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

applications/solvers/incompressible/pimpleFoam/pimpleDyMFoam/UEqn.H

@@ -5,7 +5,7 @@ tmp<fvVectorMatrix> UEqn
     fvm::ddt(U)
   + fvm::div(phi, U)
   + turbulence->divDevReff(U)
-  ==
+ ==
     fvOptions(U)
 );
 
@@ -17,7 +17,7 @@ rAU = 1.0/UEqn().A();
 
 if (pimple.momentumPredictor())
 {
-    solve(UEqn() == -fvc::grad(p) + fvOptions(U));
+    solve(UEqn() == -fvc::grad(p));
 
     fvOptions.correct(U);
 }

applications/utilities/postProcessing/graphics/PV398Readers/Allwmake

@@ -2,21 +2,26 @@
 cd ${0%/*} || exit 1    # run from this directory
 #set -x
 
-if [ -d "$ParaView_DIR" -a -r "$ParaView_DIR" ]
-then
-    [ -n "$PV_PLUGIN_PATH" ] || {
-        echo "$0 : PV_PLUGIN_PATH not valid - it is unset"
-        exit 1
-    }
+if [ "$ParaView_VERSION" == "3.98.1" ]
+    then
+    if [ -d "$ParaView_DIR" -a -r "$ParaView_DIR" ]
+    then
+        [ -n "$PV_PLUGIN_PATH" ] || {
+            echo "$0 : PV_PLUGIN_PATH not valid - it is unset"
+            exit 1
+        }
 
-    # ensure CMake gets the correct C++ compiler
-    [ -n "$WM_CXX" ] && export CXX="$WM_CXX"
+        # ensure CMake gets the correct C++ compiler
+        [ -n "$WM_CXX" ] && export CXX="$WM_CXX"
 
-    wmake libso vtkPV398Readers
-    PV398blockMeshReader/Allwmake
-    PV398FoamReader/Allwmake
+        wmake libso vtkPV398Readers
+        PV398blockMeshReader/Allwmake
+        PV398FoamReader/Allwmake
+    else
+        echo "ERROR: ParaView not found in $ParaView_DIR"
+    fi
 else
-    echo "ERROR: ParaView not found in $ParaView_DIR"
+    echo "WARN: PV398 readers not building: ParaView_VERSION=$ParaView_VERSION"
 fi
 
 # ----------------------------------------------------------------- end-of-file

applications/utilities/postProcessing/graphics/PV3Readers/Allwmake

@@ -2,21 +2,26 @@
 cd ${0%/*} || exit 1    # run from this directory
 #set -x
 
-if [ -d "$ParaView_DIR" -a -r "$ParaView_DIR" ]
-then
-    [ -n "$PV_PLUGIN_PATH" ] || {
-        echo "$0 : PV_PLUGIN_PATH not valid - it is unset"
-        exit 1
-    }
+if [ "$ParaView_VERSION" != "3.98.1" ]
+    then
+    if [ -d "$ParaView_DIR" -a -r "$ParaView_DIR" ]
+    then
+        [ -n "$PV_PLUGIN_PATH" ] || {
+            echo "$0 : PV_PLUGIN_PATH not valid - it is unset"
+            exit 1
+        }
 
-    # ensure CMake gets the correct C++ compiler
-    [ -n "$WM_CXX" ] && export CXX="$WM_CXX"
+        # ensure CMake gets the correct C++ compiler
+        [ -n "$WM_CXX" ] && export CXX="$WM_CXX"
 
-    wmake libso vtkPV3Readers
-    PV3blockMeshReader/Allwmake
-    PV3FoamReader/Allwmake
+        wmake libso vtkPV3Readers
+        PV3blockMeshReader/Allwmake
+        PV3FoamReader/Allwmake
+    else
+        echo "ERROR: ParaView not found in $ParaView_DIR"
+    fi
 else
-    echo "ERROR: ParaView not found in $ParaView_DIR"
+    echo "WARN: PV3 readers not building: ParaView_VERSION=$ParaView_VERSION"
 fi
 
 # ----------------------------------------------------------------- end-of-file

src/OpenFOAM/meshes/polyMesh/polyPatches/constraint/processorCyclic/processorCyclicPolyPatch.H

@@ -45,7 +45,7 @@ namespace Foam
 {
 
 /*---------------------------------------------------------------------------*\
-                           Class processorCyclicPolyPatch Declaration
+                  Class processorCyclicPolyPatch Declaration
 \*---------------------------------------------------------------------------*/
 
 class processorCyclicPolyPatch
@@ -63,8 +63,6 @@ class processorCyclicPolyPatch
         //- Index of originating patch
         mutable label referPatchID_;
 
-    // Private member functions
-
 
 protected:
 
@@ -223,8 +221,7 @@ public:
 
 
     // Destructor
-
-        virtual ~processorCyclicPolyPatch();
+    virtual ~processorCyclicPolyPatch();
 
 
     // Member functions

src/edgeMesh/extendedFeatureEdgeMesh/extendedFeatureEdgeMeshTemplates.C

@@ -65,8 +65,7 @@ void Foam::extendedFeatureEdgeMesh::sortPointsAndEdges
     labelListList featurePointFeatureEdges(nFeatPts);
     forAll(featurePointFeatureEdges, pI)
     {
-        featurePointFeatureEdges[pI] =
-            labelList(pointEdges[featurePoints[pI]].size(), -1);
+        featurePointFeatureEdges[pI] = pointEdges[featurePoints[pI]];
     }
 
     // Mapping between old and new indices, there is entry in the map for each
@@ -74,6 +73,10 @@ void Foam::extendedFeatureEdgeMesh::sortPointsAndEdges
     // >= 0 corresponds to the index
     labelList pointMap(sFeatLocalPts.size(), -1);
 
+    // Mapping between surface edge index and its feature edge index. -1 if it
+    // is not a feature edge
+    labelList edgeMap(sFeatEds.size(), -1);
+
     // Noting when the normal of a face has been used so not to duplicate
     labelList faceMap(surf.size(), -1);
 
@@ -98,6 +101,8 @@ void Foam::extendedFeatureEdgeMesh::sortPointsAndEdges
     {
         label sFEI = featureEdges[i];
 
+        edgeMap[sFEI] = i;
+
         const edge& fE(sFeatEds[sFEI]);
 
         // Check to see if the points have been already used
@@ -156,43 +161,31 @@ void Foam::extendedFeatureEdgeMesh::sortPointsAndEdges
         {
             regionEdges.append(i);
         }
-
-        forAll(featurePointFeatureEdges, pI)
-        {
-            const labelList& fpfEdges = pointEdges[featurePoints[pI]];
-
-            labelList& fpfe = featurePointFeatureEdges[pI];
-
-            forAll(fpfEdges, eI)
-            {
-                if (sFEI == fpfEdges[eI])
-                {
-                    fpfe[eI] = i;
-                }
-            }
-        }
     }
 
+    // Populate feature point feature edges
+    DynamicList<label> newFeatureEdges;
+
     forAll(featurePointFeatureEdges, pI)
     {
         const labelList& fpfe = featurePointFeatureEdges[pI];
 
-        DynamicList<label> newFeatureEdges(fpfe.size());
+        newFeatureEdges.setCapacity(fpfe.size());
 
         forAll(fpfe, eI)
         {
-            const label edgeIndex = fpfe[eI];
+            const label oldEdgeIndex = fpfe[eI];
+            const label newFeatureEdgeIndex = edgeMap[oldEdgeIndex];
 
-            if (edgeIndex != -1)
+            if (newFeatureEdgeIndex != -1)
             {
-                newFeatureEdges.append(edgeIndex);
+                newFeatureEdges.append(newFeatureEdgeIndex);
             }
         }
 
-        featurePointFeatureEdges[pI] = newFeatureEdges;
+        featurePointFeatureEdges[pI].transfer(newFeatureEdges);
     }
 
-
     // Reorder the edges by classification
 
     List<DynamicList<label> > allEds(nEdgeTypes);
@@ -277,7 +270,7 @@ void Foam::extendedFeatureEdgeMesh::sortPointsAndEdges
     edgeMesh::operator=(edgeMesh(pts, eds));
 
     // Initialise sorted edge related data
-    edgeDirections_ = edgeDirections/mag(edgeDirections);
+    edgeDirections_ = edgeDirections/(mag(edgeDirections) + VSMALL);
     edgeNormals_ = edgeNormals;
     regionEdges_ = regionEdges;
 

src/finiteVolume/finiteVolume/gradSchemes/fourthGrad/fourthGrad.C

@@ -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
@@ -62,7 +62,11 @@ Foam::fv::fourthGrad<Type>::calcGrad
     // Assemble the second-order least-square gradient
     // Calculate the second-order least-square gradient
     tmp<GeometricField<GradType, fvPatchField, volMesh> > tsecondfGrad
-        = leastSquaresGrad<Type>(mesh).grad(vsf);
+      = leastSquaresGrad<Type>(mesh).grad
+        (
+            vsf,
+            "leastSquaresGrad(" + vsf.name() + ")"
+        );
     const GeometricField<GradType, fvPatchField, volMesh>& secondfGrad =
         tsecondfGrad();
 

src/finiteVolume/finiteVolume/snGradSchemes/CentredFitSnGrad/CentredFitSnGradData.C

@@ -25,9 +25,7 @@ License
 
 #include "CentredFitSnGradData.H"
 #include "surfaceFields.H"
-#include "volFields.H"
 #include "SVD.H"
-#include "syncTools.H"
 #include "extendedCentredCellToFaceStencil.H"
 
 // * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
@@ -226,7 +224,7 @@ void Foam::CentredFitSnGradData<Polynomial>::calcFit()
     // find the fit coefficients for every face in the mesh
 
     const surfaceScalarField& w = mesh.surfaceInterpolation::weights();
-    const surfaceScalarField& dC = mesh.deltaCoeffs();
+    const surfaceScalarField& dC = mesh.nonOrthDeltaCoeffs();
 
     for (label facei = 0; facei < mesh.nInternalFaces(); facei++)
     {

src/finiteVolume/finiteVolume/snGradSchemes/CentredFitSnGrad/CentredFitSnGradData.H

@@ -25,7 +25,7 @@ Class
     Foam::CentredFitSnGradData
 
 Description
-    Data for the quadratic fit correction interpolation scheme
+    Data for centred fit snGrad schemes
 
 SourceFiles
     CentredFitSnGradData.C
@@ -64,6 +64,7 @@ class CentredFitSnGradData
         //  values of the stencil to obtain the gradient for each direction
         List<scalarList> coeffs_;
 
+
 public:
 
     TypeName("CentredFitSnGradData");

src/finiteVolume/finiteVolume/snGradSchemes/CentredFitSnGrad/CentredFitSnGradScheme.H

@@ -100,7 +100,7 @@ public:
             const GeometricField<Type, fvPatchField, volMesh>&
         ) const
         {
-            return this->mesh().deltaCoeffs();
+            return this->mesh().nonOrthDeltaCoeffs();
         }
 
         //- Return true if this scheme uses an explicit correction
@@ -124,18 +124,18 @@ public:
             );
 
             const CentredFitSnGradData<Polynomial>& cfd =
-            CentredFitSnGradData<Polynomial>::New
-            (
-                mesh,
-                stencil,
-                linearLimitFactor_,
-                centralWeight_
-            );
-
-            const List<scalarList>& f = cfd.coeffs();
+                CentredFitSnGradData<Polynomial>::New
+                (
+                    mesh,
+                    stencil,
+                    linearLimitFactor_,
+                    centralWeight_
+                );
 
             tmp<GeometricField<Type, fvsPatchField, surfaceMesh> > sft
-                = stencil.weightedSum(vf, f);
+            (
+                stencil.weightedSum(vf, cfd.coeffs())
+            );
 
             sft().dimensions() /= dimLength;
 
@@ -143,6 +143,7 @@ public:
         }
 };
 
+
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
 } // End namespace fv

src/sampling/sampledSurface/sampledSurfaces/sampledSurfacesTemplates.C

@@ -168,18 +168,32 @@ void Foam::sampledSurfaces::sampleAndWrite
 template<class GeoField>
 void Foam::sampledSurfaces::sampleAndWrite(const IOobjectList& objects)
 {
+    wordList names;
     if (loadFromFiles_)
     {
         IOobjectList fieldObjects(objects.lookupClass(GeoField::typeName));
+        names = fieldObjects.names();
+    }
+    else
+    {
+        names = mesh_.thisDb().names<GeoField>();
+    }
+
+    labelList nameIDs(findStrings(fieldSelection_, names));
 
-        wordList names(fieldObjects.names());
+    wordHashSet fieldNames(wordList(names, nameIDs));
 
-        labelList fieldNames(findStrings(fieldSelection_, names));
+    forAllConstIter(wordHashSet, fieldNames, iter)
+    {
+        const word& fieldName = iter.key();
 
-        forAll(fieldNames, fieldI)
+        if ((Pstream::master()) && verbose_)
         {
-            const word& fieldName = names[fieldNames[fieldI]];
+            Pout<< "sampleAndWrite: " << fieldName << endl;
+        }
 
+        if (loadFromFiles_)
+        {
             const GeoField fld
             (
                 IOobject
@@ -192,30 +206,10 @@ void Foam::sampledSurfaces::sampleAndWrite(const IOobjectList& objects)
                 mesh_
             );
 
-            if ((Pstream::master()) && verbose_)
-            {
-                Pout<< "sampleAndWrite: " << fieldName << endl;
-            }
-
             sampleAndWrite(fld);
         }
-    }
-    else
-    {
-        const wordList fieldNames
-        (
-            mesh_.thisDb().names<GeoField>(fieldSelection_)
-        );
-
-        forAll(fieldNames, i)
+        else
         {
-            const word& fieldName = fieldNames[i];
-
-            if ((Pstream::master()) && verbose_)
-            {
-                Pout<< "sampleAndWrite: " << fieldName << endl;
-            }
-
             sampleAndWrite
             (
                 mesh_.thisDb().lookupObject<GeoField>(fieldName)

src/thermophysicalModels/solidChemistryModel/basicSolidChemistryModel/basicSolidChemistryModelNew.C

@@ -53,11 +53,12 @@ New
 
     Info<< "Selecting chemistry type " << chemistryTypeDict << endl;
 
-    const int nCmpt = 12;
+    const int nCmpt = 13;
     const char* cmptNames[nCmpt] =
     {
         "chemistrySolver",
         "chemistryThermo",
+        "baseChemistry",
         "transport",
         "thermo",
         "equationOfState",
@@ -107,8 +108,9 @@ New
     word chemistryTypeName
     (
         word(chemistryTypeDict.lookup("chemistrySolver")) + '<'
-      + word(chemistryTypeDict.lookup("chemistryThermo")) + ','
-      + solidThermoTypeName + ',' + gasThermoTypeName + ">"
+      + word(chemistryTypeDict.lookup("chemistryThermo")) + '<'
+      + typeName + ','
+      + solidThermoTypeName + ',' + gasThermoTypeName + ">>"
     );
 
     Info<< "chemistryTypeName " << chemistryTypeName << endl;

src/thermophysicalModels/solidChemistryModel/makeSolidChemistryModel.H

@@ -48,7 +48,8 @@ namespace Foam
     defineTemplateTypeNameAndDebugWithName                                    \
     (                                                                         \
         sChemistryl##Comp##SThermo,                                           \
-        (#sChemistry"<"#Comp"," + SThermo::typeName() + ">").c_str(),         \
+        (word(sChemistry::typeName_()) + "<"#Comp"," + SThermo::typeName() +  \
+        + ">").c_str(),                                                       \
         0                                                                     \
     );                                                                        \
                                                                               \

src/thermophysicalModels/solidChemistryModel/solidChemistrySolver/makeSolidChemistrySolverType.H

@@ -47,8 +47,8 @@ namespace Foam
     defineTemplateTypeNameAndDebugWithName                                    \
     (                                                                         \
         SS##Schem##Comp##SThermo##GThermo,                                    \
-        (#SS"<"#Schem"<"#Comp"," + SThermo::typeName() + ","                  \
-      + GThermo::typeName() + ">>").c_str(),                                  \
+        (#SS"<" + word(Schem::typeName_()) +"<"#Comp"," + SThermo::typeName() \
+        + ","  + GThermo::typeName() + ">>").c_str(),                         \
         0                                                                     \
     );                                                                        \
                                                                               \

src/triSurface/triSurface/triSurface.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
@@ -175,6 +175,7 @@ class triSurface
         void writeDXGeometry(const bool, Ostream&) const;
         void writeDXTrailer(Ostream&) const;
 
+
     // Static private functions
 
         //- Convert faces to labelledTri. All get same region.
@@ -203,6 +204,7 @@ class triSurface
         //- read non-comment line
         static string getLineNoComment(IFstream&);
 
+
 protected:
 
     // Protected Member Functions
@@ -219,6 +221,7 @@ protected:
             return static_cast<List<Face>&>(*this);
         }
 
+
 public:
 
     // Public typedefs
@@ -287,7 +290,6 @@ public:
         triSurface(const triSurface&);
 
 
-
     //- Destructor
     ~triSurface();
 
@@ -324,6 +326,7 @@ public:
             //  If >2 neighbours: undetermined.
             const labelList& edgeOwner() const;
 
+
         // Edit
 
             //- Move points
@@ -381,6 +384,7 @@ public:
                 labelList& faceMap
             ) const;
 
+
         // Write
 
             //- Write to Ostream in simple FOAM format

src/turbulenceModels/compressible/RAS/derivedFvPatchFields/wallFunctions/alphatWallFunctions/alphatJayatillekeWallFunction/alphatJayatillekeWallFunctionFvPatchScalarField.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
@@ -122,7 +122,7 @@ class alphatJayatillekeWallFunctionFvPatchScalarField
 public:
 
     //- Runtime type information
-    TypeName("alphatJayatillekeWallFunction");
+    TypeName("compressible::alphatJayatillekeWallFunction");
 
 
     // Constructors

src/turbulenceModels/compressible/RAS/derivedFvPatchFields/wallFunctions/alphatWallFunctions/alphatWallFunction/alphatWallFunctionFvPatchScalarField.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
@@ -105,7 +105,7 @@ class alphatWallFunctionFvPatchScalarField
 public:
 
     //- Runtime type information
-    TypeName("alphatWallFunction");
+    TypeName("compressible::alphatWallFunction");
 
 
     // Constructors

tutorials/combustion/PDRFoam/flamePropagationWithObstacles/0.org/alphat

@@ -28,19 +28,19 @@ boundaryField
     }
     ground
     {
-        type            alphatWallFunction;
+        type            compressible::alphatWallFunction;
         Prt             0.85;
         value           uniform 0;
     }
     blockedFaces
     {
-        type            alphatWallFunction;
+        type            compressible::alphatWallFunction;
         Prt             0.85;
         value           nonuniform 0();
     }
     baffleWall
     {
-        type            alphatWallFunction;
+        type            compressible::alphatWallFunction;
         Prt             0.85;
         value           nonuniform 0();
     }

tutorials/combustion/engineFoam/kivaTest/-180/alphat

@@ -23,19 +23,19 @@ boundaryField
 {
     piston
     {
-        type            alphatWallFunction;
+        type            compressible::alphatWallFunction;
         Prt             0.85;
         value           uniform 0;
     }
     liner
     {
-        type            alphatWallFunction;
+        type            compressible::alphatWallFunction;
         Prt             0.85;
         value           uniform 0;
     }
     cylinderHead
     {
-        type            alphatWallFunction;
+        type            compressible::alphatWallFunction;
         Prt             0.85;
         value           uniform 0;
     }

tutorials/combustion/fireFoam/les/oppositeBurningPanels/0/alphaSgs

@@ -23,7 +23,7 @@ boundaryField
 {
     ground
     {
-        type        alphatWallFunction;
+        type        compressible::alphatWallFunction;
         mut         muSgs;
         value       uniform 0;
     }
@@ -45,7 +45,7 @@ boundaryField
 
     "(region0_to.*)"
     {
-        type        alphatWallFunction;
+        type        compressible::alphatWallFunction;
         mut         muSgs;
         value       uniform 0;
     }