From c324e4a1d538b0cc49b6e50d82b1bc3c967d8094 Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Mon, 2 Jul 2012 13:48:19 +0100
Subject: [PATCH 01/38] ENH: ptscotchDecomp: get coeffs from scotchCoeffs
 instead of ptscotchCoeffs

---
 src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C b/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C
index 81d3851837..56a669b119 100644
--- a/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C
+++ b/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C
@@ -401,10 +401,10 @@ Foam::label Foam::ptscotchDecomp::decompose
     }
 
     // Dump graph
-    if (decompositionDict_.found("ptscotchCoeffs"))
+    if (decompositionDict_.found("scotchCoeffs"))
     {
         const dictionary& scotchCoeffs =
-            decompositionDict_.subDict("ptscotchCoeffs");
+            decompositionDict_.subDict("scotchCoeffs");
 
         if (scotchCoeffs.lookupOrDefault("writeGraph", false))
         {

From cc1d0d27e461e8d8c670a0b9b83869c93ba14db2 Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Mon, 2 Jul 2012 13:55:57 +0100
Subject: [PATCH 02/38] ENH: mixerAMI: use reconstructPar as well

---
 tutorials/incompressible/pimpleDyMFoam/mixerVesselAMI2D/Allrun | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tutorials/incompressible/pimpleDyMFoam/mixerVesselAMI2D/Allrun b/tutorials/incompressible/pimpleDyMFoam/mixerVesselAMI2D/Allrun
index 0df20956c9..3aa63c00d9 100755
--- a/tutorials/incompressible/pimpleDyMFoam/mixerVesselAMI2D/Allrun
+++ b/tutorials/incompressible/pimpleDyMFoam/mixerVesselAMI2D/Allrun
@@ -12,5 +12,6 @@ application=`getApplication`
 #runApplication $application
 runApplication decomposePar
 runParallel $application 4
+runApplication reconstructPar
 
 # ----------------------------------------------------------------- end-of-file

From 83c412403c3c9945da2332298c565332f6e83562 Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Mon, 2 Jul 2012 13:56:55 +0100
Subject: [PATCH 03/38] STYLE: redistributePar: remove commented out code

---
 .../redistributePar/redistributePar.C         | 302 +-----------------
 1 file changed, 6 insertions(+), 296 deletions(-)

diff --git a/applications/utilities/parallelProcessing/redistributePar/redistributePar.C b/applications/utilities/parallelProcessing/redistributePar/redistributePar.C
index 9a337d7573..0412b67f15 100644
--- a/applications/utilities/parallelProcessing/redistributePar/redistributePar.C
+++ b/applications/utilities/parallelProcessing/redistributePar/redistributePar.C
@@ -63,294 +63,6 @@ Description
 static const scalar defaultMergeTol = 1e-6;
 
 
-//// Read mesh if available. Otherwise create empty mesh with same non-proc
-//// patches as proc0 mesh. Requires all processors to have all patches
-//// (and in same order).
-//autoPtr<fvMesh> createMesh
-//(
-//    const Time& runTime,
-//    const word& regionName,
-//    const fileName& instDir,
-//    const bool haveMesh
-//)
-//{
-//    //Pout<< "Create mesh for time = "
-//    //    << runTime.timeName() << nl << endl;
-//
-//    IOobject io
-//    (
-//        regionName,
-//        instDir,
-//        runTime,
-//        IOobject::MUST_READ
-//    );
-//
-//    if (!haveMesh)
-//    {
-//        // Create dummy mesh. Only used on procs that don't have mesh.
-//        IOobject noReadIO(io);
-//        noReadIO.readOpt() = IOobject::NO_READ;
-//        fvMesh dummyMesh
-//        (
-//            noReadIO,
-//            xferCopy(pointField()),
-//            xferCopy(faceList()),
-//            xferCopy(labelList()),
-//            xferCopy(labelList()),
-//            false
-//        );
-//        // Add some dummy zones so upon reading it does not read them
-//        // from the undecomposed case. Should be done as extra argument to
-//        // regIOobject::readStream?
-//        List<pointZone*> pz
-//        (
-//            1,
-//            new pointZone
-//            (
-//                "dummyPointZone",
-//                labelList(0),
-//                0,
-//                dummyMesh.pointZones()
-//            )
-//        );
-//        List<faceZone*> fz
-//        (
-//            1,
-//            new faceZone
-//            (
-//                "dummyFaceZone",
-//                labelList(0),
-//                boolList(0),
-//                0,
-//                dummyMesh.faceZones()
-//            )
-//        );
-//        List<cellZone*> cz
-//        (
-//            1,
-//            new cellZone
-//            (
-//                "dummyCellZone",
-//                labelList(0),
-//                0,
-//                dummyMesh.cellZones()
-//            )
-//        );
-//        dummyMesh.addZones(pz, fz, cz);
-//        //Pout<< "Writing dummy mesh to " << dummyMesh.polyMesh::objectPath()
-//        //    << endl;
-//        dummyMesh.write();
-//    }
-//
-//    //Pout<< "Reading mesh from " << io.objectPath() << endl;
-//    autoPtr<fvMesh> meshPtr(new fvMesh(io));
-//    fvMesh& mesh = meshPtr();
-//
-//
-//    // Sync patches
-//    // ~~~~~~~~~~~~
-//
-//    if (Pstream::master())
-//    {
-//        // Send patches
-//        for
-//        (
-//            int slave=Pstream::firstSlave();
-//            slave<=Pstream::lastSlave();
-//            slave++
-//        )
-//        {
-//            OPstream toSlave(Pstream::scheduled, slave);
-//            toSlave << mesh.boundaryMesh();
-//        }
-//    }
-//    else
-//    {
-//        // Receive patches
-//        IPstream fromMaster(Pstream::scheduled, Pstream::masterNo());
-//        PtrList<entry> patchEntries(fromMaster);
-//
-//        if (haveMesh)
-//        {
-//            // Check master names against mine
-//
-//            const polyBoundaryMesh& patches = mesh.boundaryMesh();
-//
-//            forAll(patchEntries, patchI)
-//            {
-//                const entry& e = patchEntries[patchI];
-//                const word type(e.dict().lookup("type"));
-//                const word& name = e.keyword();
-//
-//                if (type == processorPolyPatch::typeName)
-//                {
-//                    break;
-//                }
-//
-//                if (patchI >= patches.size())
-//                {
-//                    FatalErrorIn
-//                    (
-//                        "createMesh(const Time&, const fileName&, const bool)"
-//                    )   << "Non-processor patches not synchronised."
-//                        << endl
-//                        << "Processor " << Pstream::myProcNo()
-//                        << " has only " << patches.size()
-//                        << " patches, master has "
-//                        << patchI
-//                        << exit(FatalError);
-//                }
-//
-//                if
-//                (
-//                    type != patches[patchI].type()
-//                 || name != patches[patchI].name()
-//                )
-//                {
-//                    FatalErrorIn
-//                    (
-//                        "createMesh(const Time&, const fileName&, const bool)"
-//                    )   << "Non-processor patches not synchronised."
-//                        << endl
-//                        << "Master patch " << patchI
-//                        << " name:" << type
-//                        << " type:" << type << endl
-//                        << "Processor " << Pstream::myProcNo()
-//                        << " patch " << patchI
-//                        << " has name:" << patches[patchI].name()
-//                        << " type:" << patches[patchI].type()
-//                        << exit(FatalError);
-//                }
-//            }
-//        }
-//        else
-//        {
-//            // Add patch
-//            List<polyPatch*> patches(patchEntries.size());
-//            label nPatches = 0;
-//
-//            forAll(patchEntries, patchI)
-//            {
-//                const entry& e = patchEntries[patchI];
-//                const word type(e.dict().lookup("type"));
-//                const word& name = e.keyword();
-//
-//                if (type == processorPolyPatch::typeName)
-//                {
-//                    break;
-//                }
-//
-//                //Pout<< "Adding patch:" << nPatches
-//                //    << " name:" << name << " type:" << type << endl;
-//
-//                dictionary patchDict(e.dict());
-//                patchDict.remove("nFaces");
-//                patchDict.add("nFaces", 0);
-//                patchDict.remove("startFace");
-//                patchDict.add("startFace", 0);
-//
-//                patches[patchI] = polyPatch::New
-//                (
-//                    name,
-//                    patchDict,
-//                    nPatches++,
-//                    mesh.boundaryMesh()
-//                ).ptr();
-//            }
-//            patches.setSize(nPatches);
-//            mesh.addFvPatches(patches, false);  // no parallel comms
-//
-//            //// Write empty mesh now we have correct patches
-//            //meshPtr().write();
-//        }
-//    }
-//
-//
-//    // Determine zones
-//    // ~~~~~~~~~~~~~~~
-//
-//    wordList pointZoneNames(mesh.pointZones().names());
-//    Pstream::scatter(pointZoneNames);
-//    wordList faceZoneNames(mesh.faceZones().names());
-//    Pstream::scatter(faceZoneNames);
-//    wordList cellZoneNames(mesh.cellZones().names());
-//    Pstream::scatter(cellZoneNames);
-//
-//    if (!haveMesh)
-//    {
-//        // Add the zones. Make sure to remove the old dummy ones first
-//        mesh.pointZones().clear();
-//        mesh.faceZones().clear();
-//        mesh.cellZones().clear();
-//
-//        List<pointZone*> pz(pointZoneNames.size());
-//        forAll(pointZoneNames, i)
-//        {
-//            pz[i] = new pointZone
-//            (
-//                pointZoneNames[i],
-//                labelList(0),
-//                i,
-//                mesh.pointZones()
-//            );
-//        }
-//        List<faceZone*> fz(faceZoneNames.size());
-//        forAll(faceZoneNames, i)
-//        {
-//            fz[i] = new faceZone
-//            (
-//                faceZoneNames[i],
-//                labelList(0),
-//                boolList(0),
-//                i,
-//                mesh.faceZones()
-//            );
-//        }
-//        List<cellZone*> cz(cellZoneNames.size());
-//        forAll(cellZoneNames, i)
-//        {
-//            cz[i] = new cellZone
-//            (
-//                cellZoneNames[i],
-//                labelList(0),
-//                i,
-//                mesh.cellZones()
-//            );
-//        }
-//        mesh.addZones(pz, fz, cz);
-//    }
-//
-//
-//    if (!haveMesh)
-//    {
-//        // We created a dummy mesh file above. Delete it.
-//        //Pout<< "Removing dummy mesh " << io.objectPath() << endl;
-//        rmDir(io.objectPath());
-//    }
-//
-//    // Force recreation of globalMeshData.
-//    mesh.clearOut();
-//    mesh.globalData();
-//
-//
-//    // Do some checks.
-//
-//    // Check if the boundary definition is unique
-//    mesh.boundaryMesh().checkDefinition(true);
-//    // Check if the boundary processor patches are correct
-//    mesh.boundaryMesh().checkParallelSync(true);
-//    // Check names of zones are equal
-//    mesh.cellZones().checkDefinition(true);
-//    mesh.cellZones().checkParallelSync(true);
-//    mesh.faceZones().checkDefinition(true);
-//    mesh.faceZones().checkParallelSync(true);
-//    mesh.pointZones().checkDefinition(true);
-//    mesh.pointZones().checkParallelSync(true);
-//
-//    return meshPtr;
-//}
-
-
 // Get merging distance when matching face centres
 scalar getMergeDistance
 (
@@ -786,14 +498,6 @@ int main(int argc, char *argv[])
     Info<< "Per processor mesh availability : " << haveMesh << endl;
     const bool allHaveMesh = (findIndex(haveMesh, false) == -1);
 
-    // Create mesh
-    //autoPtr<fvMesh> meshPtr = createMesh
-    //(
-    //    runTime,
-    //    regionName,
-    //    masterInstDir,
-    //    haveMesh[Pstream::myProcNo()]
-    //);
     autoPtr<fvMesh> meshPtr = loadOrCreateMesh
     (
         IOobject
@@ -908,6 +612,9 @@ int main(int argc, char *argv[])
         objects.erase(iter);
     }
 
+
+    // volFields
+
     PtrList<volScalarField> volScalarFields;
     readFields
     (
@@ -958,6 +665,9 @@ int main(int argc, char *argv[])
         volTensorFields
     );
 
+
+    // surfaceFields
+
     PtrList<surfaceScalarField> surfScalarFields;
     readFields
     (

From e9de9f87d240cc2d33dcca0b15a2de83aa533f94 Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Mon, 2 Jul 2012 15:30:19 +0100
Subject: [PATCH 04/38] STYLE: polyMeshClear: use polyBoundaryMesh
 functionality

---
 src/OpenFOAM/meshes/polyMesh/polyMeshClear.C | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/src/OpenFOAM/meshes/polyMesh/polyMeshClear.C b/src/OpenFOAM/meshes/polyMesh/polyMeshClear.C
index 8960e932ab..9a9830545e 100644
--- a/src/OpenFOAM/meshes/polyMesh/polyMeshClear.C
+++ b/src/OpenFOAM/meshes/polyMesh/polyMeshClear.C
@@ -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) 2011-2012 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -63,10 +63,7 @@ void Foam::polyMesh::clearGeom()
 
     primitiveMesh::clearGeom();
 
-    forAll(boundary_, patchI)
-    {
-        boundary_[patchI].clearGeom();
-    }
+    boundary_.clearGeom();
 
     // Reset valid directions (could change with rotation)
     geometricD_ = Vector<label>::zero;

From 91dca0eb2f1a03f8187551d145b782b169f78522 Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Mon, 2 Jul 2012 15:31:01 +0100
Subject: [PATCH 05/38] ENH: polyPatch: make clearing of geometry virtual

---
 .../meshes/polyMesh/polyPatches/polyPatch/polyPatch.C     | 8 +++++++-
 .../meshes/polyMesh/polyPatches/polyPatch/polyPatch.H     | 7 +++++--
 2 files changed, 12 insertions(+), 3 deletions(-)

diff --git a/src/OpenFOAM/meshes/polyMesh/polyPatches/polyPatch/polyPatch.C b/src/OpenFOAM/meshes/polyMesh/polyPatches/polyPatch/polyPatch.C
index 711461d352..e22381b7dd 100644
--- a/src/OpenFOAM/meshes/polyMesh/polyPatches/polyPatch/polyPatch.C
+++ b/src/OpenFOAM/meshes/polyMesh/polyPatches/polyPatch/polyPatch.C
@@ -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) 2011-2012 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -65,6 +65,12 @@ void Foam::polyPatch::updateMesh(PstreamBuffers&)
 }
 
 
+void Foam::polyPatch::clearGeom()
+{
+    primitivePatch::clearGeom();
+}
+
+
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
 Foam::polyPatch::polyPatch
diff --git a/src/OpenFOAM/meshes/polyMesh/polyPatches/polyPatch/polyPatch.H b/src/OpenFOAM/meshes/polyMesh/polyPatches/polyPatch/polyPatch.H
index 0fa859bddb..dd06c03195 100644
--- a/src/OpenFOAM/meshes/polyMesh/polyPatches/polyPatch/polyPatch.H
+++ b/src/OpenFOAM/meshes/polyMesh/polyPatches/polyPatch/polyPatch.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) 2011-2012 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -116,6 +116,9 @@ protected:
         //- Update of the patch topology
         virtual void updateMesh(PstreamBuffers&);
 
+        //- Clear geometry
+        virtual void clearGeom();
+
 
 public:
 
@@ -338,7 +341,7 @@ public:
             const labelList& meshEdges() const;
 
             //- Clear addressing
-            void clearAddressing();
+            virtual void clearAddressing();
 
 
         // Other patch operations

From ec29827f2928b6ba7ed965553da00e53d4e9a9bf Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Mon, 2 Jul 2012 15:31:39 +0100
Subject: [PATCH 06/38] ENH: fvPatch: make coupled virtual so AMI can
 manipulate it

---
 src/finiteVolume/fvMesh/fvPatches/fvPatch/fvPatch.H | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/finiteVolume/fvMesh/fvPatches/fvPatch/fvPatch.H b/src/finiteVolume/fvMesh/fvPatches/fvPatch/fvPatch.H
index 28a07343e5..d135007da0 100644
--- a/src/finiteVolume/fvMesh/fvPatches/fvPatch/fvPatch.H
+++ b/src/finiteVolume/fvMesh/fvPatches/fvPatch/fvPatch.H
@@ -165,7 +165,7 @@ public:
             }
 
             //- Return true if this patch is coupled
-            bool coupled() const
+            virtual bool coupled() const
             {
                 return polyPatch_.coupled();
             }

From fddfec04c3106e7321a411e2552dad6b64b0f83e Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Mon, 2 Jul 2012 15:32:32 +0100
Subject: [PATCH 07/38] ENH: AMI: behave uncoupled wherever necessary; detect
 geometry changes

---
 .../cyclicAMI/cyclicAMIFvPatchField.C         | 16 +---
 .../constraint/cyclicAMI/cyclicAMIFvPatch.C   | 94 ++++++++++++-------
 .../constraint/cyclicAMI/cyclicAMIFvPatch.H   |  7 +-
 .../AMIInterpolation/AMIInterpolation.C       | 12 ++-
 .../cyclicAMIPolyPatch/cyclicAMIPolyPatch.C   | 31 +++---
 .../cyclicAMIPolyPatch/cyclicAMIPolyPatch.H   |  5 +-
 6 files changed, 95 insertions(+), 70 deletions(-)

diff --git a/src/finiteVolume/fields/fvPatchFields/constraint/cyclicAMI/cyclicAMIFvPatchField.C b/src/finiteVolume/fields/fvPatchFields/constraint/cyclicAMI/cyclicAMIFvPatchField.C
index fc48848757..197179a115 100644
--- a/src/finiteVolume/fields/fvPatchFields/constraint/cyclicAMI/cyclicAMIFvPatchField.C
+++ b/src/finiteVolume/fields/fvPatchFields/constraint/cyclicAMI/cyclicAMIFvPatchField.C
@@ -143,21 +143,7 @@ Foam::cyclicAMIFvPatchField<Type>::cyclicAMIFvPatchField
 template<class Type>
 bool Foam::cyclicAMIFvPatchField<Type>::coupled() const
 {
-    if
-    (
-        Pstream::parRun()
-     || (
-            this->cyclicAMIPatch_.size()
-         && this->cyclicAMIPatch_.cyclicAMIPatch().neighbPatch().size()
-        )
-    )
-    {
-        return true;
-    }
-    else
-    {
-        return false;
-    }
+    return cyclicAMIPatch_.coupled();
 }
 
 
diff --git a/src/finiteVolume/fvMesh/fvPatches/constraint/cyclicAMI/cyclicAMIFvPatch.C b/src/finiteVolume/fvMesh/fvPatches/constraint/cyclicAMI/cyclicAMIFvPatch.C
index 7b11172119..8d2f1b4cdd 100644
--- a/src/finiteVolume/fvMesh/fvPatches/constraint/cyclicAMI/cyclicAMIFvPatch.C
+++ b/src/finiteVolume/fvMesh/fvPatches/constraint/cyclicAMI/cyclicAMIFvPatch.C
@@ -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) 2011-2012 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -39,60 +39,82 @@ namespace Foam
 
 // * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
 
+bool Foam::cyclicAMIFvPatch::coupled() const
+{
+    return Pstream::parRun() || (this->size() && neighbFvPatch().size());
+}
+
+
 void Foam::cyclicAMIFvPatch::makeWeights(scalarField& w) const
 {
-    const cyclicAMIFvPatch& nbrPatch = neighbFvPatch();
-
-    const scalarField deltas(nf() & fvPatch::delta());
-
-    const scalarField nbrDeltas
-    (
-        interpolate(nbrPatch.nf() & nbrPatch.fvPatch::delta())
-    );
-
-    forAll(deltas, faceI)
+    if (coupled())
     {
-        scalar di = deltas[faceI];
-        scalar dni = nbrDeltas[faceI];
+        const cyclicAMIFvPatch& nbrPatch = neighbFvPatch();
 
-        w[faceI] = dni/(di + dni);
+        const scalarField deltas(nf() & fvPatch::delta());
+
+        const scalarField nbrDeltas
+        (
+            interpolate(nbrPatch.nf() & nbrPatch.fvPatch::delta())
+        );
+
+        forAll(deltas, faceI)
+        {
+            scalar di = deltas[faceI];
+            scalar dni = nbrDeltas[faceI];
+
+            w[faceI] = dni/(di + dni);
+        }
+    }
+    else
+    {
+        // Behave as uncoupled patch
+        fvPatch::makeWeights(w);
     }
 }
 
 
 Foam::tmp<Foam::vectorField> Foam::cyclicAMIFvPatch::delta() const
 {
-    const vectorField patchD(fvPatch::delta());
-
     const cyclicAMIFvPatch& nbrPatch = neighbFvPatch();
-    const vectorField nbrPatchD(interpolate(nbrPatch.fvPatch::delta()));
 
-    tmp<vectorField> tpdv(new vectorField(patchD.size()));
-    vectorField& pdv = tpdv();
-
-    // do the transformation if necessary
-    if (parallel())
+    if (coupled())
     {
-        forAll(patchD, faceI)
-        {
-            const vector& ddi = patchD[faceI];
-            const vector& dni = nbrPatchD[faceI];
+        const vectorField patchD(fvPatch::delta());
 
-            pdv[faceI] = ddi - dni;
+        const vectorField nbrPatchD(interpolate(nbrPatch.fvPatch::delta()));
+
+        tmp<vectorField> tpdv(new vectorField(patchD.size()));
+        vectorField& pdv = tpdv();
+
+        // do the transformation if necessary
+        if (parallel())
+        {
+            forAll(patchD, faceI)
+            {
+                const vector& ddi = patchD[faceI];
+                const vector& dni = nbrPatchD[faceI];
+
+                pdv[faceI] = ddi - dni;
+            }
         }
+        else
+        {
+            forAll(patchD, faceI)
+            {
+                const vector& ddi = patchD[faceI];
+                const vector& dni = nbrPatchD[faceI];
+
+                pdv[faceI] = ddi - transform(forwardT()[0], dni);
+            }
+        }
+
+        return tpdv;
     }
     else
     {
-        forAll(patchD, faceI)
-        {
-            const vector& ddi = patchD[faceI];
-            const vector& dni = nbrPatchD[faceI];
-
-            pdv[faceI] = ddi - transform(forwardT()[0], dni);
-        }
+        return fvPatch::delta();
     }
-
-    return tpdv;
 }
 
 
diff --git a/src/finiteVolume/fvMesh/fvPatches/constraint/cyclicAMI/cyclicAMIFvPatch.H b/src/finiteVolume/fvMesh/fvPatches/constraint/cyclicAMI/cyclicAMIFvPatch.H
index 02317e09a7..a44049077e 100644
--- a/src/finiteVolume/fvMesh/fvPatches/constraint/cyclicAMI/cyclicAMIFvPatch.H
+++ b/src/finiteVolume/fvMesh/fvPatches/constraint/cyclicAMI/cyclicAMIFvPatch.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) 2011-2012 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -146,6 +146,11 @@ public:
                 );
             }
 
+            //- Return true if this patch is coupled. This is equivalent
+            //  to the coupledPolyPatch::coupled() if parallel running or
+            //  both sides present, false otherwise
+            virtual bool coupled() const;
+
             //- Return delta (P to N) vectors across coupled patch
             virtual tmp<vectorField> delta() const;
 
diff --git a/src/meshTools/AMIInterpolation/AMIInterpolation/AMIInterpolation.C b/src/meshTools/AMIInterpolation/AMIInterpolation/AMIInterpolation.C
index ad5a974ed7..5781ef9911 100644
--- a/src/meshTools/AMIInterpolation/AMIInterpolation/AMIInterpolation.C
+++ b/src/meshTools/AMIInterpolation/AMIInterpolation/AMIInterpolation.C
@@ -965,6 +965,13 @@ void Foam::AMIInterpolation<SourcePatch, TargetPatch>::calcAddressing
     label tgtFaceI
 )
 {
+    // Pre-size to handle early exit
+    srcAddress_.setSize(srcPatch.size());
+    srcWeights_.setSize(srcPatch.size());
+    tgtAddress_.setSize(tgtPatch.size());
+    tgtWeights_.setSize(tgtPatch.size());
+
+
     if (debug && (!srcPatch.size() || !tgtPatch.size()))
     {
         Pout<< "AMI: Patches not on processor: Source faces = "
@@ -1134,16 +1141,11 @@ void Foam::AMIInterpolation<SourcePatch, TargetPatch>::calcAddressing
     }
 
     // transfer data to persistent storage
-    srcAddress_.setSize(srcPatch.size());
-    srcWeights_.setSize(srcPatch.size());
     forAll(srcAddr, i)
     {
         srcAddress_[i].transfer(srcAddr[i]);
         srcWeights_[i].transfer(srcWght[i]);
     }
-
-    tgtAddress_.setSize(tgtPatch.size());
-    tgtWeights_.setSize(tgtPatch.size());
     forAll(tgtAddr, i)
     {
         tgtAddress_[i].transfer(tgtAddr[i]);
diff --git a/src/meshTools/AMIInterpolation/patches/cyclic/cyclicAMIPolyPatch/cyclicAMIPolyPatch.C b/src/meshTools/AMIInterpolation/patches/cyclic/cyclicAMIPolyPatch/cyclicAMIPolyPatch.C
index 67414fa432..61125254b0 100644
--- a/src/meshTools/AMIInterpolation/patches/cyclic/cyclicAMIPolyPatch/cyclicAMIPolyPatch.C
+++ b/src/meshTools/AMIInterpolation/patches/cyclic/cyclicAMIPolyPatch/cyclicAMIPolyPatch.C
@@ -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) 2011-2012 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -208,7 +208,7 @@ void Foam::cyclicAMIPolyPatch::calcTransforms
         {
             if (debug)
             {
-                Pout<< " patch:" << name()
+                Pout<< "patch:" << name()
                     << " Assuming cyclic AMI pairs are colocated" << endl;
             }
 
@@ -282,6 +282,16 @@ void Foam::cyclicAMIPolyPatch::resetAMI() const
                 AMIReverse_
             )
         );
+
+        if (debug)
+        {
+            Pout<< "cyclicAMIPolyPatch : " << name()
+                << " constructed AMI with " << nl
+                << "    " << ":srcAddress:" << AMIPtr_().srcAddress().size()
+                << nl
+                << "    " << " tgAddress :" << AMIPtr_().tgtAddress().size()
+                << nl << endl;
+        }
     }
 }
 
@@ -345,6 +355,13 @@ void Foam::cyclicAMIPolyPatch::updateMesh(PstreamBuffers& pBufs)
 }
 
 
+void Foam::cyclicAMIPolyPatch::clearGeom()
+{
+    AMIPtr_.clear();
+    polyPatch::clearGeom();
+}
+
+
 // * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * * * //
 
 Foam::cyclicAMIPolyPatch::cyclicAMIPolyPatch
@@ -645,16 +662,6 @@ const Foam::AMIPatchToPatchInterpolation& Foam::cyclicAMIPolyPatch::AMI() const
         resetAMI();
     }
 
-
-    if (debug)
-    {
-        Pout<< "cyclicAMIPolyPatch : " << name()
-            << " constructed AMI with " << endl
-            << "    " << ":srcAddress:" << AMIPtr_().srcAddress().size() << endl
-            << "    " << " tgAddress :" << AMIPtr_().tgtAddress().size() << endl
-            << endl;
-    }
-
     return AMIPtr_();
 }
 
diff --git a/src/meshTools/AMIInterpolation/patches/cyclic/cyclicAMIPolyPatch/cyclicAMIPolyPatch.H b/src/meshTools/AMIInterpolation/patches/cyclic/cyclicAMIPolyPatch/cyclicAMIPolyPatch.H
index 7765ba2ac2..f1418c6f04 100644
--- a/src/meshTools/AMIInterpolation/patches/cyclic/cyclicAMIPolyPatch/cyclicAMIPolyPatch.H
+++ b/src/meshTools/AMIInterpolation/patches/cyclic/cyclicAMIPolyPatch/cyclicAMIPolyPatch.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) 2011-2012 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -141,6 +141,9 @@ protected:
         //- Update of the patch topology
         virtual void updateMesh(PstreamBuffers&);
 
+        //- Clear geometry
+        virtual void clearGeom();
+
 
 public:
 

From 32f31a4fefbdb8f5e733bd0ffdd2adc3560fcfed Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Mon, 2 Jul 2012 15:33:50 +0100
Subject: [PATCH 08/38] ENH: reconstructPar: -newTimes cleanup

---
 .../reconstructPar/reconstructPar.C           | 33 +++++++++++++++----
 1 file changed, 27 insertions(+), 6 deletions(-)

diff --git a/applications/utilities/parallelProcessing/reconstructPar/reconstructPar.C b/applications/utilities/parallelProcessing/reconstructPar/reconstructPar.C
index b47a15a6e1..916a0845e5 100644
--- a/applications/utilities/parallelProcessing/reconstructPar/reconstructPar.C
+++ b/applications/utilities/parallelProcessing/reconstructPar/reconstructPar.C
@@ -143,8 +143,6 @@ int main(int argc, char *argv[])
         args
     );
 
-    instantList masterTimeDirs = runTime.times();
-
     if (timeDirs.empty())
     {
         FatalErrorIn(args.executable())
@@ -152,6 +150,16 @@ int main(int argc, char *argv[])
             << exit(FatalError);
     }
 
+
+    // Get current times if -newTimes
+    instantList masterTimeDirs;
+    if (newTimes)
+    {
+        masterTimeDirs = runTime.times();
+    }
+
+
+
 #   include "createNamedMesh.H"
     word regionDir = word::null;
     if (regionName != fvMesh::defaultRegion)
@@ -176,11 +184,24 @@ int main(int argc, char *argv[])
     // Loop over all times
     forAll(timeDirs, timeI)
     {
-        if (newTimes && findIndex(masterTimeDirs, timeDirs[timeI]) != -1)
+        if (newTimes)
         {
-            Info<< "Skipping time " << timeDirs[timeI].name()
-                << endl << endl;
-            continue;
+            // Compare on timeName, not value
+            bool foundTime = false;
+            forAll(masterTimeDirs, i)
+            {
+                if (masterTimeDirs[i].name() == timeDirs[timeI].name())
+                {
+                    foundTime = true;
+                    break;
+                }
+            }
+            if (foundTime)
+            {
+                Info<< "Skipping time " << timeDirs[timeI].name()
+                    << endl << endl;
+                continue;
+            }
         }
 
 

From 6e818675629627ce1fc3e78fe77c483084a9e21f Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Mon, 2 Jul 2012 17:18:52 +0100
Subject: [PATCH 09/38] ENH: meshToMesh: allow deeper patch octree

---
 .../meshToMesh/calculateMeshToMeshAddressing.C            | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/src/sampling/meshToMeshInterpolation/meshToMesh/calculateMeshToMeshAddressing.C b/src/sampling/meshToMeshInterpolation/meshToMesh/calculateMeshToMeshAddressing.C
index fda5525f09..83716c95c4 100644
--- a/src/sampling/meshToMeshInterpolation/meshToMesh/calculateMeshToMeshAddressing.C
+++ b/src/sampling/meshToMeshInterpolation/meshToMesh/calculateMeshToMeshAddressing.C
@@ -171,13 +171,15 @@ void Foam::meshToMesh::calcAddressing()
                     wallBb.max() + vector(typDim, typDim, typDim)
                 );
 
+                // Note: allow more levels than in meshSearch. Assume patch
+                // is not as big as all boundary faces
                 indexedOctree<treeDataFace> oc
                 (
                     treeDataFace(false, fromPatch),
                     shiftedBb,  // overall search domain
-                    8,          // maxLevel
+                    12,         // maxLevel
                     10,         // leafsize
-                    3.0         // duplicity
+                    6.0         // duplicity
                 );
 
                 const vectorField::subField centresToBoundary =
@@ -185,7 +187,7 @@ void Foam::meshToMesh::calcAddressing()
 
                 boundaryAddressing_[patchi].setSize(toPatch.size());
 
-                scalar distSqr = sqr(GREAT);
+                scalar distSqr = sqr(wallBb.mag());
 
                 forAll(toPatch, toi)
                 {

From 17ca48dcd6f5136babc458263e131be1408963d5 Mon Sep 17 00:00:00 2001
From: Henry <Henry>
Date: Tue, 3 Jul 2012 15:04:43 +0100
Subject: [PATCH 10/38] fvMatrix: Removed temporary hack

---
 src/finiteVolume/fvMatrices/fvMatrix/fvMatrix.H | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/finiteVolume/fvMatrices/fvMatrix/fvMatrix.H b/src/finiteVolume/fvMatrices/fvMatrix/fvMatrix.H
index ce214e60c8..3f747fcb82 100644
--- a/src/finiteVolume/fvMatrices/fvMatrix/fvMatrix.H
+++ b/src/finiteVolume/fvMatrices/fvMatrix/fvMatrix.H
@@ -142,8 +142,8 @@ class fvMatrix
         mutable GeometricField<Type, fvsPatchField, surfaceMesh>
             *faceFluxCorrectionPtr_;
 
-// ***HGW for testing LduMatrix protected:
-public:
+
+protected:
 
     //- Declare friendship with the fvSolver class
     friend class fvSolver;

From f0d5bf1a3a8bc4deaa6aca7c186210985455ab46 Mon Sep 17 00:00:00 2001
From: Henry <Henry>
Date: Tue, 3 Jul 2012 15:05:07 +0100
Subject: [PATCH 11/38] interRegionHeatTransferModel: Updated temporary code

---
 .../interRegionHeatTransferModel.C                             | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/fieldSources/basicSource/interRegionHeatTransferModel/interRegionHeatTransferModel/interRegionHeatTransferModel.C b/src/fieldSources/basicSource/interRegionHeatTransferModel/interRegionHeatTransferModel/interRegionHeatTransferModel.C
index 772f26094a..9105347079 100644
--- a/src/fieldSources/basicSource/interRegionHeatTransferModel/interRegionHeatTransferModel/interRegionHeatTransferModel.C
+++ b/src/fieldSources/basicSource/interRegionHeatTransferModel/interRegionHeatTransferModel/interRegionHeatTransferModel.C
@@ -198,8 +198,7 @@ void Foam::interRegionHeatTransferModel::addSup
                 << endl;
         }
 
-        //SAF: temporarily output
-        if (mesh_.time().outputTime())
+        if (debug && mesh_.time().outputTime())
         {
             Tmapped.write();
             htc_.write();

From 9a0b88fbbcbe4c3a6a0ea748b2cc97b8c4dddc64 Mon Sep 17 00:00:00 2001
From: Henry <Henry>
Date: Tue, 3 Jul 2012 15:05:18 +0100
Subject: [PATCH 12/38] Updated header

---
 .../interRegionHeatTransferModel/interRegionHeatTransferModel.C | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/fieldSources/basicSource/interRegionHeatTransferModel/interRegionHeatTransferModel/interRegionHeatTransferModel.C b/src/fieldSources/basicSource/interRegionHeatTransferModel/interRegionHeatTransferModel/interRegionHeatTransferModel.C
index 9105347079..f9ffec2938 100644
--- a/src/fieldSources/basicSource/interRegionHeatTransferModel/interRegionHeatTransferModel/interRegionHeatTransferModel.C
+++ b/src/fieldSources/basicSource/interRegionHeatTransferModel/interRegionHeatTransferModel/interRegionHeatTransferModel.C
@@ -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) 2011-2012 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License

From aaf2b3973b53f11591add4ece91c604cadb0398d Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Wed, 4 Jul 2012 09:58:56 +0100
Subject: [PATCH 13/38] STYLE: manualDecomp: corrected message

---
 .../decompositionMethods/manualDecomp/manualDecomp.H          | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/parallel/decompose/decompositionMethods/manualDecomp/manualDecomp.H b/src/parallel/decompose/decompositionMethods/manualDecomp/manualDecomp.H
index 28a1d4c539..cd2ba9b430 100644
--- a/src/parallel/decompose/decompositionMethods/manualDecomp/manualDecomp.H
+++ b/src/parallel/decompose/decompositionMethods/manualDecomp/manualDecomp.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) 2011-2012 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -111,7 +111,7 @@ public:
             notImplemented
             (
                 "decompose(const labelListList&, const pointField&"
-                ", const scalarField)"
+                ", const scalarField&)"
             );
             return labelList(0);
         }

From 82ec0dbe6b0d3f6bb5a2099a17250d9ce6950953 Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Wed, 4 Jul 2012 10:00:31 +0100
Subject: [PATCH 14/38] ENH: decompositionMethods: added none method

---
 .../decompose/decompositionMethods/Make/files |   1 +
 .../decompositionMethods/noDecomp/noDecomp.C  |  53 +++++++
 .../decompositionMethods/noDecomp/noDecomp.H  | 134 ++++++++++++++++++
 3 files changed, 188 insertions(+)
 create mode 100644 src/parallel/decompose/decompositionMethods/noDecomp/noDecomp.C
 create mode 100644 src/parallel/decompose/decompositionMethods/noDecomp/noDecomp.H

diff --git a/src/parallel/decompose/decompositionMethods/Make/files b/src/parallel/decompose/decompositionMethods/Make/files
index b21f2c70bd..5e54b366af 100644
--- a/src/parallel/decompose/decompositionMethods/Make/files
+++ b/src/parallel/decompose/decompositionMethods/Make/files
@@ -6,5 +6,6 @@ manualDecomp/manualDecomp.C
 multiLevelDecomp/multiLevelDecomp.C
 structuredDecomp/topoDistanceData.C
 structuredDecomp/structuredDecomp.C
+noDecomp/noDecomp.C
 
 LIB = $(FOAM_LIBBIN)/libdecompositionMethods
diff --git a/src/parallel/decompose/decompositionMethods/noDecomp/noDecomp.C b/src/parallel/decompose/decompositionMethods/noDecomp/noDecomp.C
new file mode 100644
index 0000000000..e62e588b9e
--- /dev/null
+++ b/src/parallel/decompose/decompositionMethods/noDecomp/noDecomp.C
@@ -0,0 +1,53 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 2012 OpenFOAM Foundation
+     \\/     M anipulation  |
+-------------------------------------------------------------------------------
+License
+    This file is part of OpenFOAM.
+
+    OpenFOAM is free software: you can redistribute it and/or modify it
+    under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
+    ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+    FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
+    for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
+
+\*---------------------------------------------------------------------------*/
+
+#include "noDecomp.H"
+#include "addToRunTimeSelectionTable.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+    defineTypeName(noDecomp);
+
+    addNamedToRunTimeSelectionTable
+    (
+        decompositionMethod,
+        noDecomp,
+        dictionary,
+        none
+    );
+}
+
+
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+Foam::noDecomp::noDecomp(const dictionary& decompositionDict)
+:
+    decompositionMethod(decompositionDict)
+{}
+
+
+// ************************************************************************* //
diff --git a/src/parallel/decompose/decompositionMethods/noDecomp/noDecomp.H b/src/parallel/decompose/decompositionMethods/noDecomp/noDecomp.H
new file mode 100644
index 0000000000..13368c9970
--- /dev/null
+++ b/src/parallel/decompose/decompositionMethods/noDecomp/noDecomp.H
@@ -0,0 +1,134 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 2012 OpenFOAM Foundation
+     \\/     M anipulation  |
+-------------------------------------------------------------------------------
+License
+    This file is part of OpenFOAM.
+
+    OpenFOAM is free software: you can redistribute it and/or modify it
+    under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
+    ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+    FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
+    for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
+
+Class
+    Foam::noDecomp
+
+Description
+    Dummy decomposition method
+
+SourceFiles
+    noDecomp.C
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef noDecomp_H
+#define noDecomp_H
+
+#include "decompositionMethod.H"
+
+namespace Foam
+{
+
+/*---------------------------------------------------------------------------*\
+                           Class noDecomp Declaration
+\*---------------------------------------------------------------------------*/
+
+class noDecomp
+:
+    public decompositionMethod
+{
+
+    // Private Member Functions
+
+        //- Disallow default bitwise copy construct and assignment
+        void operator=(const noDecomp&);
+        noDecomp(const noDecomp&);
+
+
+public:
+
+    //- Runtime type information
+    TypeName("noDecomp");
+
+
+    // Constructors
+
+        //- Construct given the decomposition dictionary
+        noDecomp(const dictionary& decompositionDict);
+
+    //- Destructor
+    virtual ~noDecomp()
+    {}
+
+
+    // Member Functions
+
+        //- manual decompose does not care about proc boundaries - is all
+        //  up to the user.
+        virtual bool parallelAware() const
+        {
+            return false;
+        }
+
+        //- Return for every coordinate the wanted processor number. Use the
+        //  mesh connectivity (if needed)
+        virtual labelList decompose
+        (
+            const polyMesh& mesh,
+            const pointField& cc,
+            const scalarField& cWeights
+        )
+        {
+            notImplemented
+            (
+                "decompose(const polyMesh&, const pointField&"
+                ", const scalarField&)"
+            );
+            return labelList(0);
+        }
+
+        //- Return for every coordinate the wanted processor number. Explicitly
+        //  provided connectivity - does not use mesh_.
+        //  The connectivity is equal to mesh.cellCells() except for
+        //  - in parallel the cell numbers are global cell numbers (starting
+        //    from 0 at processor0 and then incrementing all through the
+        //    processors)
+        //  - the connections are across coupled patches
+        virtual labelList decompose
+        (
+            const labelListList& globalCellCells,
+            const pointField& cc,
+            const scalarField& cWeights
+        )
+        {
+            notImplemented
+            (
+                "decompose(const labelListList&, const pointField&"
+                ", const scalarField&)"
+            );
+            return labelList(0);
+        }
+
+};
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#endif
+
+// ************************************************************************* //

From 33656b39691a96f9032c2596ad96a2c2c2edfced Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Wed, 4 Jul 2012 10:01:25 +0100
Subject: [PATCH 15/38] ENH: snappyHexMesh: run without decomposeParDict

---
 .../generation/snappyHexMesh/snappyHexMesh.C  | 21 ++++++++++++++-----
 1 file changed, 16 insertions(+), 5 deletions(-)

diff --git a/applications/utilities/mesh/generation/snappyHexMesh/snappyHexMesh.C b/applications/utilities/mesh/generation/snappyHexMesh/snappyHexMesh.C
index 279808bff1..d991719071 100644
--- a/applications/utilities/mesh/generation/snappyHexMesh/snappyHexMesh.C
+++ b/applications/utilities/mesh/generation/snappyHexMesh/snappyHexMesh.C
@@ -40,6 +40,7 @@ Description
 #include "refinementFeatures.H"
 #include "shellSurfaces.H"
 #include "decompositionMethod.H"
+#include "noDecomp.H"
 #include "fvMeshDistribute.H"
 #include "wallPolyPatch.H"
 #include "refinementParameters.H"
@@ -176,17 +177,27 @@ int main(int argc, char *argv[])
 
 
     // Read decomposePar dictionary
-    IOdictionary decomposeDict
-    (
-        IOobject
+    dictionary decomposeDict;
+    {
+        IOobject io
         (
             "decomposeParDict",
             runTime.system(),
             mesh,
             IOobject::MUST_READ_IF_MODIFIED,
             IOobject::NO_WRITE
-        )
-    );
+        );
+
+        if (io.headerOk())
+        {
+            decomposeDict = IOdictionary(io);
+        }
+        else
+        {
+            decomposeDict.add("method", "none");
+            decomposeDict.add("numberOfSubdomains", 1);
+        }
+    }
 
 
     // Debug

From f64b5a1b77185f436ba9298e135afd0a41a2f1a1 Mon Sep 17 00:00:00 2001
From: sergio <sergio>
Date: Wed, 4 Jul 2012 14:22:08 +0100
Subject: [PATCH 16/38] BUG: Re-arrenging the solidThermo interface

---
 .../reactingOneDim/reactingOneDim.C           |  4 +-
 .../thermoBaffle2D/thermoBaffle2D.C           |  2 +-
 .../basic/basicThermo/basicThermo.C           | 55 -----------
 .../basic/rhoThermo/rhoThermo/rhoThermo.C     | 19 ++++
 .../basic/rhoThermo/rhoThermo/rhoThermo.H     |  3 +
 .../heSolidThermo/heSolidThermo.H             |  3 -
 .../solidThermo/solidThermo.C                 | 78 +---------------
 .../solidThermo/solidThermo.H                 | 92 +------------------
 8 files changed, 29 insertions(+), 227 deletions(-)

diff --git a/src/regionModels/pyrolysisModels/reactingOneDim/reactingOneDim.C b/src/regionModels/pyrolysisModels/reactingOneDim/reactingOneDim.C
index e19084dd3d..65143f5d27 100644
--- a/src/regionModels/pyrolysisModels/reactingOneDim/reactingOneDim.C
+++ b/src/regionModels/pyrolysisModels/reactingOneDim/reactingOneDim.C
@@ -349,7 +349,7 @@ reactingOneDim::reactingOneDim(const word& modelType, const fvMesh& mesh)
     pyrolysisModel(modelType, mesh),
     solidChemistry_(solidChemistryModel::New(regionMesh())),
     solidThermo_(solidChemistry_->solid()),
-    rho_(solidThermo_.rhos()),
+    rho_(solidThermo_.rho()),
     Ys_(solidThermo_.composition().Y()),
     h_(solidThermo_.he()),
     primaryRadFluxName_(coeffs().lookupOrDefault<word>("radFluxName", "Qr")),
@@ -449,7 +449,7 @@ reactingOneDim::reactingOneDim
     pyrolysisModel(modelType, mesh, dict),
     solidChemistry_(solidChemistryModel::New(regionMesh())),
     solidThermo_(solidChemistry_->solid()),
-    rho_(solidThermo_.rhos()),
+    rho_(solidThermo_.rho()),
     Ys_(solidThermo_.composition().Y()),
     h_(solidThermo_.he()),
     primaryRadFluxName_(dict.lookupOrDefault<word>("radFluxName", "Qr")),
diff --git a/src/regionModels/thermoBaffleModels/thermoBaffle2D/thermoBaffle2D.C b/src/regionModels/thermoBaffleModels/thermoBaffle2D/thermoBaffle2D.C
index a0495d2d06..97faec40cb 100644
--- a/src/regionModels/thermoBaffleModels/thermoBaffle2D/thermoBaffle2D.C
+++ b/src/regionModels/thermoBaffleModels/thermoBaffle2D/thermoBaffle2D.C
@@ -359,7 +359,7 @@ void thermoBaffle2D::info() const
             (
                 mag(regionMesh().Sf().boundaryField()[patchI])
               * ph.snGrad()
-              * thermo_->alpha(patchI)
+              * thermo_->alpha().boundaryField()[patchI]
             ) << endl;
     }
 }
diff --git a/src/thermophysicalModels/basic/basicThermo/basicThermo.C b/src/thermophysicalModels/basic/basicThermo/basicThermo.C
index aa90283d51..1390c214a2 100644
--- a/src/thermophysicalModels/basic/basicThermo/basicThermo.C
+++ b/src/thermophysicalModels/basic/basicThermo/basicThermo.C
@@ -40,62 +40,7 @@ namespace Foam
     defineTypeNameAndDebug(basicThermo, 0);
     defineRunTimeSelectionTable(basicThermo, fvMesh);
 }
-/*
-// * * * * * * * * * * * * Protected Member Functions  * * * * * * * * * * * //
 
-Foam::wordList Foam::basicThermo::heBoundaryTypes()
-{
-    const volScalarField::GeometricBoundaryField& tbf = T_.boundaryField();
-
-    wordList hbt = tbf.types();
-
-    forAll(tbf, patchi)
-    {
-        if (isA<fixedValueFvPatchScalarField>(tbf[patchi]))
-        {
-            hbt[patchi] = fixedEnergyFvPatchScalarField::typeName;
-        }
-        else if
-        (
-            isA<zeroGradientFvPatchScalarField>(tbf[patchi])
-         || isA<fixedGradientFvPatchScalarField>(tbf[patchi])
-        )
-        {
-            hbt[patchi] = gradientEnergyFvPatchScalarField::typeName;
-        }
-        else if(isA<mixedFvPatchScalarField>(tbf[patchi]))
-        {
-            hbt[patchi] = mixedEnergyFvPatchScalarField::typeName;
-        }
-        else if (isA<temperatureJumpFvPatchScalarField>(tbf[patchi]))
-        {
-            hbt[patchi] = energyJumpFvPatchScalarField::typeName;
-        }
-    }
-
-    return hbt;
-}
-
-
-void Foam::basicThermo::heBoundaryCorrection(volScalarField& h)
-{
-    volScalarField::GeometricBoundaryField& hbf = h.boundaryField();
-
-    forAll(hbf, patchi)
-    {
-        if (isA<gradientEnergyFvPatchScalarField>(hbf[patchi]))
-        {
-            refCast<gradientEnergyFvPatchScalarField>(hbf[patchi]).gradient()
-                = hbf[patchi].fvPatchField::snGrad();
-        }
-        else if (isA<mixedEnergyFvPatchScalarField>(hbf[patchi]))
-        {
-            refCast<mixedEnergyFvPatchScalarField>(hbf[patchi]).refGrad()
-                = hbf[patchi].fvPatchField::snGrad();
-        }
-    }
-}
-*/
 
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
diff --git a/src/thermophysicalModels/basic/rhoThermo/rhoThermo/rhoThermo.C b/src/thermophysicalModels/basic/rhoThermo/rhoThermo/rhoThermo.C
index 8cafa9454c..33c7905fee 100644
--- a/src/thermophysicalModels/basic/rhoThermo/rhoThermo/rhoThermo.C
+++ b/src/thermophysicalModels/basic/rhoThermo/rhoThermo/rhoThermo.C
@@ -55,6 +55,25 @@ Foam::rhoThermo::rhoThermo(const fvMesh& mesh)
 {}
 
 
+Foam::rhoThermo::rhoThermo(const fvMesh& mesh, const dictionary& dicy)
+:
+    basicThermo(mesh, dict),
+    rho_
+    (
+        IOobject
+        (
+            "rhoThermo",
+            mesh.time().timeName(),
+            mesh,
+            IOobject::NO_READ,
+            IOobject::NO_WRITE
+        ),
+        mesh,
+        dimDensity
+    )
+{}
+
+
 // * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
 
 Foam::rhoThermo::~rhoThermo()
diff --git a/src/thermophysicalModels/basic/rhoThermo/rhoThermo/rhoThermo.H b/src/thermophysicalModels/basic/rhoThermo/rhoThermo/rhoThermo.H
index 098e2ec0f1..77a4c4fd12 100644
--- a/src/thermophysicalModels/basic/rhoThermo/rhoThermo/rhoThermo.H
+++ b/src/thermophysicalModels/basic/rhoThermo/rhoThermo/rhoThermo.H
@@ -90,6 +90,9 @@ public:
         //- Construct from mesh
         rhoThermo(const fvMesh&);
 
+        //- Construct from mesh
+        rhoThermo(const fvMesh&, const dictionary&);
+
 
     //- Selector
     static autoPtr<rhoThermo> New(const fvMesh&);
diff --git a/src/thermophysicalModels/basicSolidThermo/heSolidThermo/heSolidThermo.H b/src/thermophysicalModels/basicSolidThermo/heSolidThermo/heSolidThermo.H
index fac27226ff..88a8d8aab6 100644
--- a/src/thermophysicalModels/basicSolidThermo/heSolidThermo/heSolidThermo.H
+++ b/src/thermophysicalModels/basicSolidThermo/heSolidThermo/heSolidThermo.H
@@ -89,9 +89,6 @@ public:
 
         // Derived thermal properties
 
-            //- Isotropic thermal conductivity [W/m/K]
-            //virtual tmp<volScalarField> kappa() const;
-
             //- Anisotropic thermal conductivity [W/m/K]
             virtual tmp<volVectorField> Kappa() const;
 
diff --git a/src/thermophysicalModels/basicSolidThermo/solidThermo/solidThermo.C b/src/thermophysicalModels/basicSolidThermo/solidThermo/solidThermo.C
index 24220ee9bb..7a791b59cc 100644
--- a/src/thermophysicalModels/basicSolidThermo/solidThermo/solidThermo.C
+++ b/src/thermophysicalModels/basicSolidThermo/solidThermo/solidThermo.C
@@ -42,20 +42,7 @@ namespace Foam
 
 Foam::solidThermo::solidThermo(const fvMesh& mesh)
 :
-    basicThermo(mesh),
-    rho_
-    (
-        IOobject
-        (
-            "rho",
-            mesh.time().timeName(),
-            mesh,
-            IOobject::NO_READ,
-            IOobject::NO_WRITE
-        ),
-        mesh,
-        dimMass/dimVolume
-    )
+    rhoThermo(mesh)
 {}
 
 
@@ -65,20 +52,7 @@ Foam::solidThermo::solidThermo
     const dictionary& dict
 )
 :
-    basicThermo(mesh, dict),
-    rho_
-    (
-        IOobject
-        (
-            "rho",
-            mesh.time().timeName(),
-            mesh,
-            IOobject::NO_READ,
-            IOobject::NO_WRITE
-        ),
-        mesh,
-        dimMass/dimVolume
-    )
+    rhoThermo(mesh, dict)
 {}
 
 
@@ -90,54 +64,6 @@ Foam::solidThermo::~solidThermo()
 
 // * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
 
-Foam::volScalarField& Foam::solidThermo::T()
-{
-    return this->T_;
-}
-
-
-const Foam::volScalarField& Foam::solidThermo::T() const
-{
-    return this->T_;
-}
-
-
-const Foam::volScalarField& Foam::solidThermo::rhos() const
-{
-    return rho_;
-}
-
-
-Foam::volScalarField& Foam::solidThermo::rhos()
-{
-    return rho_;
-}
-
-
-const Foam::volScalarField& Foam::solidThermo::p() const
-{
-    return this->p_;
-}
-
-
-Foam::volScalarField& Foam::solidThermo::p()
-{
-    return this->p_;
-}
-
-
-const Foam::volScalarField& Foam::solidThermo::alpha() const
-{
-    return this->alpha_;
-}
-
-
-Foam::tmp<Foam::volScalarField> Foam::solidThermo::rho() const
-{
-    return tmp<volScalarField>(rho_);
-}
-
-
 bool Foam::solidThermo::read()
 {
     return regIOobject::read();
diff --git a/src/thermophysicalModels/basicSolidThermo/solidThermo/solidThermo.H b/src/thermophysicalModels/basicSolidThermo/solidThermo/solidThermo.H
index 79741f466f..08b9f82ab4 100644
--- a/src/thermophysicalModels/basicSolidThermo/solidThermo/solidThermo.H
+++ b/src/thermophysicalModels/basicSolidThermo/solidThermo/solidThermo.H
@@ -41,7 +41,7 @@ SourceFiles
 #include "IOdictionary.H"
 #include "autoPtr.H"
 #include "basicSolidMixture.H"
-#include "basicThermo.H"
+#include "rhoThermo.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
@@ -54,18 +54,9 @@ namespace Foam
 
 class solidThermo
 :
-    public basicThermo
+    public rhoThermo
 {
 
-protected:
-
-
-        // Fields
-
-            //- Density [kg/m3]
-            volScalarField rho_;
-
-
 public:
 
     //- Runtime type information
@@ -116,50 +107,9 @@ public:
 
     // Member functions
 
-        //- Update properties
-        virtual void correct() = 0;
-
-
-        // Access to thermodynamic state variables
-
-            //- Constant access to temperature [K]
-            virtual const volScalarField& T() const;
-
-            //- Non constant access to temperature [K]
-            virtual volScalarField& T();
-
-            //- Solid density [kg/m3]
-            virtual const volScalarField& rhos() const;
-
-            //- Non-const access for solid density [kg/m3]
-            virtual volScalarField& rhos();
-
-
-            //- Constant access to p [Pa]
-            virtual const volScalarField& p() const;
-
-            //- Non-constant access to p [Pa]
-            virtual volScalarField& p();
-
-
-        // Access to transport state variables
-
-            //- Thermal diffusivity for enthalpy of mixture [kg/m/s]
-            virtual const volScalarField& alpha() const;
-
 
         // Derived thermal properties
 
-            //- Enthalpy/Internal energy [J/kg]
-            virtual const volScalarField& he() const = 0;
-
-            //- Enthalpy/Internal energy [J/kg]
-            //  Non-const access allowed for transport equations
-            virtual volScalarField& he() = 0;
-
-            //- Thermal conductivity [W/m/K]
-            virtual tmp<volScalarField> kappa() const = 0;
-
             //- Thermal conductivity [W/m/K]
             virtual tmp<volVectorField> Kappa() const = 0;
 
@@ -172,50 +122,12 @@ public:
             //- Emissivity coefficient [1/m]
             virtual tmp<volScalarField> emissivity() const = 0;
 
-            //- Specific heat capacity [J/kg/K]
-            virtual tmp<volScalarField> Cp() const = 0;
-
-            //- Heat of formation [J/kg]
-            virtual tmp<volScalarField> hc() const = 0;
-
-             //- Density [kg/m^3]
-            virtual tmp<volScalarField> rho() const;
-
 
         // Per patch calculation
 
-            //- Enthalpy/Internal energy [J/kg]
-            virtual tmp<scalarField> he
-            (
-                const scalarField& p,
-                const scalarField& T,
-                const label patchi
-            ) const = 0;
-
-
-            //- Specific heat capacity [J/kg/K)]
-            virtual tmp<scalarField> Cp
-            (
-                const scalarField& p,
-                const scalarField& T,
-                const label patchI
-            ) const = 0;
-
-
-            //- Isotropic thermal conductivity [W//m/K]
-            virtual tmp<scalarField> kappa
-            (
-                const label patchI
-            ) const = 0;
 
             //- Anisotropic thermal conductivity [W/m/K]
             virtual tmp<vectorField> Kappa
-            (
-                const label patchI
-            ) const = 0;
-
-            //- Thermal diffusivity for enthalpy of mixture [kg/m/s]
-            virtual tmp<scalarField> alpha
             (
                 const label patchI
             ) const = 0;

From 0607d6a9aa3037534a1bd822e24fe2fe969162f0 Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Wed, 4 Jul 2012 16:06:29 +0100
Subject: [PATCH 17/38] BUG: patchSummary: no output if no patch groups

---
 .../miscellaneous/patchSummary/patchSummary.C    | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/applications/utilities/miscellaneous/patchSummary/patchSummary.C b/applications/utilities/miscellaneous/patchSummary/patchSummary.C
index d23acc6a69..e26fc10988 100644
--- a/applications/utilities/miscellaneous/patchSummary/patchSummary.C
+++ b/applications/utilities/miscellaneous/patchSummary/patchSummary.C
@@ -191,6 +191,22 @@ int main(int argc, char *argv[])
                     outputFieldList<tensor>(vtf, patchIDs[0]);
                     Info<< endl;
                 }
+                else
+                {
+                    // No group.
+                    forAll(patchIDs, i)
+                    {
+                        label patchI = patchIDs[i];
+                        Info<< bm[patchI].type()
+                            << "\t: " << bm[patchI].name() << nl;
+                        outputFieldList<scalar>(vsf, patchI);
+                        outputFieldList<vector>(vvf, patchI);
+                        outputFieldList<sphericalTensor>(vsptf, patchI);
+                        outputFieldList<symmTensor>(vsytf, patchI);
+                        outputFieldList<tensor>(vtf, patchI);
+                        Info<< endl;
+                    }
+                }
             }
         }
     }

From cc9fbe7393338c12bdd06357b85c451f2fdd9638 Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Thu, 5 Jul 2012 12:16:19 +0100
Subject: [PATCH 18/38] ENH: FaceCellWave: check on supplied sizes

---
 .../algorithms/MeshWave/FaceCellWave.C        | 44 ++++++++++++++++++-
 1 file changed, 42 insertions(+), 2 deletions(-)

diff --git a/src/meshTools/algorithms/MeshWave/FaceCellWave.C b/src/meshTools/algorithms/MeshWave/FaceCellWave.C
index 2177382a38..27218a474a 100644
--- a/src/meshTools/algorithms/MeshWave/FaceCellWave.C
+++ b/src/meshTools/algorithms/MeshWave/FaceCellWave.C
@@ -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) 2011-2012 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -814,7 +814,27 @@ Foam::FaceCellWave<Type, TrackingData>::FaceCellWave
     nEvals_(0),
     nUnvisitedCells_(mesh_.nCells()),
     nUnvisitedFaces_(mesh_.nFaces())
-{}
+{
+    if
+    (
+        allFaceInfo.size() != mesh_.nFaces()
+     || allCellInfo.size() != mesh_.nCells()
+    )
+    {
+        FatalErrorIn
+        (
+            "FaceCellWave<Type, TrackingData>::FaceCellWave"
+            "(const polyMesh&, const labelList&, const List<Type>,"
+            " UList<Type>&, UList<Type>&, const label maxIter)"
+        )   << "face and cell storage not the size of mesh faces, cells:"
+            << endl
+            << "    allFaceInfo   :" << allFaceInfo.size() << endl
+            << "    mesh_.nFaces():" << mesh_.nFaces() << endl
+            << "    allCellInfo   :" << allCellInfo.size() << endl
+            << "    mesh_.nCells():" << mesh_.nCells()
+            << exit(FatalError);
+    }
+}
 
 
 // Iterate, propagating changedFacesInfo across mesh, until no change (or
@@ -850,6 +870,26 @@ Foam::FaceCellWave<Type, TrackingData>::FaceCellWave
     nUnvisitedCells_(mesh_.nCells()),
     nUnvisitedFaces_(mesh_.nFaces())
 {
+    if
+    (
+        allFaceInfo.size() != mesh_.nFaces()
+     || allCellInfo.size() != mesh_.nCells()
+    )
+    {
+        FatalErrorIn
+        (
+            "FaceCellWave<Type, TrackingData>::FaceCellWave"
+            "(const polyMesh&, const labelList&, const List<Type>,"
+            " UList<Type>&, UList<Type>&, const label maxIter)"
+        )   << "face and cell storage not the size of mesh faces, cells:"
+            << endl
+            << "    allFaceInfo   :" << allFaceInfo.size() << endl
+            << "    mesh_.nFaces():" << mesh_.nFaces() << endl
+            << "    allCellInfo   :" << allCellInfo.size() << endl
+            << "    mesh_.nCells():" << mesh_.nCells()
+            << exit(FatalError);
+    }
+
     // Copy initial changed faces data
     setFaceInfo(changedFaces, changedFacesInfo);
 

From 2e2c8d32d54d54e74033bf36ed0b164659b91fab Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Thu, 5 Jul 2012 12:23:42 +0100
Subject: [PATCH 19/38] BUG: rhoThermo.C: misspelled argument

---
 src/thermophysicalModels/basic/rhoThermo/rhoThermo/rhoThermo.C | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/thermophysicalModels/basic/rhoThermo/rhoThermo/rhoThermo.C b/src/thermophysicalModels/basic/rhoThermo/rhoThermo/rhoThermo.C
index 33c7905fee..75b6f1f363 100644
--- a/src/thermophysicalModels/basic/rhoThermo/rhoThermo/rhoThermo.C
+++ b/src/thermophysicalModels/basic/rhoThermo/rhoThermo/rhoThermo.C
@@ -55,7 +55,7 @@ Foam::rhoThermo::rhoThermo(const fvMesh& mesh)
 {}
 
 
-Foam::rhoThermo::rhoThermo(const fvMesh& mesh, const dictionary& dicy)
+Foam::rhoThermo::rhoThermo(const fvMesh& mesh, const dictionary& dict)
 :
     basicThermo(mesh, dict),
     rho_

From 15188397e87253bedfb6943a9d9d6e32341a903f Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Thu, 5 Jul 2012 12:26:51 +0100
Subject: [PATCH 20/38] BUG: createFields: non-const ref to T

---
 .../postProcessing/wall/solidWallHeatFlux/createFields.H        | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/applications/utilities/postProcessing/wall/solidWallHeatFlux/createFields.H b/applications/utilities/postProcessing/wall/solidWallHeatFlux/createFields.H
index 712dd51050..88adcd8e54 100644
--- a/applications/utilities/postProcessing/wall/solidWallHeatFlux/createFields.H
+++ b/applications/utilities/postProcessing/wall/solidWallHeatFlux/createFields.H
@@ -3,4 +3,4 @@ autoPtr<solidThermo> thermo
     solidThermo::New(mesh)
 );
 
-volScalarField& T = thermo->T();
+const volScalarField& T = thermo->T();

From 3e26473b5db93981dfa7683efa1822f0518da686 Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Fri, 6 Jul 2012 11:57:46 +0100
Subject: [PATCH 21/38] STYLE: solidThermo: indenting

---
 .../basicSolidThermo/solidReactionThermo/solidReactionThermo.C  | 2 ++
 .../basicSolidThermo/solidThermo/solidThermo.C                  | 1 +
 2 files changed, 3 insertions(+)

diff --git a/src/thermophysicalModels/basicSolidThermo/solidReactionThermo/solidReactionThermo.C b/src/thermophysicalModels/basicSolidThermo/solidReactionThermo/solidReactionThermo.C
index 6cf0fef12b..00f75ac7cc 100644
--- a/src/thermophysicalModels/basicSolidThermo/solidReactionThermo/solidReactionThermo.C
+++ b/src/thermophysicalModels/basicSolidThermo/solidReactionThermo/solidReactionThermo.C
@@ -35,6 +35,7 @@ namespace Foam
     defineRunTimeSelectionTable(solidReactionThermo, dictionary);
 }
 
+
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
 Foam::solidReactionThermo::solidReactionThermo(const fvMesh& mesh)
@@ -52,6 +53,7 @@ Foam::solidReactionThermo::solidReactionThermo
     solidThermo(mesh, dict)
 {}
 
+
 // * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
 
 Foam::solidReactionThermo::~solidReactionThermo()
diff --git a/src/thermophysicalModels/basicSolidThermo/solidThermo/solidThermo.C b/src/thermophysicalModels/basicSolidThermo/solidThermo/solidThermo.C
index 7a791b59cc..d1e6af4e2b 100644
--- a/src/thermophysicalModels/basicSolidThermo/solidThermo/solidThermo.C
+++ b/src/thermophysicalModels/basicSolidThermo/solidThermo/solidThermo.C
@@ -69,4 +69,5 @@ bool Foam::solidThermo::read()
     return regIOobject::read();
 }
 
+
 // ************************************************************************* //

From c380d6d423e1153f250395502d9469ce7a337dc3 Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Fri, 6 Jul 2012 12:03:47 +0100
Subject: [PATCH 22/38] BUG: extendedLeastSquares: incorrect indexing. Added 2D
 detection.

---
 .../extendedLeastSquaresVectors.C             | 136 +++++++++++++++---
 1 file changed, 114 insertions(+), 22 deletions(-)

diff --git a/src/finiteVolume/finiteVolume/gradSchemes/extendedLeastSquaresGrad/extendedLeastSquaresVectors.C b/src/finiteVolume/finiteVolume/gradSchemes/extendedLeastSquaresGrad/extendedLeastSquaresVectors.C
index efc6559d79..e9ecd484c3 100644
--- a/src/finiteVolume/finiteVolume/gradSchemes/extendedLeastSquaresGrad/extendedLeastSquaresVectors.C
+++ b/src/finiteVolume/finiteVolume/gradSchemes/extendedLeastSquaresGrad/extendedLeastSquaresVectors.C
@@ -110,6 +110,38 @@ void Foam::extendedLeastSquaresVectors::makeLeastSquaresVectors() const
     const labelUList& owner = mesh_.owner();
     const labelUList& neighbour = mesh_.neighbour();
 
+
+    // Determine number of dimensions and (for 2D) missing dimension
+    label nDims = 0;
+    label twoD = -1;
+    for (direction dir = 0; dir < vector::nComponents; dir++)
+    {
+        if (mesh.geometricD()[dir] == 1)
+        {
+            nDims++;
+        }
+        else
+        {
+            twoD = dir;
+        }
+    }
+
+    if (nDims == 1)
+    {
+        FatalErrorIn
+        (
+            "extendedLeastSquaresVectors::makeLeastSquaresVectors() const"
+        )   << "Found a mesh with only one geometric dimension : "
+            << mesh.geometricD()
+            << exit(FatalError);
+    }
+    else if (nDims == 2)
+    {
+        Info<< "extendedLeastSquares : detected " << nDims
+            << " valid directions. Missing direction " << twoD << nl << endl;
+    }
+
+
     const volVectorField& C = mesh.C();
 
     // Set up temporary storage for the dd tensor (before inversion)
@@ -122,7 +154,7 @@ void Foam::extendedLeastSquaresVectors::makeLeastSquaresVectors() const
 
         vector d = C[nei] - C[own];
 
-        const symmTensor wdd(1.0/magSqr(d[facei])*sqr(d[facei]));
+        const symmTensor wdd(1.0/magSqr(d)*sqr(d));
 
         dd[own] += wdd;
         dd[nei] += wdd;
@@ -147,6 +179,28 @@ void Foam::extendedLeastSquaresVectors::makeLeastSquaresVectors() const
         }
     }
 
+
+    // Check for missing dimensions
+    // Add the missing eigenvector (such that it does not
+    // affect the determinant)
+    if (nDims == 2)
+    {
+        forAll(dd, cellI)
+        {
+            if (twoD == 0)
+            {
+                dd[cellI].xx() = 1;
+            }
+            else if (twoD == 1)
+            {
+                dd[cellI].yy() = 1;
+            }
+            else
+            {
+                dd[cellI].zz() = 1;
+            }
+        }
+    }
     scalarField detdd(det(dd));
 
     Info<< "max(detdd) = " << max(detdd) << nl
@@ -170,7 +224,8 @@ void Foam::extendedLeastSquaresVectors::makeLeastSquaresVectors() const
                 (
                     "extendedLeastSquaresVectors::"
                     "makeLeastSquaresVectors() const"
-                )   << "nAddCells exceeds maxNaddCells"
+                )   << "nAddCells exceeds maxNaddCells ("
+                    << maxNaddCells << ")"
                     << exit(FatalError);
             }
 
@@ -188,20 +243,35 @@ void Foam::extendedLeastSquaresVectors::makeLeastSquaresVectors() const
 
                     if (cellj != i)
                     {
-                        if (cellj != -1)
+                        vector dCij = (mesh.C()[cellj] - mesh.C()[i]);
+
+                        symmTensor ddij =
+                            dd[i] + (1.0/magSqr(dCij))*sqr(dCij);
+
+                        // Add the missing eigenvector (such that it does not
+                        // affect the determinant)
+                        if (nDims == 2)
                         {
-                            vector dCij = (mesh.C()[cellj] - mesh.C()[i]);
-
-                            symmTensor ddij =
-                                dd[i] + (1.0/magSqr(dCij))*sqr(dCij);
-
-                            scalar detddij = det(ddij);
-
-                            if (detddij > maxDetddij)
+                            if (twoD == 0)
                             {
-                                addCell = cellj;
-                                maxDetddij = detddij;
+                                ddij.xx() = 1;
                             }
+                            else if (twoD == 1)
+                            {
+                                ddij.yy() = 1;
+                            }
+                            else
+                            {
+                                ddij.zz() = 1;
+                            }
+                        }
+
+                        scalar detddij = det(ddij);
+
+                        if (detddij > maxDetddij)
+                        {
+                            addCell = cellj;
+                            maxDetddij = detddij;
                         }
                     }
                 }
@@ -213,6 +283,25 @@ void Foam::extendedLeastSquaresVectors::makeLeastSquaresVectors() const
                 additionalCells_[nAddCells++][1] = addCell;
                 vector dCij = mesh.C()[addCell] - mesh.C()[i];
                 dd[i] += (1.0/magSqr(dCij))*sqr(dCij);
+
+                // Add the missing eigenvector (such that it does not
+                // affect the determinant)
+                if (nDims == 2)
+                {
+                    if (twoD == 0)
+                    {
+                        dd[i].xx() = 1;
+                    }
+                    else if (twoD == 1)
+                    {
+                        dd[i].yy() = 1;
+                    }
+                    else
+                    {
+                        dd[i].zz() = 1;
+                    }
+                }
+
                 detdd[i] = det(dd[i]);
             }
         }
@@ -220,10 +309,16 @@ void Foam::extendedLeastSquaresVectors::makeLeastSquaresVectors() const
 
     additionalCells_.setSize(nAddCells);
 
-    Info<< "max(detdd) = " << max(detdd) << nl
-        << "min(detdd) = " << min(detdd) << nl
-        << "average(detdd) = " << average(detdd) << nl
-        << "nAddCells/nCells = " << scalar(nAddCells)/mesh.nCells() << endl;
+    reduce(nAddCells, sumOp<label>());
+    if (nAddCells)
+    {
+        Info<< "max(detdd) = " << max(detdd) << nl
+            << "min(detdd) = " << min(detdd) << nl
+            << "average(detdd) = " << average(detdd) << nl
+            << "nAddCells/nCells = "
+            << scalar(nAddCells)/mesh.globalData().nTotalCells()
+            << endl;
+    }
 
     // Invert the dd tensor
     const symmTensorField invDd(inv(dd));
@@ -237,11 +332,8 @@ void Foam::extendedLeastSquaresVectors::makeLeastSquaresVectors() const
 
         vector d = C[nei] - C[own];
 
-        lsP[facei] =
-            (1.0/magSqr(d[facei]))*(invDd[owner[facei]] & d);
-
-        lsN[facei] =
-            ((-1.0)/magSqr(d[facei]))*(invDd[neighbour[facei]] & d);
+        lsP[facei] = (1.0/magSqr(d))*(invDd[own] & d);
+        lsN[facei] = ((-1.0)/magSqr(d))*(invDd[nei] & d);
     }
 
     forAll(blsP, patchI)

From 45ca1c067c2db6c5e9ce7d555eb23a0c545988b8 Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Fri, 6 Jul 2012 12:39:35 +0100
Subject: [PATCH 23/38] BUG: fieldMinMax: accessing uninitialised data (data
 not scattered)

---
 .../field/fieldMinMax/fieldMinMaxTemplates.C  | 33 +++++++++----------
 1 file changed, 16 insertions(+), 17 deletions(-)

diff --git a/src/postProcessing/functionObjects/field/fieldMinMax/fieldMinMaxTemplates.C b/src/postProcessing/functionObjects/field/fieldMinMax/fieldMinMaxTemplates.C
index be16e3a5c0..cf76cbda0e 100644
--- a/src/postProcessing/functionObjects/field/fieldMinMax/fieldMinMaxTemplates.C
+++ b/src/postProcessing/functionObjects/field/fieldMinMax/fieldMinMaxTemplates.C
@@ -73,16 +73,16 @@ void Foam::fieldMinMax::calcMinMaxFields
                 Pstream::gatherList(maxVs);
                 Pstream::gatherList(maxCs);
 
-                label minI = findMin(minVs);
-                scalar minValue = minVs[minI];
-                const vector& minC = minCs[minI];
-
-                label maxI = findMax(maxVs);
-                scalar maxValue = maxVs[maxI];
-                const vector& maxC = maxCs[maxI];
-
                 if (Pstream::master())
                 {
+                    label minI = findMin(minVs);
+                    scalar minValue = minVs[minI];
+                    const vector& minC = minCs[minI];
+
+                    label maxI = findMax(maxVs);
+                    scalar maxValue = maxVs[maxI];
+                    const vector& maxC = maxCs[maxI];
+
                     if (write_)
                     {
                         fieldMinMaxFilePtr_()
@@ -153,17 +153,16 @@ void Foam::fieldMinMax::calcMinMaxFields
                 Pstream::gatherList(maxVs);
                 Pstream::gatherList(maxCs);
 
-                label minI = findMin(minVs);
-                Type minValue = minVs[minI];
-                const vector& minC = minCs[minI];
-
-                label maxI = findMax(maxVs);
-                Type maxValue = maxVs[maxI];
-                const vector& maxC = maxCs[maxI];
-
-
                 if (Pstream::master())
                 {
+                    label minI = findMin(minVs);
+                    Type minValue = minVs[minI];
+                    const vector& minC = minCs[minI];
+
+                    label maxI = findMax(maxVs);
+                    Type maxValue = maxVs[maxI];
+                    const vector& maxC = maxCs[maxI];
+
                     if (write_)
                     {
                         fieldMinMaxFilePtr_()

From a40ebc83ea1ed9646cc69b2c26c26caf8fc180bd Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Fri, 6 Jul 2012 15:15:00 +0100
Subject: [PATCH 24/38] ENH: motorBike: correct application

---
 .../pisoFoam/les/motorBike/motorBike/system/controlDict         | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tutorials/incompressible/pisoFoam/les/motorBike/motorBike/system/controlDict b/tutorials/incompressible/pisoFoam/les/motorBike/motorBike/system/controlDict
index 6569a100b7..d7759e4112 100644
--- a/tutorials/incompressible/pisoFoam/les/motorBike/motorBike/system/controlDict
+++ b/tutorials/incompressible/pisoFoam/les/motorBike/motorBike/system/controlDict
@@ -17,7 +17,7 @@ FoamFile
 
 libs            ("libOpenFOAM.so" "libfieldFunctionObjects.so");
 
-application     simpleFoam;
+application     pisoFoam;
 
 startFrom       latestTime;
 

From c0882aef0c95ad0d47184e9969fc42c475d78e96 Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Fri, 6 Jul 2012 17:42:22 +0100
Subject: [PATCH 25/38] ENH: flange: tighten min-tet volume since has little
 effect

---
 tutorials/mesh/snappyHexMesh/flange/system/snappyHexMeshDict | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tutorials/mesh/snappyHexMesh/flange/system/snappyHexMeshDict b/tutorials/mesh/snappyHexMesh/flange/system/snappyHexMeshDict
index feb4f2f871..66499680bd 100644
--- a/tutorials/mesh/snappyHexMesh/flange/system/snappyHexMeshDict
+++ b/tutorials/mesh/snappyHexMesh/flange/system/snappyHexMeshDict
@@ -292,7 +292,7 @@ meshQualityControls
     //     <0 = inside out tet,
     //      0 = flat tet
     //      1 = regular tet
-    minTetQuality 1e-30;
+    minTetQuality 1e-9;
 
     //- Minimum face area. Set to <0 to disable.
     minArea -1;

From 1d05413348ed36f1b43b11dd8c2992aa84bc5ac0 Mon Sep 17 00:00:00 2001
From: Henry <Henry>
Date: Mon, 9 Jul 2012 08:52:37 +0100
Subject: [PATCH 26/38] fvPatchField: Reorganisation of macros

---
 .../fvPatchFields/fvPatchField/fvPatchField.H       | 13 +++++++++++++
 .../fvPatchFields/fvPatchField/fvPatchFields.C      | 12 ------------
 2 files changed, 13 insertions(+), 12 deletions(-)

diff --git a/src/finiteVolume/fields/fvPatchFields/fvPatchField/fvPatchField.H b/src/finiteVolume/fields/fvPatchFields/fvPatchField/fvPatchField.H
index 369246d3b0..4dc1041ffc 100644
--- a/src/finiteVolume/fields/fvPatchFields/fvPatchField/fvPatchField.H
+++ b/src/finiteVolume/fields/fvPatchFields/fvPatchField/fvPatchField.H
@@ -498,6 +498,19 @@ public:
 #endif
 
 
+#define makeFvPatchField(fvPatchTypeField)                                    \
+                                                                              \
+defineNamedTemplateTypeNameAndDebug(fvPatchTypeField, 0);                     \
+template<>                                                                    \
+int fvPatchTypeField::disallowGenericFvPatchField                             \
+(                                                                             \
+    debug::debugSwitch("disallowGenericFvPatchField", 0)                      \
+);                                                                            \
+defineTemplateRunTimeSelectionTable(fvPatchTypeField, patch);                 \
+defineTemplateRunTimeSelectionTable(fvPatchTypeField, patchMapper);           \
+defineTemplateRunTimeSelectionTable(fvPatchTypeField, dictionary);
+
+
 #define addToPatchFieldRunTimeSelection(PatchTypeField, typePatchTypeField)   \
     addToRunTimeSelectionTable                                                \
     (                                                                         \
diff --git a/src/finiteVolume/fields/fvPatchFields/fvPatchField/fvPatchFields.C b/src/finiteVolume/fields/fvPatchFields/fvPatchField/fvPatchFields.C
index 023213cc48..62788f5b42 100644
--- a/src/finiteVolume/fields/fvPatchFields/fvPatchField/fvPatchFields.C
+++ b/src/finiteVolume/fields/fvPatchFields/fvPatchField/fvPatchFields.C
@@ -32,18 +32,6 @@ namespace Foam
 
 // * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
 
-#define makeFvPatchField(fvPatchTypeField)                                    \
-                                                                              \
-defineNamedTemplateTypeNameAndDebug(fvPatchTypeField, 0);                     \
-template<>                                                                    \
-int fvPatchTypeField::disallowGenericFvPatchField                             \
-(                                                                             \
-    debug::debugSwitch("disallowGenericFvPatchField", 0)                      \
-);                                                                            \
-defineTemplateRunTimeSelectionTable(fvPatchTypeField, patch);                 \
-defineTemplateRunTimeSelectionTable(fvPatchTypeField, patchMapper);           \
-defineTemplateRunTimeSelectionTable(fvPatchTypeField, dictionary);
-
 makeFvPatchField(fvPatchScalarField)
 makeFvPatchField(fvPatchVectorField)
 makeFvPatchField(fvPatchSphericalTensorField)

From 327ebcbcfa7f12bb7ef565768029f7b389de237d Mon Sep 17 00:00:00 2001
From: Henry <Henry>
Date: Mon, 9 Jul 2012 08:52:45 +0100
Subject: [PATCH 27/38] Update headers

---
 .../fields/fvPatchFields/fvPatchField/fvPatchFields.C           | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/finiteVolume/fields/fvPatchFields/fvPatchField/fvPatchFields.C b/src/finiteVolume/fields/fvPatchFields/fvPatchField/fvPatchFields.C
index 62788f5b42..fb4dbe8531 100644
--- a/src/finiteVolume/fields/fvPatchFields/fvPatchField/fvPatchFields.C
+++ b/src/finiteVolume/fields/fvPatchFields/fvPatchField/fvPatchFields.C
@@ -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) 2011-2012 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License

From 8f2874056886185c7d1e00ca3c4c6e5293142784 Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Mon, 9 Jul 2012 09:06:41 +0100
Subject: [PATCH 28/38] COMP: Intel: add add-needed link flags for modern linux
 platforms

---
 wmake/rules/linux64Icc/c   | 2 +-
 wmake/rules/linux64Icc/c++ | 4 ++--
 wmake/rules/linuxIcc/c     | 2 +-
 wmake/rules/linuxIcc/c++   | 4 ++--
 4 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/wmake/rules/linux64Icc/c b/wmake/rules/linux64Icc/c
index 08ea0f8049..1085d50498 100644
--- a/wmake/rules/linux64Icc/c
+++ b/wmake/rules/linux64Icc/c
@@ -13,4 +13,4 @@ ctoo        = $(WM_SCHEDULER) $(cc) $(cFLAGS) -c $$SOURCE -o $@
 LINK_LIBS   = $(cDBUG) -L$(IA32ROOT)/lib
 
 LINKLIBSO   = $(cc) $(cFLAGS) -shared
-LINKEXE     = $(cc) $(cFLAGS)
+LINKEXE     = $(cc) $(cFLAGS) -Xlinker --add-needed -Xlinker -z -Xlinker nodefs
diff --git a/wmake/rules/linux64Icc/c++ b/wmake/rules/linux64Icc/c++
index 5ad41fd9b4..dfad97cee6 100644
--- a/wmake/rules/linux64Icc/c++
+++ b/wmake/rules/linux64Icc/c++
@@ -17,5 +17,5 @@ cpptoo      = $(Ctoo)
 
 LINK_LIBS   = $(c++DBUG) -L$(IA64ROOT)/lib
 
-LINKLIBSO   = $(CC) $(c++FLAGS) -shared
-LINKEXE     = $(CC) $(c++FLAGS)
+LINKLIBSO   = $(CC) $(c++FLAGS) -shared -Xlinker --add-needed -Xlinker --no-as-needed
+LINKEXE     = $(CC) $(c++FLAGS) -Xlinker --add-needed -Xlinker --no-as-needed
diff --git a/wmake/rules/linuxIcc/c b/wmake/rules/linuxIcc/c
index 269eeaba47..e8059d9dbb 100644
--- a/wmake/rules/linuxIcc/c
+++ b/wmake/rules/linuxIcc/c
@@ -13,4 +13,4 @@ ctoo        = $(WM_SCHEDULER) $(cc) $(cFLAGS) -c $$SOURCE -o $@
 LINK_LIBS   = $(cDBUG) -L$(IA32ROOT)/lib
 
 LINKLIBSO   = $(cc) $(cFLAGS) -shared
-LINKEXE     = $(cc) $(cFLAGS)
+LINKEXE     = $(cc) $(cFLAGS) -Xlinker --add-needed -Xlinker -z -Xlinker nodefs
diff --git a/wmake/rules/linuxIcc/c++ b/wmake/rules/linuxIcc/c++
index 409e289014..d06a874848 100644
--- a/wmake/rules/linuxIcc/c++
+++ b/wmake/rules/linuxIcc/c++
@@ -19,5 +19,5 @@ cpptoo      = $(Ctoo)
 #LINK_LIBS   = $(c++DBUG) -lstdc++
 LINK_LIBS   = $(c++DBUG) -L$(IA32ROOT)/lib
 
-LINKLIBSO   = $(CC) $(c++FLAGS) -shared
-LINKEXE     = $(CC) $(c++FLAGS)
+LINKLIBSO   = $(CC) $(c++FLAGS) -shared -Xlinker --add-needed -Xlinker --no-as-needed
+LINKEXE     = $(CC) $(c++FLAGS) -Xlinker --add-needed -Xlinker --no-as-needed

From 2587c7d641a1dc4757b43c1301bb8d94b99b5f50 Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Mon, 9 Jul 2012 09:24:23 +0100
Subject: [PATCH 29/38] GIT: boundary: not needed

---
 .../icoFoam/cavity/constant/polyMesh/boundary | 40 -------------------
 1 file changed, 40 deletions(-)
 delete mode 100644 tutorials/incompressible/icoFoam/cavity/constant/polyMesh/boundary

diff --git a/tutorials/incompressible/icoFoam/cavity/constant/polyMesh/boundary b/tutorials/incompressible/icoFoam/cavity/constant/polyMesh/boundary
deleted file mode 100644
index 61feadd974..0000000000
--- a/tutorials/incompressible/icoFoam/cavity/constant/polyMesh/boundary
+++ /dev/null
@@ -1,40 +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       polyBoundaryMesh;
-    location    "constant/polyMesh";
-    object      boundary;
-}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-3
-(
-    movingWall
-    {
-        type            wall;
-        nFaces          20;
-        startFace       760;
-    }
-    fixedWalls
-    {
-        type            wall;
-        nFaces          60;
-        startFace       780;
-    }
-    frontAndBack
-    {
-        type            empty;
-        nFaces          800;
-        startFace       840;
-    }
-)
-
-// ************************************************************************* //

From c030c5e40a8548292bc12f63e32973dfd3c82ba5 Mon Sep 17 00:00:00 2001
From: laurence <laurence>
Date: Mon, 9 Jul 2012 12:31:30 +0100
Subject: [PATCH 30/38] ENH: Add rotation tensor constructor to quaternion
 class

---
 .../primitives/quaternion/quaternion.H        |  3 +
 .../primitives/quaternion/quaternionI.H       | 75 +++++++++++++++++++
 2 files changed, 78 insertions(+)

diff --git a/src/OpenFOAM/primitives/quaternion/quaternion.H b/src/OpenFOAM/primitives/quaternion/quaternion.H
index 9a7c297189..1c2bfb1d2e 100644
--- a/src/OpenFOAM/primitives/quaternion/quaternion.H
+++ b/src/OpenFOAM/primitives/quaternion/quaternion.H
@@ -109,6 +109,9 @@ public:
             const scalar angleZ
         );
 
+        //- Construct a quaternion from a rotation tensor
+        inline explicit quaternion(const tensor& rotationTensor);
+
         //- Construct from Istream
         quaternion(Istream&);
 
diff --git a/src/OpenFOAM/primitives/quaternion/quaternionI.H b/src/OpenFOAM/primitives/quaternion/quaternionI.H
index 19b5c79130..01c5b74bc2 100644
--- a/src/OpenFOAM/primitives/quaternion/quaternionI.H
+++ b/src/OpenFOAM/primitives/quaternion/quaternionI.H
@@ -66,6 +66,81 @@ inline Foam::quaternion::quaternion
     operator*=(quaternion(vector(0, 0, 1), angleZ));
 }
 
+inline Foam::quaternion::quaternion
+(
+    const tensor& rotationTensor
+)
+{
+    scalar trace = rotationTensor.xx()
+                 + rotationTensor.yy()
+                 + rotationTensor.zz();
+
+    if (trace > 0)
+    {
+        scalar s = 0.5/Foam::sqrt(trace + 1.0);
+
+        w_ = 0.25/s;
+        v_[0] = (rotationTensor.zy() - rotationTensor.yz())*s;
+        v_[1] = (rotationTensor.xz() - rotationTensor.zx())*s;
+        v_[2] = (rotationTensor.yx() - rotationTensor.xy())*s;
+    }
+    else
+    {
+        if
+        (
+            rotationTensor.xx() > rotationTensor.yy()
+         && rotationTensor.xx() > rotationTensor.zz()
+        )
+        {
+            scalar s = 2.0*Foam::sqrt
+            (
+                1.0
+              + rotationTensor.xx()
+              - rotationTensor.yy()
+              - rotationTensor.zz()
+            );
+
+            w_ = (rotationTensor.zy() - rotationTensor.yz())/s;
+            v_[0] = 0.25*s;
+            v_[1] = (rotationTensor.xy() + rotationTensor.yx())/s;
+            v_[2] = (rotationTensor.xz() + rotationTensor.zx())/s;
+        }
+        else if
+        (
+            rotationTensor.yy() > rotationTensor.zz()
+        )
+        {
+            scalar s = 2.0*Foam::sqrt
+            (
+                1.0
+              + rotationTensor.yy()
+              - rotationTensor.xx()
+              - rotationTensor.zz()
+            );
+
+            w_ = (rotationTensor.xz() - rotationTensor.xz())/s;
+            v_[0] = (rotationTensor.xy() + rotationTensor.yx())/s;
+            v_[1] = 0.25*s;
+            v_[2] = (rotationTensor.yz() + rotationTensor.zy())/s;
+        }
+        else
+        {
+            scalar s = 2.0*Foam::sqrt
+            (
+                1.0
+              + rotationTensor.zz()
+              - rotationTensor.xx()
+              - rotationTensor.yy()
+            );
+
+            w_ = (rotationTensor.yx() - rotationTensor.xy())/s;
+            v_[0] = (rotationTensor.xz() + rotationTensor.zx())/s;
+            v_[1] = (rotationTensor.yz() + rotationTensor.zy())/s;
+            v_[2] = 0.25*s;
+        }
+    }
+}
+
 
 // * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
 

From 70f4d345caf025aed34b16281d9c90726f2373df Mon Sep 17 00:00:00 2001
From: Henry <Henry>
Date: Mon, 9 Jul 2012 12:34:03 +0100
Subject: [PATCH 31/38] quaternion: Adding members required by GeometricField

---
 src/OpenFOAM/primitives/quaternion/quaternion.H | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/src/OpenFOAM/primitives/quaternion/quaternion.H b/src/OpenFOAM/primitives/quaternion/quaternion.H
index 9a7c297189..b2012d6bd1 100644
--- a/src/OpenFOAM/primitives/quaternion/quaternion.H
+++ b/src/OpenFOAM/primitives/quaternion/quaternion.H
@@ -75,6 +75,17 @@ class quaternion
 
 public:
 
+    //- Component type
+    typedef scalar cmptType;
+
+    // Member constants
+
+        enum
+        {
+            rank = 1 // Rank of quaternion is 1
+        };
+
+
     // Static data members
 
         static const char* const typeName;

From 495f5eee74bcb426b92d4e3de746eced12b2be32 Mon Sep 17 00:00:00 2001
From: Henry <Henry>
Date: Mon, 9 Jul 2012 12:34:37 +0100
Subject: [PATCH 32/38] Updated header

---
 src/OpenFOAM/primitives/quaternion/quaternion.H | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/OpenFOAM/primitives/quaternion/quaternion.H b/src/OpenFOAM/primitives/quaternion/quaternion.H
index b2012d6bd1..be6b68fa93 100644
--- a/src/OpenFOAM/primitives/quaternion/quaternion.H
+++ b/src/OpenFOAM/primitives/quaternion/quaternion.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) 2011-2012 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License

From 58cf28ffe5938fdb35309a62a5cebcad0d6e079d Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Mon, 9 Jul 2012 14:34:59 +0100
Subject: [PATCH 33/38] BUG: extendedLeastSquares: determinant is 0..8 only for
 face-area weighted

---
 .../extendedLeastSquaresGrad.H                      |  6 +++---
 .../extendedLeastSquaresVectors.C                   | 13 ++++++++++++-
 2 files changed, 15 insertions(+), 4 deletions(-)

diff --git a/src/finiteVolume/finiteVolume/gradSchemes/extendedLeastSquaresGrad/extendedLeastSquaresGrad.H b/src/finiteVolume/finiteVolume/gradSchemes/extendedLeastSquaresGrad/extendedLeastSquaresGrad.H
index 43c398bbf1..f734409d09 100644
--- a/src/finiteVolume/finiteVolume/gradSchemes/extendedLeastSquaresGrad/extendedLeastSquaresGrad.H
+++ b/src/finiteVolume/finiteVolume/gradSchemes/extendedLeastSquaresGrad/extendedLeastSquaresGrad.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) 2011-2012 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -85,7 +85,7 @@ public:
             gradScheme<Type>(mesh),
             minDet_(readScalar(schemeData))
         {
-            if (minDet_ < 0 || minDet_ > 8)
+            if (minDet_ < 0)    //-for facearea weighted: || minDet_ > 8)
             {
                 FatalIOErrorIn
                 (
@@ -93,7 +93,7 @@ public:
                     "(const fvMesh&, Istream& schemeData)",
                     schemeData
                 )   << "Minimum determinant = " << minDet_
-                    << " should be >= 0 and <= 8"
+                    << " should be >= 0"    // and <= 8"
                     << exit(FatalIOError);
             }
         }
diff --git a/src/finiteVolume/finiteVolume/gradSchemes/extendedLeastSquaresGrad/extendedLeastSquaresVectors.C b/src/finiteVolume/finiteVolume/gradSchemes/extendedLeastSquaresGrad/extendedLeastSquaresVectors.C
index e9ecd484c3..254038b3fa 100644
--- a/src/finiteVolume/finiteVolume/gradSchemes/extendedLeastSquaresGrad/extendedLeastSquaresVectors.C
+++ b/src/finiteVolume/finiteVolume/gradSchemes/extendedLeastSquaresGrad/extendedLeastSquaresVectors.C
@@ -138,7 +138,7 @@ void Foam::extendedLeastSquaresVectors::makeLeastSquaresVectors() const
     else if (nDims == 2)
     {
         Info<< "extendedLeastSquares : detected " << nDims
-            << " valid directions. Missing direction " << twoD << nl << endl;
+            << " valid directions. Missing direction " << twoD << endl;
     }
 
 
@@ -207,6 +207,7 @@ void Foam::extendedLeastSquaresVectors::makeLeastSquaresVectors() const
         << "min(detdd) = " << min(detdd) << nl
         << "average(detdd) = " << average(detdd) << endl;
 
+    label nAdaptedCells = 0;
     label nAddCells = 0;
     label maxNaddCells = 4*detdd.size();
     additionalCellsPtr_ = new List<labelPair>(maxNaddCells);
@@ -216,6 +217,8 @@ void Foam::extendedLeastSquaresVectors::makeLeastSquaresVectors() const
     {
         label count = 0;
 
+        label oldNAddCells = nAddCells;
+
         while (++count < 100 && detdd[i] < minDet_)
         {
             if (nAddCells == maxNaddCells)
@@ -305,16 +308,24 @@ void Foam::extendedLeastSquaresVectors::makeLeastSquaresVectors() const
                 detdd[i] = det(dd[i]);
             }
         }
+
+        if (oldNAddCells < nAddCells)
+        {
+            nAdaptedCells++;
+        }
     }
 
     additionalCells_.setSize(nAddCells);
 
     reduce(nAddCells, sumOp<label>());
+    reduce(nAdaptedCells, sumOp<label>());
     if (nAddCells)
     {
         Info<< "max(detdd) = " << max(detdd) << nl
             << "min(detdd) = " << min(detdd) << nl
             << "average(detdd) = " << average(detdd) << nl
+            << "nAdapted/nCells = "
+            << scalar(nAdaptedCells)/mesh.globalData().nTotalCells() << nl
             << "nAddCells/nCells = "
             << scalar(nAddCells)/mesh.globalData().nTotalCells()
             << endl;

From d490f9608620272f1bbebf63649e82eac006d098 Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Tue, 10 Jul 2012 10:00:52 +0100
Subject: [PATCH 34/38] STYLE: SLList: make construct from type explicit to
 avoid nasty conversions

---
 .../mesh/conversion/star3ToFoam/createCoupleMatches.C     | 8 ++++----
 src/OpenFOAM/containers/LinkedLists/user/SLList.H         | 6 +++---
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/applications/utilities/mesh/conversion/star3ToFoam/createCoupleMatches.C b/applications/utilities/mesh/conversion/star3ToFoam/createCoupleMatches.C
index f852c06ec4..139aa65f9b 100644
--- a/applications/utilities/mesh/conversion/star3ToFoam/createCoupleMatches.C
+++ b/applications/utilities/mesh/conversion/star3ToFoam/createCoupleMatches.C
@@ -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) 2011-2012 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -123,7 +123,7 @@ void starMesh::createCoupleMatches()
                 cellRemovedFaces.insert
                 (
                     fp.masterCell(),
-                    fp.masterFace()
+                    SLList<label>(fp.masterFace())
                 );
             }
             else
@@ -1362,7 +1362,7 @@ void starMesh::createCoupleMatches()
                 cellRemovedFaces.insert
                 (
                     fp.masterCell(),
-                    fp.masterFace()
+                    SLList<label>(fp.masterFace())
                 );
             }
             else
@@ -1378,7 +1378,7 @@ void starMesh::createCoupleMatches()
                 cellRemovedFaces.insert
                 (
                     fp.slaveCell(),
-                    fp.slaveFace()
+                    SLList<label>(fp.slaveFace())
                 );
             }
             else
diff --git a/src/OpenFOAM/containers/LinkedLists/user/SLList.H b/src/OpenFOAM/containers/LinkedLists/user/SLList.H
index 2b88b5eff0..6cb3d6ac62 100644
--- a/src/OpenFOAM/containers/LinkedLists/user/SLList.H
+++ b/src/OpenFOAM/containers/LinkedLists/user/SLList.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) 2011-2012 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -59,13 +59,13 @@ public:
         {}
 
         //- Construct given initial T
-        SLList(T a)
+        explicit SLList(T a)
         :
             LList<SLListBase, T>(a)
         {}
 
         //- Construct from Istream
-        SLList(Istream& is)
+        explicit SLList(Istream& is)
         :
             LList<SLListBase, T>(is)
         {}

From 413d25fbd225731547fb2cc2d4c1e7e9de14ce63 Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Tue, 10 Jul 2012 10:02:01 +0100
Subject: [PATCH 35/38] ENH: boxToCell/face/point: have 'boxes' for multiple
 boxes

---
 .../mesh/manipulation/topoSet/topoSetDict     |  9 ++++---
 .../sets/cellSources/boxToCell/boxToCell.C    | 27 ++++++++++++-------
 .../sets/cellSources/boxToCell/boxToCell.H    | 10 +++----
 .../sets/faceSources/boxToFace/boxToFace.C    | 27 ++++++++++++-------
 .../sets/faceSources/boxToFace/boxToFace.H    |  8 +++---
 .../sets/pointSources/boxToPoint/boxToPoint.C | 26 +++++++++++-------
 .../sets/pointSources/boxToPoint/boxToPoint.H |  8 +++---
 7 files changed, 72 insertions(+), 43 deletions(-)

diff --git a/applications/utilities/mesh/manipulation/topoSet/topoSetDict b/applications/utilities/mesh/manipulation/topoSet/topoSetDict
index 1f58d59dde..562c006ab1 100644
--- a/applications/utilities/mesh/manipulation/topoSet/topoSetDict
+++ b/applications/utilities/mesh/manipulation/topoSet/topoSetDict
@@ -95,11 +95,12 @@ FoamFile
 //        type hex;           // hex/wedge/prism/pyr/tet/tetWedge/splitHex
 //    }
 //
-//    // Cells with cell centre within box
+//    // Cells with cell centre within box ('box') or multiple boxes ('boxes')
 //    source boxToCell;
 //    sourceInfo
 //    {
 //       box   (0 0 0) (1 1 1);
+//       //boxes   ((0 0 0) (1 1 1) (10 10 10)(11 11 11));
 //    }
 //
 //    // Cells with cell centre within box
@@ -223,11 +224,12 @@ FoamFile
 //        name ".*Zone1";     // Name of faceZone, regular expressions allowed
 //    }
 //
-//    // Faces with face centre within box
+//    // Faces with face centre within box ('box') or multiple boxes ('boxes')
 //    source boxToFace;
 //    sourceInfo
 //    {
 //        box  (0 0 0) (1 1 1);
+//       //boxes   ((0 0 0) (1 1 1) (10 10 10)(11 11 11));
 //    }
 //
 //    // Faces with normal to within certain angle aligned with vector.
@@ -295,11 +297,12 @@ FoamFile
 //       points ((0 0 0) (1 1 1));
 //    }
 //
-//    // Points with coordinate within box
+//    // Points with coordinate within box ('box') or multiple boxes ('boxes')
 //    source boxToPoint;
 //    sourceInfo
 //    {
 //       box   (0 0 0) (1 1 1);
+//       //boxes   ((0 0 0) (1 1 1) (10 10 10)(11 11 11));
 //    }
 //
 //    // Select based on surface
diff --git a/src/meshTools/sets/cellSources/boxToCell/boxToCell.C b/src/meshTools/sets/cellSources/boxToCell/boxToCell.C
index 58f62f93d7..28bec358bc 100644
--- a/src/meshTools/sets/cellSources/boxToCell/boxToCell.C
+++ b/src/meshTools/sets/cellSources/boxToCell/boxToCell.C
@@ -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) 2011-2012 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -58,9 +58,13 @@ void Foam::boxToCell::combine(topoSet& set, const bool add) const
 
     forAll(ctrs, cellI)
     {
-        if (bb_.contains(ctrs[cellI]))
+        forAll(bbs_, i)
         {
-            addOrDelete(set, cellI, add);
+            if (bbs_[i].contains(ctrs[cellI]))
+            {
+                addOrDelete(set, cellI, add);
+                break;
+            }
         }
     }
 }
@@ -72,11 +76,11 @@ void Foam::boxToCell::combine(topoSet& set, const bool add) const
 Foam::boxToCell::boxToCell
 (
     const polyMesh& mesh,
-    const treeBoundBox& bb
+    const treeBoundBoxList& bbs
 )
 :
     topoSetSource(mesh),
-    bb_(bb)
+    bbs_(bbs)
 {}
 
 
@@ -88,7 +92,12 @@ Foam::boxToCell::boxToCell
 )
 :
     topoSetSource(mesh),
-    bb_(dict.lookup("box"))
+    bbs_
+    (
+        dict.found("box")
+      ? treeBoundBoxList(1, treeBoundBox(dict.lookup("box")))
+      : dict.lookup("boxes")
+    )
 {}
 
 
@@ -100,7 +109,7 @@ Foam::boxToCell::boxToCell
 )
 :
     topoSetSource(mesh),
-    bb_(checkIs(is))
+    bbs_(1, treeBoundBox(checkIs(is)))
 {}
 
 // * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
@@ -119,13 +128,13 @@ void Foam::boxToCell::applyToSet
 {
     if ((action == topoSetSource::NEW) || (action == topoSetSource::ADD))
     {
-        Info<< "    Adding cells with center within box " << bb_ << endl;
+        Info<< "    Adding cells with center within boxes " << bbs_ << endl;
 
         combine(set, true);
     }
     else if (action == topoSetSource::DELETE)
     {
-        Info<< "    Removing cells with center within box " << bb_ << endl;
+        Info<< "    Removing cells with center within boxes " << bbs_ << endl;
 
         combine(set, false);
     }
diff --git a/src/meshTools/sets/cellSources/boxToCell/boxToCell.H b/src/meshTools/sets/cellSources/boxToCell/boxToCell.H
index ee1d0deb12..488ceb934f 100644
--- a/src/meshTools/sets/cellSources/boxToCell/boxToCell.H
+++ b/src/meshTools/sets/cellSources/boxToCell/boxToCell.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) 2011-2012 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -25,7 +25,7 @@ Class
     Foam::boxToCell
 
 Description
-    A topoSetSource to select cells based on cell centres inside box.
+    A topoSetSource to select cells based on cell centres inside box(es).
 
 SourceFiles
     boxToCell.C
@@ -36,7 +36,7 @@ SourceFiles
 #define boxToCell_H
 
 #include "topoSetSource.H"
-#include "treeBoundBox.H"
+#include "treeBoundBoxList.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
@@ -59,7 +59,7 @@ class boxToCell
 
 
         //- bounding box.
-        treeBoundBox bb_;
+        treeBoundBoxList bbs_;
 
 
     // Private Member Functions
@@ -78,7 +78,7 @@ public:
         boxToCell
         (
             const polyMesh& mesh,
-            const treeBoundBox& bb
+            const treeBoundBoxList& bbs
         );
 
         //- Construct from dictionary
diff --git a/src/meshTools/sets/faceSources/boxToFace/boxToFace.C b/src/meshTools/sets/faceSources/boxToFace/boxToFace.C
index f46c1dd0b2..698bb5c311 100644
--- a/src/meshTools/sets/faceSources/boxToFace/boxToFace.C
+++ b/src/meshTools/sets/faceSources/boxToFace/boxToFace.C
@@ -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) 2011-2012 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -58,9 +58,13 @@ void Foam::boxToFace::combine(topoSet& set, const bool add) const
 
     forAll(ctrs, faceI)
     {
-        if (bb_.contains(ctrs[faceI]))
+        forAll(bbs_, i)
         {
-            addOrDelete(set, faceI, add);
+            if (bbs_[i].contains(ctrs[faceI]))
+            {
+                addOrDelete(set, faceI, add);
+                break;
+            }
         }
     }
 }
@@ -72,11 +76,11 @@ void Foam::boxToFace::combine(topoSet& set, const bool add) const
 Foam::boxToFace::boxToFace
 (
     const polyMesh& mesh,
-    const treeBoundBox& bb
+    const treeBoundBoxList& bbs
 )
 :
     topoSetSource(mesh),
-    bb_(bb)
+    bbs_(bbs)
 {}
 
 
@@ -88,7 +92,12 @@ Foam::boxToFace::boxToFace
 )
 :
     topoSetSource(mesh),
-    bb_(dict.lookup("box"))
+    bbs_
+    (
+        dict.found("box")
+      ? treeBoundBoxList(1, treeBoundBox(dict.lookup("box")))
+      : dict.lookup("boxes")
+    )
 {}
 
 
@@ -100,7 +109,7 @@ Foam::boxToFace::boxToFace
 )
 :
     topoSetSource(mesh),
-    bb_(checkIs(is))
+    bbs_(1, treeBoundBox(checkIs(is)))
 {}
 
 
@@ -120,13 +129,13 @@ void Foam::boxToFace::applyToSet
 {
     if ((action == topoSetSource::NEW) || (action == topoSetSource::ADD))
     {
-        Info<< "    Adding faces with centre within box " << bb_ << endl;
+        Info<< "    Adding faces with centre within boxes " << bbs_ << endl;
 
         combine(set, true);
     }
     else if (action == topoSetSource::DELETE)
     {
-        Info<< "    Removing faces with centre within box " << bb_ << endl;
+        Info<< "    Removing faces with centre within boxes " << bbs_ << endl;
 
         combine(set, false);
     }
diff --git a/src/meshTools/sets/faceSources/boxToFace/boxToFace.H b/src/meshTools/sets/faceSources/boxToFace/boxToFace.H
index 16685861ea..056dbac118 100644
--- a/src/meshTools/sets/faceSources/boxToFace/boxToFace.H
+++ b/src/meshTools/sets/faceSources/boxToFace/boxToFace.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) 2011-2012 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -36,7 +36,7 @@ SourceFiles
 #define boxToFace_H
 
 #include "topoSetSource.H"
-#include "treeBoundBox.H"
+#include "treeBoundBoxList.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
@@ -58,7 +58,7 @@ class boxToFace
         static addToUsageTable usage_;
 
         //- bounding box.
-        treeBoundBox bb_;
+        treeBoundBoxList bbs_;
 
 
     // Private Member Functions
@@ -77,7 +77,7 @@ public:
         boxToFace
         (
             const polyMesh& mesh,
-            const treeBoundBox& bb
+            const treeBoundBoxList& bbs
         );
 
         //- Construct from dictionary
diff --git a/src/meshTools/sets/pointSources/boxToPoint/boxToPoint.C b/src/meshTools/sets/pointSources/boxToPoint/boxToPoint.C
index 56975ded6e..53bb9b41fe 100644
--- a/src/meshTools/sets/pointSources/boxToPoint/boxToPoint.C
+++ b/src/meshTools/sets/pointSources/boxToPoint/boxToPoint.C
@@ -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) 2011-2012 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -58,9 +58,12 @@ void Foam::boxToPoint::combine(topoSet& set, const bool add) const
 
     forAll(pts, pointI)
     {
-        if (bb_.contains(pts[pointI]))
+        forAll(bbs_, i)
         {
-            addOrDelete(set, pointI, add);
+            if (bbs_[i].contains(pts[pointI]))
+            {
+                addOrDelete(set, pointI, add);
+            }
         }
     }
 }
@@ -72,11 +75,11 @@ void Foam::boxToPoint::combine(topoSet& set, const bool add) const
 Foam::boxToPoint::boxToPoint
 (
     const polyMesh& mesh,
-    const treeBoundBox& bb
+    const treeBoundBoxList& bbs
 )
 :
     topoSetSource(mesh),
-    bb_(bb)
+    bbs_(bbs)
 {}
 
 
@@ -88,7 +91,12 @@ Foam::boxToPoint::boxToPoint
 )
 :
     topoSetSource(mesh),
-    bb_(dict.lookup("box"))
+    bbs_
+    (
+        dict.found("box")
+      ? treeBoundBoxList(1, treeBoundBox(dict.lookup("box")))
+      : dict.lookup("boxes")
+    )
 {}
 
 
@@ -100,7 +108,7 @@ Foam::boxToPoint::boxToPoint
 )
 :
     topoSetSource(mesh),
-    bb_(checkIs(is))
+    bbs_(1, treeBoundBox(checkIs(is)))
 {}
 
 
@@ -120,14 +128,14 @@ void Foam::boxToPoint::applyToSet
 {
     if ((action == topoSetSource::NEW) || (action == topoSetSource::ADD))
     {
-        Info<< "    Adding points that are within box " << bb_ << " ..."
+        Info<< "    Adding points that are within boxes " << bbs_ << " ..."
             << endl;
 
         combine(set, true);
     }
     else if (action == topoSetSource::DELETE)
     {
-        Info<< "    Removing points that are within box " << bb_ << " ..."
+        Info<< "    Removing points that are within boxes " << bbs_ << " ..."
             << endl;
 
         combine(set, false);
diff --git a/src/meshTools/sets/pointSources/boxToPoint/boxToPoint.H b/src/meshTools/sets/pointSources/boxToPoint/boxToPoint.H
index d40eb2e052..e5f5cfc559 100644
--- a/src/meshTools/sets/pointSources/boxToPoint/boxToPoint.H
+++ b/src/meshTools/sets/pointSources/boxToPoint/boxToPoint.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) 2011-2012 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -36,7 +36,7 @@ SourceFiles
 #define boxToPoint_H
 
 #include "topoSetSource.H"
-#include "treeBoundBox.H"
+#include "treeBoundBoxList.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
@@ -58,7 +58,7 @@ class boxToPoint
         static addToUsageTable usage_;
 
         //- bounding box.
-        treeBoundBox bb_;
+        treeBoundBoxList bbs_;
 
 
     // Private Member Functions
@@ -77,7 +77,7 @@ public:
         boxToPoint
         (
             const polyMesh& mesh,
-            const treeBoundBox& bb
+            const treeBoundBoxList& bb
         );
 
         //- Construct from dictionary

From 1f7d24e617a73f72f8ceae0a72e7db3c92a64f44 Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Tue, 10 Jul 2012 10:03:15 +0100
Subject: [PATCH 36/38] STYLE: decomposeParDict: added comment

---
 .../utilities/parallelProcessing/decomposePar/decomposeParDict | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/applications/utilities/parallelProcessing/decomposePar/decomposeParDict b/applications/utilities/parallelProcessing/decomposePar/decomposeParDict
index b3270edb6b..b383a6efe3 100644
--- a/applications/utilities/parallelProcessing/decomposePar/decomposeParDict
+++ b/applications/utilities/parallelProcessing/decomposePar/decomposeParDict
@@ -122,7 +122,8 @@ structuredCoeffs
     patches     (bottomPatch);
 }
 
-//// Is the case distributed
+//// Is the case distributed? Note: command-line argument -roots takes
+//// precedence
 //distributed     yes;
 //// Per slave (so nProcs-1 entries) the directory above the case.
 //roots

From 2d1efdaa6c03a382ff19600cb728d07474e84ca9 Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Tue, 10 Jul 2012 10:03:32 +0100
Subject: [PATCH 37/38] ENH: snappyHexMesh: run without decomposeParDict

---
 .../generation/snappyHexMesh/snappyHexMesh.C  | 23 ++++++++++---------
 1 file changed, 12 insertions(+), 11 deletions(-)

diff --git a/applications/utilities/mesh/generation/snappyHexMesh/snappyHexMesh.C b/applications/utilities/mesh/generation/snappyHexMesh/snappyHexMesh.C
index d991719071..9080f58e67 100644
--- a/applications/utilities/mesh/generation/snappyHexMesh/snappyHexMesh.C
+++ b/applications/utilities/mesh/generation/snappyHexMesh/snappyHexMesh.C
@@ -179,18 +179,19 @@ int main(int argc, char *argv[])
     // Read decomposePar dictionary
     dictionary decomposeDict;
     {
-        IOobject io
-        (
-            "decomposeParDict",
-            runTime.system(),
-            mesh,
-            IOobject::MUST_READ_IF_MODIFIED,
-            IOobject::NO_WRITE
-        );
-
-        if (io.headerOk())
+        if (Pstream::parRun())
         {
-            decomposeDict = IOdictionary(io);
+            decomposeDict = IOdictionary
+            (
+                IOobject
+                (
+                    "decomposeParDict",
+                    runTime.system(),
+                    mesh,
+                    IOobject::MUST_READ_IF_MODIFIED,
+                    IOobject::NO_WRITE
+                )
+            );
         }
         else
         {

From 0e1e599bfe56fd5a38ed32c591cfe267cd90d9db Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Tue, 10 Jul 2012 10:03:57 +0100
Subject: [PATCH 38/38] STYLE: setRegionSolidFields: remove commented out old
 code

---
 .../chtMultiRegionFoam/solid/setRegionSolidFields.H            | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/applications/solvers/heatTransfer/chtMultiRegionFoam/solid/setRegionSolidFields.H b/applications/solvers/heatTransfer/chtMultiRegionFoam/solid/setRegionSolidFields.H
index 3b94c89e31..0968002e55 100644
--- a/applications/solvers/heatTransfer/chtMultiRegionFoam/solid/setRegionSolidFields.H
+++ b/applications/solvers/heatTransfer/chtMultiRegionFoam/solid/setRegionSolidFields.H
@@ -12,7 +12,4 @@
     tmp<volScalarField> tkappa = thermo.kappa();
     const volScalarField& kappa = tkappa();
 
-    //tmp<volSymmTensorField> tkappa = thermo.directionalKappa();
-    //const volSymmTensorField& kappa = tkappa();
-
     volScalarField& h = thermo.he();