Merge branch 'master' of /home/dm4/OpenFOAM/OpenFOAM-dev

applications/solvers/compressible/rhoPimpleFoam/rhoLTSPimpleFoam/Make/options

@@ -1,5 +1,4 @@
 EXE_INC = \
-    -I../rhoPorousMRFPimpleFoam \
     -I.. \
     -I$(LIB_SRC)/thermophysicalModels/basic/lnInclude \
     -I$(LIB_SRC)/turbulenceModels/compressible/turbulenceModel \

applications/utilities/mesh/advanced/autoRefineMesh/autoRefineMesh.C

@@ -269,9 +269,10 @@ void selectCurvatureCells
         querySurf.surface(),
         querySurf,
         pointField(1, mesh.cellCentres()[0]),
-        false,
+        false,              // includeCut
-        false,
+        false,              // includeInside
-        false,
+        false,              // includeOutside
+        false,              // geometricOnly
         nearDist,
         curvature
     );

applications/utilities/mesh/manipulation/topoSet/topoSetDict

@@ -143,6 +143,9 @@ FoamFile
 //    sourceInfo
 //    {
 //        file            "www.avl.com-geometry.stl";
+//        useSurfaceOrientation false;  // use closed surface inside/outside
+//                                      // test (ignores includeCut,
+//                                      // outsidePoints)
 //        outsidePoints   ((-99 -99 -59));    // definition of outside
 //        includeCut      false;              // cells cut by surface
 //        includeInside   false;              // cells not on outside of surf

applications/utilities/postProcessing/sampling/sample/sampleDict

@@ -165,6 +165,10 @@ surfaces
 
         //- Optional: restrict to a particular zone
         // zone        zone1;
+
+        //- Optional: do not triangulate (only for surfaceFormats that support
+        //            polygons)
+        //triangulate     false;
     }
 
     interpolatedPlane

src/OpenFOAM/db/dictionary/functionEntries/codeStream/codeStream.C

@@ -39,6 +39,14 @@ namespace functionEntries
 {
     defineTypeNameAndDebug(codeStream, 0);
 
+    addToMemberFunctionSelectionTable
+    (
+        functionEntry,
+        codeStream,
+        execute,
+        dictionaryIstream
+    );
+
     addToMemberFunctionSelectionTable
     (
         functionEntry,
@@ -364,6 +372,38 @@ bool Foam::functionEntries::codeStream::execute
     IStringStream resultStream(os.str());
     entry.read(parentDict, resultStream);
 
+    return true;
+}
+
+
+bool Foam::functionEntries::codeStream::execute
+(
+    dictionary& parentDict,
+    Istream& is
+)
+{
+    Info<< "Using #codeStream at line " << is.lineNumber()
+        << " in file " <<  parentDict.name() << endl;
+
+    dynamicCode::checkSecurity
+    (
+        "functionEntries::codeStream::execute(..)",
+        parentDict
+    );
+
+    // get code dictionary
+    // must reference parent for stringOps::expand to work nicely
+    dictionary codeDict("#codeStream", parentDict, is);
+
+    streamingFunctionType function = getFunction(parentDict, codeDict);
+
+    // use function to write stream
+    OStringStream os(is.format());
+    (*function)(os, parentDict);
+
+    // get the entry from this stream
+    IStringStream resultStream(os.str());
+    parentDict.read(resultStream);
 
     return true;
 }

src/OpenFOAM/db/dictionary/functionEntries/codeStream/codeStream.H

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2011 OpenFOAM Foundation
+    \\  /    A nd           | Copyright (C) 2011-2013 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -160,6 +160,10 @@ public:
 
     // Member Functions
 
+        //- Execute the functionEntry in a sub-dict context
+        static bool execute(dictionary& parentDict, Istream&);
+
+        //- Execute the functionEntry in a primitiveEntry context
         static bool execute
         (
             const dictionary& parentDict,

src/meshTools/sets/cellSources/surfaceToCell/surfaceToCell.C

@@ -157,7 +157,30 @@ void Foam::surfaceToCell::combine(topoSet& set, const bool add) const
 {
     cpuTime timer;
 
-    if (includeCut_ || includeInside_ || includeOutside_)
+
+    if (useSurfaceOrientation_ && (includeInside_ || includeOutside_))
+    {
+        const meshSearch queryMesh(mesh_);
+
+        //- Calculate for each searchPoint inside/outside status.
+        boolList isInside(querySurf().calcInside(mesh_.cellCentres()));
+
+        Info<< "    Marked inside/outside using surface orientation in = "
+            << timer.cpuTimeIncrement() << " s" << endl << endl;
+
+        forAll(isInside, cellI)
+        {
+            if (isInside[cellI] && includeInside_)
+            {
+                addOrDelete(set, cellI, add);
+            }
+            else if (!isInside[cellI] && includeOutside_)
+            {
+                addOrDelete(set, cellI, add);
+            }
+        }
+    }
+    else if (includeCut_ || includeInside_ || includeOutside_)
     {
         //
         // Cut cells with surface and classify cells
@@ -166,7 +189,7 @@ void Foam::surfaceToCell::combine(topoSet& set, const bool add) const
 
         // Construct search engine on mesh
 
-        meshSearch queryMesh(mesh_);
+        const meshSearch queryMesh(mesh_);
 
 
         // Check all 'outside' points
@@ -196,10 +219,10 @@ void Foam::surfaceToCell::combine(topoSet& set, const bool add) const
         );
 
 
-        Info<< "    Marked inside/outside in = "
+        Info<< "    Marked inside/outside using surface intersection in = "
             << timer.cpuTimeIncrement() << " s" << endl << endl;
 
-
+        //- Add/remove cells using set
         forAll(cellType, cellI)
         {
             label cType = cellType[cellI];
@@ -326,6 +349,18 @@ void Foam::surfaceToCell::checkSettings() const
             << " or set curvature to a value -1 .. 1."
             << exit(FatalError);
     }
+
+    if (useSurfaceOrientation_ && includeCut_)
+    {
+        FatalErrorIn
+        (
+            "surfaceToCell:checkSettings()"
+        )   << "Illegal include cell specification."
+            << " You cannot specify both 'useSurfaceOrientation'"
+            << " and 'includeCut'"
+            << " since 'includeCut' specifies a topological split"
+            << exit(FatalError);
+    }
 }
 
 
@@ -340,6 +375,7 @@ Foam::surfaceToCell::surfaceToCell
     const bool includeCut,
     const bool includeInside,
     const bool includeOutside,
+    const bool useSurfaceOrientation,
     const scalar nearDist,
     const scalar curvature
 )
@@ -350,6 +386,7 @@ Foam::surfaceToCell::surfaceToCell
     includeCut_(includeCut),
     includeInside_(includeInside),
     includeOutside_(includeOutside),
+    useSurfaceOrientation_(useSurfaceOrientation),
     nearDist_(nearDist),
     curvature_(curvature),
     surfPtr_(new triSurface(surfName_)),
@@ -371,6 +408,7 @@ Foam::surfaceToCell::surfaceToCell
     const bool includeCut,
     const bool includeInside,
     const bool includeOutside,
+    const bool useSurfaceOrientation,
     const scalar nearDist,
     const scalar curvature
 )
@@ -381,6 +419,7 @@ Foam::surfaceToCell::surfaceToCell
     includeCut_(includeCut),
     includeInside_(includeInside),
     includeOutside_(includeOutside),
+    useSurfaceOrientation_(useSurfaceOrientation),
     nearDist_(nearDist),
     curvature_(curvature),
     surfPtr_(&surf),
@@ -404,6 +443,10 @@ Foam::surfaceToCell::surfaceToCell
     includeCut_(readBool(dict.lookup("includeCut"))),
     includeInside_(readBool(dict.lookup("includeInside"))),
     includeOutside_(readBool(dict.lookup("includeOutside"))),
+    useSurfaceOrientation_
+    (
+        dict.lookupOrDefault<bool>("useSurfaceOrientation", false)
+    ),
     nearDist_(readScalar(dict.lookup("nearDistance"))),
     curvature_(readScalar(dict.lookup("curvature"))),
     surfPtr_(new triSurface(surfName_)),
@@ -427,6 +470,7 @@ Foam::surfaceToCell::surfaceToCell
     includeCut_(readBool(checkIs(is))),
     includeInside_(readBool(checkIs(is))),
     includeOutside_(readBool(checkIs(is))),
+    useSurfaceOrientation_(false),
     nearDist_(readScalar(checkIs(is))),
     curvature_(readScalar(checkIs(is))),
     surfPtr_(new triSurface(surfName_)),

src/meshTools/sets/cellSources/surfaceToCell/surfaceToCell.H

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2011 OpenFOAM Foundation
+    \\  /    A nd           | Copyright (C) 2011-2013 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -29,6 +29,8 @@ Description
 
     Selects:
     - all cells inside/outside/cut by surface
+    - all cells inside/outside surface ('useSurfaceOrientation', requires closed
+      surface)
     - cells with centre nearer than XXX to surface
     - cells with centre nearer than XXX to surface \b and with normal
       at nearest point to centre and cell-corners differing by
@@ -67,27 +69,31 @@ class surfaceToCell
         static addToUsageTable usage_;
 
         //- Name of surface file
-        fileName surfName_;
+        const fileName surfName_;
 
         //- Points which are outside
-        pointField outsidePoints_;
+        const pointField outsidePoints_;
 
         //- Include cut cells
-        bool includeCut_;
+        const bool includeCut_;
 
         //- Include inside cells
-        bool includeInside_;
+        const bool includeInside_;
 
         //- Include outside cells
-        bool includeOutside_;
+        const bool includeOutside_;
+
+        //- Determine inside/outside purely using geometric test
+        //  (does not allow includeCut)
+        const bool useSurfaceOrientation_;
 
         //- if > 0 : include cells with distance from cellCentre to surface
         //  less than nearDist.
-        scalar nearDist_;
+        const scalar nearDist_;
 
         //- if > -1 : include cells with normals at nearest surface points
         //  varying more than curvature_.
-        scalar curvature_;
+        const scalar curvature_;
 
         //- triSurface to search on. On pointer since can be external.
         const triSurface* surfPtr_;
@@ -97,7 +103,7 @@ class surfaceToCell
 
         //- whether I allocated above surface ptrs or whether they are
         //  external.
-        bool IOwnPtrs_;
+        const bool IOwnPtrs_;
 
 
     // Private Member Functions
@@ -155,6 +161,7 @@ public:
             const bool includeCut,
             const bool includeInside,
             const bool includeOutside,
+            const bool useSurfaceOrientation,
             const scalar nearDist,
             const scalar curvature
         );
@@ -170,6 +177,7 @@ public:
             const bool includeCut,
             const bool includeInside,
             const bool includeOutside,
+            const bool useSurfaceOrientation,
             const scalar nearDist,
             const scalar curvature
         );

src/meshTools/sets/topoSets/topoSet.C

@@ -472,7 +472,6 @@ void Foam::topoSet::invert(const label maxLen)
             insert(cellI);
         }
     }
-
 }
 
 
@@ -550,20 +549,6 @@ void Foam::topoSet::writeDebug(Ostream& os, const label maxLen) const
 }
 
 
-//void Foam::topoSet::writeDebug
-//(
-//    Ostream&,
-//    const primitiveMesh&,
-//    const label
-//) const
-//{
-//    notImplemented
-//    (
-//        "topoSet::writeDebug(Ostream&, const primitiveMesh&, const label)"
-//    );
-//}
-
-
 bool Foam::topoSet::writeData(Ostream& os) const
 {
     return (os << *this).good();
@@ -576,14 +561,6 @@ void Foam::topoSet::updateMesh(const mapPolyMesh&)
 }
 
 
-////- Return max index+1.
-//label topoSet::maxSize(const polyMesh&) const
-//{
-//    notImplemented("topoSet::maxSize(const polyMesh&)");
-//
-//    return -1;
-//}
-
 // * * * * * * * * * * * * * * * Member Operators  * * * * * * * * * * * * * //
 
 void Foam::topoSet::operator=(const topoSet& rhs)

src/regionModels/pyrolysisModels/reactingOneDim/reactingOneDim.C

@@ -32,6 +32,7 @@ License
 #include "fvcVolumeIntegrate.H"
 #include "fvMatrices.H"
 #include "absorptionEmissionModel.H"
+#include "fvcLaplacian.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
@@ -61,6 +62,9 @@ void reactingOneDim::readReactingOneDimControls()
 
     coeffs().lookup("gasHSource") >> gasHSource_;
     coeffs().lookup("QrHSource") >> QrHSource_;
+    useChemistrySolvers_ =
+        coeffs().lookupOrDefault<bool>("useChemistrySolvers", true);
+
 }
 
 
@@ -321,6 +325,8 @@ void reactingOneDim::solveEnergy()
     (
         fvm::ddt(rho_, h_)
       - fvm::laplacian(alpha, h_)
+      + fvc::laplacian(alpha, h_)
+      - fvc::laplacian(kappa(), T())
      ==
         chemistrySh_
       - fvm::Sp(solidChemistry_->RRg(), h_)
@@ -462,7 +468,8 @@ reactingOneDim::reactingOneDim(const word& modelType, const fvMesh& mesh)
     totalGasMassFlux_(0.0),
     totalHeatRR_(dimensionedScalar("zero", dimEnergy/dimTime, 0.0)),
     gasHSource_(false),
-    QrHSource_(false)
+    QrHSource_(false),
+    useChemistrySolvers_(true)
 {
     if (active_)
     {
@@ -560,7 +567,8 @@ reactingOneDim::reactingOneDim
     totalGasMassFlux_(0.0),
     totalHeatRR_(dimensionedScalar("zero", dimEnergy/dimTime, 0.0)),
     gasHSource_(false),
-    QrHSource_(false)
+    QrHSource_(false),
+    useChemistrySolvers_(true)
 {
     if (active_)
     {
@@ -681,11 +689,18 @@ void reactingOneDim::evolveRegion()
 {
     Info<< "\nEvolving pyrolysis in region: " << regionMesh().name() << endl;
 
+    if (useChemistrySolvers_)
+    {
         solidChemistry_->solve
         (
             time().value() - time().deltaTValue(),
             time().deltaTValue()
         );
+    }
+    else
+    {
+        solidChemistry_->calculate();
+    }
 
     solveContinuity();
 

src/regionModels/pyrolysisModels/reactingOneDim/reactingOneDim.H

@@ -154,6 +154,9 @@ protected:
             //- Add in depth radiation source term
             bool  QrHSource_;
 
+            //- Use chemistry solvers (ode or sequential)
+            bool useChemistrySolvers_;
+
 
     // Protected member functions
 

src/sampling/sampledSurface/sampledPlane/sampledPlane.C

@@ -45,12 +45,14 @@ Foam::sampledPlane::sampledPlane
     const word& name,
     const polyMesh& mesh,
     const plane& planeDesc,
-    const keyType& zoneKey
+    const keyType& zoneKey,
+    const bool triangulate
 )
 :
     sampledSurface(name, mesh),
     cuttingPlane(planeDesc),
     zoneKey_(zoneKey),
+    triangulate_(triangulate),
     needsUpdate_(true)
 {
     if (debug && zoneKey_.size() && mesh.cellZones().findIndex(zoneKey_) < 0)
@@ -71,6 +73,7 @@ Foam::sampledPlane::sampledPlane
     sampledSurface(name, mesh, dict),
     cuttingPlane(plane(dict.lookup("basePoint"), dict.lookup("normalVector"))),
     zoneKey_(keyType::null),
+    triangulate_(dict.lookupOrDefault("triangulate", true)),
     needsUpdate_(true)
 {
     // make plane relative to the coordinateSystem (Cartesian)
@@ -138,11 +141,11 @@ bool Foam::sampledPlane::update()
 
     if (selectedCells.empty())
     {
-        reCut(mesh(), true);    // always triangulate. Note:Make option?
+        reCut(mesh(), triangulate_);
     }
     else
     {
-        reCut(mesh(), true, selectedCells);
+        reCut(mesh(), triangulate_, selectedCells);
     }
 
     if (debug)
@@ -250,6 +253,7 @@ void Foam::sampledPlane::print(Ostream& os) const
     os  << "sampledPlane: " << name() << " :"
         << "  base:" << refPoint()
         << "  normal:" << normal()
+        << "  triangulate:" << triangulate_
         << "  faces:" << faces().size()
         << "  points:" << points().size();
 }

src/sampling/sampledSurface/sampledPlane/sampledPlane.H

@@ -25,7 +25,7 @@ Class
     Foam::sampledPlane
 
 Description
-    A sampledSurface defined by a cuttingPlane. Always triangulated.
+    A sampledSurface defined by a cuttingPlane. Triangulated by default.
 
 Note
     Does not actually cut until update() called.
@@ -60,6 +60,9 @@ class sampledPlane
         //- If restricted to zones, name of this zone or a regular expression
         keyType zoneKey_;
 
+        //- Triangulated faces or keep faces as is
+        const bool triangulate_;
+
         //- Track if the surface needs an update
         mutable bool needsUpdate_;
 
@@ -92,7 +95,8 @@ public:
             const word& name,
             const polyMesh& mesh,
             const plane& planeDesc,
-            const keyType& zoneKey = word::null
+            const keyType& zoneKey = word::null,
+            const bool triangulate = true
         );
 
         //- Construct from dictionary

src/thermophysicalModels/chemistryModel/chemistryModel/basicChemistryModel/basicChemistryModel.H

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2011-2012 OpenFOAM Foundation
+    \\  /    A nd           | Copyright (C) 2011-2013 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -140,6 +140,12 @@ public:
                     const label i
                 ) const = 0;
 
+                //- Return access to chemical source terms [kg/m3/s]
+                virtual DimensionedField<scalar, volMesh>& RR
+                (
+                    const label i
+                ) = 0;
+
 
             // Chemistry solution
 

src/thermophysicalModels/chemistryModel/chemistryModel/chemistryModel/chemistryModel.H

@@ -211,6 +211,12 @@ public:
                 const label i
             ) const;
 
+            //- Return non const access to chemical source terms [kg/m3/s]
+            virtual DimensionedField<scalar, volMesh>& RR
+            (
+                const label i
+            );
+
             //- Solve the reaction system for the given start time and time
             //  step and return the characteristic time
             virtual scalar solve(const scalar t0, const scalar deltaT);

src/thermophysicalModels/chemistryModel/chemistryModel/chemistryModel/chemistryModelI.H

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2011-2012 OpenFOAM Foundation
+    \\  /    A nd           | Copyright (C) 2011-2013 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -78,5 +78,15 @@ Foam::chemistryModel<CompType, ThermoType>::RR
     return RR_[i];
 }
 
+template<class CompType, class ThermoType>
+Foam::DimensionedField<Foam::scalar, Foam::volMesh>&
+Foam::chemistryModel<CompType, ThermoType>::RR
+(
+    const label i
+)
+{
+    return RR_[i];
+}
+
 
 // ************************************************************************* //

src/thermophysicalModels/solidChemistryModel/basicSolidChemistryModel/basicSolidChemistryModel.C

@@ -53,4 +53,35 @@ Foam::basicSolidChemistryModel::~basicSolidChemistryModel()
 {}
 
 
+const Foam::DimensionedField<Foam::scalar, Foam::volMesh>&
+Foam::basicSolidChemistryModel::RR(const label i) const
+{
+    notImplemented
+    (
+        "const Foam::DimensionedField<Foam::scalar, Foam::volMesh>&"
+        "basicSolidChemistryModel::RR(const label)"
+    );
+    return (DimensionedField<scalar, volMesh>::null());
+}
+
+
+Foam::DimensionedField<Foam::scalar, Foam::volMesh>&
+Foam::basicSolidChemistryModel::RR(const label i)
+{
+    notImplemented
+    (
+        "Foam::DimensionedField<Foam::scalar, Foam::volMesh>&"
+        "basicSolidChemistryModel::RR(const label)"
+    );
+
+    return dynamic_cast<DimensionedField<scalar, volMesh>&>
+    (
+        const_cast<DimensionedField<scalar, volMesh>& >
+        (
+            DimensionedField<scalar, volMesh>::null()
+        )
+    );
+}
+
+
 // ************************************************************************* //

src/thermophysicalModels/solidChemistryModel/basicSolidChemistryModel/basicSolidChemistryModel.H

@@ -149,6 +149,15 @@ public:
 
         //- Calculates the reaction rates
         virtual void calculate() = 0;
+
+        //- Return const access to the total source terms
+        virtual const DimensionedField<scalar, volMesh>& RR
+        (
+            const label i
+        ) const;
+
+        //- Return non-const access to the total source terms
+        virtual DimensionedField<scalar, volMesh>& RR(const label i);
 };
 
 

src/thermophysicalModels/solidChemistryModel/pyrolysisChemistryModel/pyrolysisChemistryModel.C

@@ -535,14 +535,21 @@ updateConcsInReactionI
         c[si] = max(0.0, c[si]);
     }
 
+    scalar sr = 0.0;
     forAll(R.rhs(), s)
     {
         label si = R.rhs()[s].index;
         const scalar rhoR = this->solidThermo_[si].rho(p, T);
-        const scalar sr = rhoR/rhoL;
+        sr = rhoR/rhoL;
         c[si] += dt*sr*omeg;
         c[si] = max(0.0, c[si]);
     }
+
+    forAll(R.grhs(), g)
+    {
+        label gi = R.grhs()[g].index;
+        c[gi + this->nSolids_] += (1.0 - sr)*omeg*dt;
+    }
 }
 
 
@@ -561,24 +568,11 @@ updateRRInReactionI
     simpleMatrix<scalar>& RR
 ) const
 {
-    const Reaction<SolidThermo>& R = this->reactions_[index];
+    notImplemented
-    scalar rhoL = 0.0;
+    (
-    forAll(R.lhs(), s)
+        "void Foam::pyrolysisChemistryModel<CompType, SolidThermo,GasThermo>::"
-    {
+        "updateRRInReactionI"
-        label si = R.lhs()[s].index;
+    );
-        rhoL = this->solidThermo_[si].rho(p, T);
-        RR[si][rRef] -= pr*corr;
-        RR[si][lRef] += pf*corr;
-    }
-
-    forAll(R.rhs(), s)
-    {
-        label si = R.rhs()[s].index;
-        const scalar rhoR = this->solidThermo_[si].rho(p, T);
-        const scalar sr = rhoR/rhoL;
-        RR[si][lRef] -= sr*pf*corr;
-        RR[si][rRef] += sr*pr*corr;
-    }
 }
 
 
@@ -666,7 +660,6 @@ Foam::pyrolysisChemistryModel<CompType, SolidThermo, GasThermo>::solve
 
                 scalar newCp = 0.0;
                 scalar newhi = 0.0;
-                scalar invRho = 0.0;
                 scalarList dcdt = (c - c0)/dt;
 
                 for (label i=0; i<this->nSolids_; i++)
@@ -675,7 +668,6 @@ Foam::pyrolysisChemistryModel<CompType, SolidThermo, GasThermo>::solve
                     scalar Yi = c[i]/cTot;
                     newCp += Yi*this->solidThermo_[i].Cp(pi, Ti);
                     newhi -= dYi*this->solidThermo_[i].Hc();
-                    invRho += Yi/this->solidThermo_[i].rho(pi, Ti);
                 }
 
                 scalar dTi = (newhi/newCp)*dt;

src/thermophysicalModels/solidChemistryModel/pyrolysisChemistryModel/pyrolysisChemistryModel.H

@@ -137,8 +137,9 @@ public:
             const bool updateC0 = false
         ) const;
 
-        //- Return the reaction rate for reaction r and the reference
+        //- Return the reaction rate for reaction r
-        //  species and charateristic times
+        // NOTE: Currently does not calculate reference specie and
+        // characteristic times (pf, cf,l Ref, etc.)
         virtual scalar omega
         (
             const Reaction<SolidThermo>& r,
@@ -153,8 +154,10 @@ public:
             label& rRef
         ) const;
 
-        //- Return the reaction rate for iReaction and the reference
+
-        //  species and charateristic times
+        //- Return the reaction rate for iReaction
+        // NOTE: Currently does not calculate reference specie and
+        // characteristic times (pf, cf,l Ref, etc.)
         virtual scalar omegaI
         (
             label iReaction,
@@ -169,6 +172,7 @@ public:
             label& rRef
         ) const;
 
+
         //- Calculates the reaction rates
         virtual void calculate();
 
@@ -186,6 +190,7 @@ public:
 
 
         //- Update matrix RR for reaction i. Used by EulerImplicit
+        // (Not implemented)
         virtual void updateRRInReactionI
         (
             const label i,

src/thermophysicalModels/solidChemistryModel/solidChemistryModel/solidChemistryModel.H

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2011-2013 OpenFOAM Foundation
+    \\  /    A nd           | Copyright (C) 2013-2013 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -65,6 +65,9 @@ class solidChemistryModel
 {
     // Private Member Functions
 
+        //- Disallow copy constructor
+        solidChemistryModel(const solidChemistryModel&);
+
         //- Disallow default bitwise assignment
         void operator=(const solidChemistryModel&);
 
@@ -151,6 +154,7 @@ public:
             label& rRef
         ) const = 0;
 
+
         //- Return the reaction rate for iReaction and the reference
         //  species and charateristic times
         virtual scalar omegaI
@@ -167,6 +171,10 @@ public:
             label& rRef
         ) const = 0;
 
+        //- Calculates the reaction rates
+        virtual void calculate() = 0;
+
+
         //- Update concentrations in reaction i given dt and reaction rate
         // omega used by sequential solver
         virtual void updateConcsInReactionI
@@ -194,11 +202,8 @@ public:
             simpleMatrix<scalar>& RR
         ) const = 0;
 
-        //- Calculates the reaction rates
-        virtual void calculate() = 0;
 
-
+        // Solid Chemistry model functions
-        // Chemistry model functions
 
             //- Return const access to the chemical source terms for solids
             inline const DimensionedField<scalar, volMesh>& RRs
@@ -209,13 +214,6 @@ public:
             //- Return total solid source term
             inline tmp<DimensionedField<scalar, volMesh> > RRs() const;
 
-            //- Return const access to the total source terms
-            inline const DimensionedField<scalar, volMesh>& RR
-            (
-                const label i
-            ) const;
-
-
             //- Solve the reaction system for the given start time and time
             //  step and return the characteristic time
             virtual scalar solve(const scalar t0, const scalar deltaT) = 0;

src/thermophysicalModels/solidChemistryModel/solidChemistryModel/solidChemistryModelI.H

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2011-2013 OpenFOAM Foundation
+    \\  /    A nd           | Copyright (C) 2013-2013 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -95,16 +95,4 @@ Foam::solidChemistryModel<CompType, SolidThermo>::RRs() const
 }
 
 
-template<class CompType, class SolidThermo>
-inline const Foam::DimensionedField<Foam::scalar, Foam::volMesh>&
-Foam::solidChemistryModel<CompType, SolidThermo>::RR
-(
-    const label i
-) const
-{
-    notImplemented("solidChemistryModel::RR(const label)");
-    return (DimensionedField<scalar, volMesh>::null());
-}
-
-
 // ************************************************************************* //

src/thermophysicalModels/solidChemistryModel/solidChemistrySolver/makeSolidChemistrySolverType.H

@@ -52,9 +52,8 @@ namespace Foam
     defineTemplateTypeNameAndDebugWithName                                    \
     (                                                                         \
         SS##Schem##Comp##SThermo##GThermo,                                    \
-        (#SS"<" + word(Schem::typeName_())                                    \
+        (#SS"<"#Schem"<"#Comp"," + SThermo::typeName() + ","                  \
-      + "<"#Comp"," + SThermo::typeName()                                     \
+      + GThermo::typeName() + ">>").c_str(),                                  \
-      + "," + GThermo::typeName() + ">>").c_str(),                            \
         0                                                                     \
     );                                                                        \
                                                                               \
@@ -77,14 +76,6 @@ namespace Foam
         GThermo                                                               \
     );                                                                        \
                                                                               \
-    makeSolidChemistrySolverType                                              \
-    (                                                                         \
-        EulerImplicit,                                                        \
-        SolidChem,                                                            \
-        Comp,                                                                 \
-        SThermo,                                                              \
-        GThermo                                                               \
-    );                                                                        \
                                                                               \
     makeSolidChemistrySolverType                                              \
     (                                                                         \
@@ -104,7 +95,6 @@ namespace Foam
         GThermo                                                               \
     );
 
-
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
 } // End namespace Foam

src/thermophysicalModels/solidThermo/solidThermo/makeSolidThermo.H

@@ -30,7 +30,7 @@ Description
 \*---------------------------------------------------------------------------*/
 
 #ifndef makeSolidThermo_H
-#define makesolidThermo_H
+#define makeSolidThermo_H
 
 #include "addToRunTimeSelectionTable.H"
 

tutorials/multiphase/MRFMultiphaseInterFoam/mixerVessel2D/0.org/alpha.air

@@ -10,7 +10,7 @@ FoamFile
     version     2.0;
     format      ascii;
     class       volScalarField;
-    object      alpha1;
+    object      alpha.air;
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 

tutorials/multiphase/MRFMultiphaseInterFoam/mixerVessel2D/0.org/alpha.mercury

@@ -10,7 +10,7 @@ FoamFile
     version     2.0;
     format      ascii;
     class       volScalarField;
-    object      alpha1;
+    object      alpha.mercury;
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 

tutorials/multiphase/MRFMultiphaseInterFoam/mixerVessel2D/0.org/alpha.oil

@@ -10,7 +10,7 @@ FoamFile
     version     2.0;
     format      ascii;
     class       volScalarField;
-    object      alpha1;
+    object      alpha.oil;
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 

tutorials/multiphase/MRFMultiphaseInterFoam/mixerVessel2D/0.org/alphawater

@@ -1,44 +0,0 @@
-/*--------------------------------*- C++ -*----------------------------------*\
-| =========                 |                                                 |
-| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  dev                                   |
-|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
-|    \\/     M anipulation  |                                                 |
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
-    version     2.0;
-    format      ascii;
-    class       volScalarField;
-    object      alpha1;
-}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-dimensions      [0 0 0 0 0 0 0];
-
-internalField   uniform 0;
-
-boundaryField
-{
-    rotor
-    {
-        type            zeroGradient;
-    }
-
-    stator
-    {
-        type            zeroGradient;
-    }
-
-    front
-    {
-        type            empty;
-    }
-
-    back
-    {
-        type            empty;
-    }
-}
-
-// ************************************************************************* //

tutorials/multiphase/MRFMultiphaseInterFoam/mixerVessel2D/0/alpha.air

@@ -11,7 +11,7 @@ FoamFile
     format      ascii;
     class       volScalarField;
     location    "0";
-    object      alphaair;
+    object      alpha.air;
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 

tutorials/multiphase/MRFMultiphaseInterFoam/mixerVessel2D/0/alpha.mercury

@@ -11,7 +11,7 @@ FoamFile
     format      ascii;
     class       volScalarField;
     location    "0";
-    object      alphamercury;
+    object      alpha.mercury;
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 

tutorials/multiphase/MRFMultiphaseInterFoam/mixerVessel2D/0/alpha.oil

@@ -11,7 +11,7 @@ FoamFile
     format      ascii;
     class       volScalarField;
     location    "0";
-    object      alphaoil;
+    object      alpha.oil;
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 

tutorials/multiphase/MRFMultiphaseInterFoam/mixerVessel2D/0/alpha.water

@@ -11,7 +11,7 @@ FoamFile
     format      ascii;
     class       volScalarField;
     location    "0";
-    object      alphawater;
+    object      alpha.water;
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 

tutorials/multiphase/MRFMultiphaseInterFoam/mixerVessel2D/constant/polyMesh/boundary

@@ -32,12 +32,14 @@ FoamFile
     front
     {
         type            empty;
+        inGroups        1(empty);
         nFaces          3072;
         startFace       6336;
     }
     back
     {
         type            empty;
+        inGroups        1(empty);
         nFaces          3072;
         startFace       9408;
     }

tutorials/multiphase/MRFMultiphaseInterFoam/mixerVessel2D/constant/transportProperties

@@ -46,8 +46,6 @@ phases
      }
 );
 
-refPhase        air;
-
 sigmas
 (
     (air water) 0.07

tutorials/multiphase/MRFMultiphaseInterFoam/mixerVessel2D/system/setFieldsDict

@@ -17,10 +17,10 @@ FoamFile
 
 defaultFieldValues
 (
-    volScalarFieldValue alphaair 1
+    volScalarFieldValue alpha.air 1
-    volScalarFieldValue alphawater 0
+    volScalarFieldValue alpha.water 0
-    volScalarFieldValue alphaoil 0
+    volScalarFieldValue alpha.oil 0
-    volScalarFieldValue alphamercury 0
+    volScalarFieldValue alpha.mercury 0
 );
 
 regions
@@ -30,10 +30,10 @@ regions
         box (0 0 -1) (1 1 1);
         fieldValues
         (
-            volScalarFieldValue alphawater 1
+            volScalarFieldValue alpha.water 1
-            volScalarFieldValue alphaoil 0
+            volScalarFieldValue alpha.oil 0
-            volScalarFieldValue alphamercury 0
+            volScalarFieldValue alpha.mercury 0
-            volScalarFieldValue alphaair 0
+            volScalarFieldValue alpha.air 0
         );
     }
     boxToCell
@@ -41,10 +41,10 @@ regions
         box (0 -1 -1) (1 0 1);
         fieldValues
         (
-            volScalarFieldValue alphawater 0
+            volScalarFieldValue alpha.water 0
-            volScalarFieldValue alphaoil 1
+            volScalarFieldValue alpha.oil 1
-            volScalarFieldValue alphamercury 0
+            volScalarFieldValue alpha.mercury 0
-            volScalarFieldValue alphaair 0
+            volScalarFieldValue alpha.air 0
         );
     }
     boxToCell
@@ -52,10 +52,10 @@ regions
         box (-1 -1 -1) (0 0 1);
         fieldValues
         (
-            volScalarFieldValue alphawater 0
+            volScalarFieldValue alpha.water 0
-            volScalarFieldValue alphaoil 0
+            volScalarFieldValue alpha.oil 0
-            volScalarFieldValue alphamercury 1
+            volScalarFieldValue alpha.mercury 1
-            volScalarFieldValue alphaair 0
+            volScalarFieldValue alpha.air 0
         );
     }
 );