieved solution stored in Rphiq
-            for (label i=0; i<this->nSpecie(); i++)
+            for (label i=0; i<this->nSpecie(); ++i)
             {
                 c[i] = rhoi*Rphiq[i]/this->specieThermo_[i].W();
             }
@@ -713,7 +715,7 @@ Foam::scalar Foam::TDACChemistryModel<CompType, ThermoType>::solve
                 // Reduce mechanism change the number of species (only active)
                 mechRed_->reduceMechanism(c, Ti, pi);
                 nActiveSpecies += mechRed_->NsSimp();
-                nAvg++;
+                ++nAvg;
                 scalar timeIncr = clockTime_.timeIncrement();
                 reduceMechCpuTime_ += timeIncr;
                 timeTmp += timeIncr;
@@ -735,7 +737,7 @@ Foam::scalar Foam::TDACChemistryModel<CompType, ThermoType>::solve
                         simplifiedC_, Ti, pi, dt, this->deltaTChem_[celli]
                     );
 
-                    for (label i=0; i<NsDAC_; i++)
+                    for (label i=0; i<NsDAC_; ++i)
                     {
                         c[simplifiedToCompleteIndex_[i]] = simplifiedC_[i];
                     }
@@ -774,6 +776,7 @@ Foam::scalar Foam::TDACChemistryModel<CompType, ThermoType>::solve
                 }
                 label growOrAdd =
                     tabulation_->add(phiq, Rphiq, rhoi, deltaT[celli]);
+
                 if (growOrAdd)
                 {
                     this->setTabulationResultsAdd(celli);
@@ -797,7 +800,7 @@ Foam::scalar Foam::TDACChemistryModel<CompType, ThermoType>::solve
         }
 
         // Set the RR vector (used in the solver)
-        for (label i=0; i<this->nSpecie_; i++)
+        for (label i=0; i<this->nSpecie_; ++i)
         {
             this->RR_[i][celli] =
                 (c[i] - c0[i])*this->specieThermo_[i].W()/deltaT[celli];

src/thermophysicalModels/chemistryModel/chemistryModel/TDACChemistryModel/TDACChemistryModelI.H

@@ -168,9 +168,9 @@ Foam::TDACChemistryModel<CompType, ThermoType>::specieComp()
 template<class CompType, class ThermoType>
 void Foam::TDACChemistryModel<CompType, ThermoType>::resetTabulationResults()
 {
-    forAll(tabulationResults_, tabi)
+    for (auto& res : tabulationResults_)
     {
-        tabulationResults_[tabi] = 2;
+        res = 2;
     }
 }
 

src/thermophysicalModels/chemistryModel/chemistryModel/TDACChemistryModel/reduction/DAC/DAC.C

@@ -253,7 +253,7 @@ void Foam::chemistryReductionMethods::DAC<CompType, ThermoType>::reduceMechanism
 {
     scalarField& completeC(this->chemistry_.completeC());
     scalarField c1(this->chemistry_.nEqns(), 0.0);
-    for(label i=0; i<this->nSpecie_; i++)
+    for (label i=0; i<this->nSpecie_; i++)
     {
         c1[i] = c[i];
         completeC[i] = c[i];
@@ -276,9 +276,8 @@ void Foam::chemistryReductionMethods::DAC<CompType, ThermoType>::reduceMechanism
 
     scalar pf, cf, pr, cr;
     label lRef, rRef;
-    forAll(this->chemistry_.reactions(), i)
+    for (const Reaction<ThermoType>& R : this->chemistry_.reactions())
     {
-        const Reaction<ThermoType>& R = this->chemistry_.reactions()[i];
         // for each reaction compute omegai
         scalar omegai = this->chemistry_.omega
         (
@@ -511,7 +510,7 @@ void Foam::chemistryReductionMethods::DAC<CompType, ThermoType>::reduceMechanism
 
     // Set all species to inactive and activate them according
     // to rAB and initial set
-    for (label i=0; i<this->nSpecie_; i++)
+    for (label i=0; i<this->nSpecie_; ++i)
     {
         this->activeSpecies_[i] = false;
     }
@@ -530,19 +529,19 @@ void Foam::chemistryReductionMethods::DAC<CompType, ThermoType>::reduceMechanism
             // When phiLarge and phiProgress >= phiTol then
             // CO, HO2 and fuel are in the SIS
             Q.push(COId_);
-            speciesNumber++;
+            ++speciesNumber;
             this->activeSpecies_[COId_] = true;
             Rvalue[COId_] = 1.0;
             Q.push(HO2Id_);
-            speciesNumber++;
+            ++speciesNumber;
             this->activeSpecies_[HO2Id_] = true;
             Rvalue[HO2Id_] = 1.0;
-            forAll(fuelSpeciesID_,i)
+            for (const label fuelId : fuelSpeciesID_)
             {
-                Q.push(fuelSpeciesID_[i]);
-                speciesNumber++;
-                this->activeSpecies_[fuelSpeciesID_[i]] = true;
-                Rvalue[fuelSpeciesID_[i]] = 1.0;
+                Q.push(fuelId);
+                ++speciesNumber;
+                this->activeSpecies_[fuelId] = true;
+                Rvalue[fuelId] = 1.0;
             }
 
         }
@@ -551,22 +550,22 @@ void Foam::chemistryReductionMethods::DAC<CompType, ThermoType>::reduceMechanism
             // When phiLarge < phiTol and phiProgress >= phiTol then
             // CO, HO2 are in the SIS
             Q.push(COId_);
-            speciesNumber++;
+            ++speciesNumber;
             this->activeSpecies_[COId_] = true;
             Rvalue[COId_] = 1.0;
             Q.push(HO2Id_);
-            speciesNumber++;
+            ++speciesNumber;
             this->activeSpecies_[HO2Id_] = true;
             Rvalue[HO2Id_] = 1.0;
 
             if (forceFuelInclusion_)
             {
-                forAll(fuelSpeciesID_, i)
+                for (const label fuelId : fuelSpeciesID_)
                 {
-                    Q.push(fuelSpeciesID_[i]);
-                    speciesNumber++;
-                    this->activeSpecies_[fuelSpeciesID_[i]] = true;
-                    Rvalue[fuelSpeciesID_[i]] = 1.0;
+                    Q.push(fuelId);
+                    ++speciesNumber;
+                    this->activeSpecies_[fuelId] = true;
+                    Rvalue[fuelId] = 1.0;
                 }
             }
         }
@@ -585,12 +584,12 @@ void Foam::chemistryReductionMethods::DAC<CompType, ThermoType>::reduceMechanism
             Rvalue[H2OId_] = 1.0;
             if (forceFuelInclusion_)
             {
-                forAll(fuelSpeciesID_, i)
+                for (const label fuelId : fuelSpeciesID_)
                 {
-                    Q.push(fuelSpeciesID_[i]);
-                    speciesNumber++;
-                    this->activeSpecies_[fuelSpeciesID_[i]] = true;
-                    Rvalue[fuelSpeciesID_[i]] = 1.0;
+                    Q.push(fuelId);
+                    ++speciesNumber;
+                    this->activeSpecies_[fuelId] = true;
+                    Rvalue[fuelId] = 1.0;
                 }
             }
         }
@@ -598,7 +597,7 @@ void Foam::chemistryReductionMethods::DAC<CompType, ThermoType>::reduceMechanism
         if (T > NOxThreshold_ && NOId_ != -1)
         {
             Q.push(NOId_);
-            speciesNumber++;
+            ++speciesNumber;
             this->activeSpecies_[NOId_] = true;
             Rvalue[NOId_] = 1.0;
         }
@@ -609,7 +608,7 @@ void Foam::chemistryReductionMethods::DAC<CompType, ThermoType>::reduceMechanism
         {
             label q = SIS[i];
             this->activeSpecies_[q] = true;
-            speciesNumber++;
+            ++speciesNumber;
             Q.push(q);
             Rvalue[q] = 1.0;
         }
@@ -620,18 +619,23 @@ void Foam::chemistryReductionMethods::DAC<CompType, ThermoType>::reduceMechanism
     {
         label u = Q.pop();
         scalar Den = max(PA[u], CA[u]);
-        if (Den!=0.0)
+        if (Den != 0.0)
         {
-            for (label v=0; v<NbrABInit[u]; v++)
+            for (label v=0; v<NbrABInit[u]; ++v)
             {
                 label otherSpec = rABOtherSpec(u, v);
                 scalar rAB = mag(rABNum(u, v))/Den;
-                if (rAB>1)
+
+                if (rAB > 1)
                 {
                     Info<< "Badly Conditioned rAB : " << rAB
-                        << "species involved : "<<u << "," << otherSpec << endl;
-                    rAB=1.0;
+                    << " for species : "
+                    << this->chemistry_.Y()[u].name() << ","
+                    << this->chemistry_.Y()[otherSpec].name()
+                    << endl;
+                    rAB = 1.0;
                 }
+
                 // The direct link is weaker than the user-defined tolerance
                 if (rAB >= this->tolerance())
                 {
@@ -646,7 +650,7 @@ void Foam::chemistryReductionMethods::DAC<CompType, ThermoType>::reduceMechanism
                         if (!this->activeSpecies_[otherSpec])
                         {
                             this->activeSpecies_[otherSpec] = true;
-                            speciesNumber++;
+                            ++speciesNumber;
                         }
                     }
                 }

src/thermophysicalModels/chemistryModel/chemistryModel/TDACChemistryModel/reduction/DRG/DRG.C

@@ -105,8 +105,8 @@ void Foam::chemistryReductionMethods::DRG<CompType, ThermoType>::reduceMechanism
         // For each reaction compute omegai
         scalar omegai = this->chemistry_.omega
         (
-         R, c1, T, p, pf, cf, lRef, pr, cr, rRef
-         );
+            R, c1, T, p, pf, cf, lRef, pr, cr, rRef
+        );
 
 
         // Then for each pair of species composing this reaction,
@@ -253,12 +253,14 @@ void Foam::chemistryReductionMethods::DRG<CompType, ThermoType>::reduceMechanism
                 label otherSpec = rABOtherSpec(u, v);
                 scalar rAB = rABNum(u, v)/Den;
 
-                if (rAB>1)
+                if (rAB > 1)
                 {
                     Info<< "Badly Conditioned rAB : " << rAB
-                        << "species involved : " << u << "," << otherSpec
-                        << endl;
-                    rAB = 1;
+                    << " for species : "
+                    << this->chemistry_.Y()[u].name() << ","
+                    << this->chemistry_.Y()[otherSpec].name()
+                    << endl;
+                    rAB = 1.0;
                 }
 
                 // Include B only if rAB is above the tolerance and if the

src/thermophysicalModels/chemistryModel/chemistryModel/TDACChemistryModel/reduction/DRGEP/DRGEP.C

@@ -37,25 +37,25 @@ Foam::chemistryReductionMethods::DRGEP<CompType, ThermoType>::DRGEP
 :
     chemistryReductionMethod<CompType, ThermoType>(dict, chemistry),
     searchInitSet_(this->coeffsDict_.subDict("initialSet").size()),
-    sC_(this->nSpecie_,0),
-    sH_(this->nSpecie_,0),
-    sO_(this->nSpecie_,0),
-    sN_(this->nSpecie_,0),
+    sC_(this->nSpecie_, 0),
+    sH_(this->nSpecie_, 0),
+    sO_(this->nSpecie_, 0),
+    sN_(this->nSpecie_, 0),
     NGroupBased_(50)
 {
-    label j=0;
+    label j = 0;
     dictionary initSet = this->coeffsDict_.subDict("initialSet");
-    for (label i=0; i<chemistry.nSpecie(); i++)
+    for (label i=0; i<chemistry.nSpecie(); ++i)
     {
         if (initSet.found(chemistry.Y()[i].name()))
         {
-            searchInitSet_[j++]=i;
+            searchInitSet_[j++] = i;
         }
     }
     if (j<searchInitSet_.size())
     {
         FatalErrorInFunction
-            << searchInitSet_.size()-j
+            << searchInitSet_.size() - j
             << " species in the intial set is not in the mechanism "
             << initSet
             << exit(FatalError);
@@ -68,15 +68,14 @@ Foam::chemistryReductionMethods::DRGEP<CompType, ThermoType>::DRGEP
 
     const List<List<specieElement>>& specieComposition =
         this->chemistry_.specieComp();
-    for (label i=0; i<this->nSpecie_; i++)
+
+    for (label i=0; i<this->nSpecie_; ++i)
     {
-        const List<specieElement>& curSpecieComposition =
-            specieComposition[i];
+        const List<specieElement>& curSpecieComposition = specieComposition[i];
+
         // for all elements in the current species
-        forAll(curSpecieComposition, j)
+        for (const specieElement& curElement : curSpecieComposition)
         {
-            const specieElement& curElement =
-                curSpecieComposition[j];
             if (curElement.name() == "C")
             {
                 sC_[i] = curElement.nAtoms();
@@ -123,7 +122,7 @@ reduceMechanism
     scalarField& completeC(this->chemistry_.completeC());
     scalarField c1(this->chemistry_.nEqns(), 0.0);
 
-    for (label i=0; i<this->nSpecie_; i++)
+    for (label i=0; i<this->nSpecie_; ++i)
     {
         c1[i] = c[i];
         completeC[i] = c[i];
@@ -133,12 +132,12 @@ reduceMechanism
     c1[this->nSpecie_+1] = p;
 
     // Compute the rAB matrix
-    RectangularMatrix<scalar> rABNum(this->nSpecie_,this->nSpecie_,0.0);
-    scalarField PA(this->nSpecie_,0.0);
-    scalarField CA(this->nSpecie_,0.0);
+    RectangularMatrix<scalar> rABNum(this->nSpecie_, this->nSpecie_, 0.0);
+    scalarField PA(this->nSpecie_, 0.0);
+    scalarField CA(this->nSpecie_, 0.0);
 
     // Number of initialized rAB for each lines
-    Field<label> NbrABInit(this->nSpecie_,0);
+    Field<label> NbrABInit(this->nSpecie_, 0);
     // Position of the initialized rAB, -1 when not initialized
     RectangularMatrix<label> rABPos(this->nSpecie_, this->nSpecie_, -1);
     // Index of the other species involved in the rABNum
@@ -150,11 +149,12 @@ reduceMechanism
     forAll(this->chemistry_.reactions(), i)
     {
         const Reaction<ThermoType>& R = this->chemistry_.reactions()[i];
+
         // for each reaction compute omegai
         scalar omegai = this->chemistry_.omega
         (
-         R, c1, T, p, pf, cf, lRef, pr, cr, rRef
-         );
+            R, c1, T, p, pf, cf, lRef, pr, cr, rRef
+        );
         omegaV[i] = omegai;
 
         // then for each pair of species composing this reaction,
@@ -185,7 +185,7 @@ reduceMechanism
             // Disable for self reference (by definition rAA=0)
             deltaBi[ss] = false;
 
-            while(!usedIndex.empty())
+            while (!usedIndex.empty())
             {
                 label curIndex = usedIndex.pop();
                 if (deltaBi[curIndex])
@@ -193,7 +193,7 @@ reduceMechanism
                     // disable to avoid counting it more than once
                     deltaBi[curIndex] = false;
                     // test if this rAB is not initialized
-                    if (rABPos(ss, curIndex)==-1)
+                    if (rABPos(ss, curIndex) == -1)
                     {
                         rABPos(ss, curIndex) = NbrABInit[ss];
                         NbrABInit[ss]++;
@@ -209,7 +209,7 @@ reduceMechanism
             bool found(false);
             forAll(wAID, id)
             {
-                if (ss==wAID[id])
+                if (ss == wAID[id])
                 {
                     wA[id] += sl*omegai;
                     found = true;
@@ -245,7 +245,7 @@ reduceMechanism
             // Disable for self reference (by definition rAA=0)
             deltaBi[ss] = false;
 
-            while(!usedIndex.empty())
+            while (!usedIndex.empty())
             {
                 label curIndex = usedIndex.pop();
                 if (deltaBi[curIndex])
@@ -253,7 +253,7 @@ reduceMechanism
                     // disable to avoid counting it more than once
                     deltaBi[curIndex] = false;
                     // test if this rAB is not initialized
-                    if (rABPos(ss, curIndex)==-1)
+                    if (rABPos(ss, curIndex) == -1)
                     {
                         rABPos(ss, curIndex) = NbrABInit[ss];
                         NbrABInit[ss]++;
@@ -270,7 +270,7 @@ reduceMechanism
             bool found(false);
             forAll(wAID, id)
             {
-                if (ss==wAID[id])
+                if (ss == wAID[id])
                 {
                     wA[id] += sl*omegai;
                     found = true;
@@ -320,28 +320,28 @@ reduceMechanism
     scalarList Pa(nElements,0.0);
     scalarList Ca(nElements,0.0);
 
-    // for (label q=0; q<SIS.size(); q++)
-    for (label i=0; i<this->nSpecie_; i++)
+    // for (label q=0; q<SIS.size(); ++q)
+    for (label i=0; i<this->nSpecie_; ++i)
     {
-        Pa[0] += sC_[i]*max(0.0,(PA[i]-CA[i]));
+        Pa[0] += sC_[i]*max(0.0, (PA[i]-CA[i]));
         Ca[0] += sC_[i]*max(0.0,-(PA[i]-CA[i]));
-        Pa[1] += sH_[i]*max(0.0,(PA[i]-CA[i]));
+        Pa[1] += sH_[i]*max(0.0, (PA[i]-CA[i]));
         Ca[1] += sH_[i]*max(0.0,-(PA[i]-CA[i]));
-        Pa[2] += sO_[i]*max(0.0,(PA[i]-CA[i]));
+        Pa[2] += sO_[i]*max(0.0, (PA[i]-CA[i]));
         Ca[2] += sO_[i]*max(0.0,-(PA[i]-CA[i]));
-        Pa[3] += sN_[i]*max(0.0,(PA[i]-CA[i]));
+        Pa[3] += sN_[i]*max(0.0, (PA[i]-CA[i]));
         Ca[3] += sN_[i]*max(0.0,-(PA[i]-CA[i]));
     }
 
     // Using the rAB matrix (numerator and denominator separated)
     // compute the R value according to the search initiating set
-    scalarField Rvalue(this->nSpecie_,0.0);
+    scalarField Rvalue(this->nSpecie_, 0.0);
     label speciesNumber = 0;
-    List<bool> disabledSpecies(this->nSpecie_,false);
+    List<bool> disabledSpecies(this->nSpecie_, false);
 
     // set all species to inactive and activate them according
     // to rAB and initial set
-    for (label i=0; i<this->nSpecie_; i++)
+    for (label i=0; i<this->nSpecie_; ++i)
     {
         this->activeSpecies_[i] = false;
     }
@@ -353,7 +353,7 @@ reduceMechanism
 
     // Compute the alpha coefficient and initialize the R value of the species
     // in the SIS
-    for (label i=0; i<SIS.size(); i++)
+    for (label i=0; i<SIS.size(); ++i)
     {
         label q = SIS[i];
         // compute alpha
@@ -397,7 +397,7 @@ reduceMechanism
         if (alphaA > this->tolerance())
         {
             this->activeSpecies_[q] = true;
-            speciesNumber++;
+            ++speciesNumber;
             Q.push(q);
             QStart.append(q);
             alphaQ.append(1.0);
@@ -415,18 +415,19 @@ reduceMechanism
     {
         scalar Rmax=0.0;
         label specID=-1;
-        forAll(SIS, i)
+        for (const label sis : SIS)
         {
-            if (Rvalue[SIS[i]] > Rmax)
+            if (Rvalue[sis] > Rmax)
             {
-                Rmax = Rvalue[SIS[i]];
-                specID=SIS[i];
+                Rmax = Rvalue[sis];
+                specID = sis;
             }
         }
+
         Q.push(specID);
         QStart.append(specID);
         alphaQ.append(1.0);
-        speciesNumber++;
+        ++speciesNumber;
         Rvalue[specID] = 1.0;
         this->activeSpecies_[specID] = true;
     }
@@ -435,18 +436,22 @@ reduceMechanism
     while (!Q.empty())
     {
         label u = Q.pop();
-        scalar Den = max(PA[u],CA[u]);
+        scalar Den = max(PA[u], CA[u]);
         if (Den > VSMALL)
         {
-            for (label v=0; v<NbrABInit[u]; v++)
+            for (label v=0; v<NbrABInit[u]; ++v)
             {
                 label otherSpec = rABOtherSpec(u, v);
                 scalar rAB = mag(rABNum(u, v))/Den;
-                if (rAB>1)
+
+                if (rAB > 1)
                 {
                     Info<< "Badly Conditioned rAB : " << rAB
-                    << "species involved : "<<u << "," << otherSpec << endl;
-                    rAB=1.0;
+                    << " for species : "
+                    << this->chemistry_.Y()[u].name() << ","
+                    << this->chemistry_.Y()[otherSpec].name()
+                    << endl;