Merge commit 'OpenCFD/master' into merging

Conflicts:

	src/OpenFOAM/containers/misc/xferI.H
	src/OpenFOAM/fields/tmp/refCount.H
	src/OpenFOAM/memory/refCount/refCount.H
	src/OpenFOAM/memory/xfer/xferI.H
	src/finiteVolume/fvMesh/extendedStencil/extendedCentredStencil.C
	src/finiteVolume/fvMesh/extendedStencil/faceStencil/faceEdgeCellStencil.H

applications/utilities/mesh/manipulation/createPatch/createPatch.C

@@ -625,10 +625,8 @@ int main(int argc, char *argv[])
                     << " as patch " << destPatchI
                     << " from " << patchDict << endl;
 
-                patchDict.remove("nFaces");
-                patchDict.add("nFaces", 0);
-                patchDict.remove("startFace");
-                patchDict.add("startFace", startFaceI);
+                patchDict.set("nFaces", 0);
+                patchDict.set("startFace", startFaceI);
 
                 // Add an empty patch.
                 allPatches.append

applications/utilities/parallelProcessing/reconstructParMesh/Make/options

 EXE_INC = \
     -I$(LIB_SRC)/dynamicMesh/lnInclude \
+    -I$(LIB_SRC)/finiteVolume/lnInclude \
     -I$(LIB_SRC)/meshTools/lnInclude
 
 EXE_LIBS = \

applications/utilities/parallelProcessing/reconstructParMesh/reconstructParMesh.C

@@ -46,6 +46,8 @@ Description
 #include "mapAddedPolyMesh.H"
 #include "polyMeshAdder.H"
 #include "faceCoupleInfo.H"
+#include "fvMeshAdder.H"
+#include "polyTopoChange.H"
 
 using namespace Foam;
 
@@ -203,6 +205,78 @@ autoPtr<faceCoupleInfo> determineCoupledFaces
 }
 
 
+autoPtr<mapPolyMesh> mergeSharedPoints
+(
+    const scalar mergeDist,
+    polyMesh& mesh,
+    labelListList& pointProcAddressing
+)
+{
+    // Find out which sets of points get merged and create a map from
+    // mesh point to unique point.
+    Map<label> pointToMaster
+    (
+        fvMeshAdder::findSharedPoints
+        (
+            mesh,
+            mergeDist
+        )
+    );
+
+    Info<< "mergeSharedPoints : detected " << pointToMaster.size()
+        << " points that are to be merged." << endl;
+
+    if (returnReduce(pointToMaster.size(), sumOp<label>()) == 0)
+    {
+        return autoPtr<mapPolyMesh>(NULL);
+    }
+
+    polyTopoChange meshMod(mesh);
+
+    fvMeshAdder::mergePoints(mesh, pointToMaster, meshMod);
+
+    // Change the mesh (no inflation). Note: parallel comms allowed.
+    autoPtr<mapPolyMesh> map = meshMod.changeMesh(mesh, false, true);
+
+    // Update fields. No inflation, parallel sync.
+    mesh.updateMesh(map);
+
+    // pointProcAddressing give indices into the master mesh so adapt them
+    // for changed point numbering.
+
+    // Adapt constructMaps for merged points.
+    forAll(pointProcAddressing, procI)
+    {
+        labelList& constructMap = pointProcAddressing[procI];
+
+        forAll(constructMap, i)
+        {
+            label oldPointI = constructMap[i];
+
+            // New label of point after changeMesh.
+            label newPointI = map().reversePointMap()[oldPointI];
+
+            if (newPointI < -1)
+            {
+                constructMap[i] = -newPointI-2;
+            }
+            else if (newPointI >= 0)
+            {
+                constructMap[i] = newPointI;
+            }
+            else
+            {
+                FatalErrorIn("fvMeshDistribute::mergeSharedPoints()")
+                    << "Problem. oldPointI:" << oldPointI
+                    << " newPointI:" << newPointI << abort(FatalError);
+            }
+        }
+    }
+
+    return map;    
+}
+
+
 int main(int argc, char *argv[])
 {
     argList::noParallel();
@@ -214,7 +288,7 @@ int main(int argc, char *argv[])
 #   include "setRootCase.H"
 #   include "createTime.H"
 
-    Pout<< "This is an experimental tool which tries to merge"
+    Info<< "This is an experimental tool which tries to merge"
         << " individual processor" << nl
         << "meshes back into one master mesh. Use it if the original"
         << " master mesh has" << nl
@@ -246,7 +320,7 @@ int main(int argc, char *argv[])
     }
     scalar writeTol = Foam::pow(10.0, -scalar(IOstream::defaultPrecision()));
 
-    Pout<< "Merge tolerance : " << mergeTol << nl
+    Info<< "Merge tolerance : " << mergeTol << nl
         << "Write tolerance : " << writeTol << endl;
 
     if (runTime.writeFormat() == IOstream::ASCII && mergeTol < writeTol)
@@ -267,11 +341,11 @@ int main(int argc, char *argv[])
 
     if (fullMatch)
     {
-        Pout<< "Doing geometric matching on all boundary faces." << nl << endl;
+        Info<< "Doing geometric matching on all boundary faces." << nl << endl;
     }
     else
     {
-        Pout<< "Doing geometric matching on correct procBoundaries only."
+        Info<< "Doing geometric matching on correct procBoundaries only."
             << nl << "This assumes a correct decomposition." << endl;
     }
 
@@ -292,7 +366,7 @@ int main(int argc, char *argv[])
         nProcs++;
     }
 
-    Pout<< "Found " << nProcs << " processor directories" << nl << endl;
+    Info<< "Found " << nProcs << " processor directories" << nl << endl;
 
 
     // Read all databases.
@@ -300,7 +374,7 @@ int main(int argc, char *argv[])
 
     forAll (databases, procI)
     {
-        Pout<< "Reading database "
+        Info<< "Reading database "
             << args.caseName()/fileName(word("processor") + name(procI))
             << endl;
 
@@ -337,7 +411,7 @@ int main(int argc, char *argv[])
     }
 
     // Set master time
-    Pout<< "Setting master time to " << databases[0].timeName() << nl << endl;
+    Info<< "Setting master time to " << databases[0].timeName() << nl << endl;
     runTime.setTime(databases[0]);
 
 
@@ -373,7 +447,7 @@ int main(int argc, char *argv[])
                 << endl << exit(FatalError);
         }
 
-        Pout<< "Reading points from "
+        Info<< "Reading points from "
             << databases[procI].caseName()
             << " for time = " << databases[procI].timeName()
             << nl << endl;
@@ -403,7 +477,7 @@ int main(int argc, char *argv[])
     }
     const scalar mergeDist = mergeTol*mag(bb.max() - bb.min());
 
-    Pout<< "Overall mesh bounding box  : " << bb << nl
+    Info<< "Overall mesh bounding box  : " << bb << nl
         << "Relative tolerance         : " << mergeTol << nl
         << "Absolute matching distance : " << mergeDist << nl
         << endl;
@@ -422,7 +496,7 @@ int main(int argc, char *argv[])
 
     {
         // Construct empty mesh.
-        Pout<< "Constructing empty mesh to add to." << nl << endl;
+        Info<< "Constructing empty mesh to add to." << nl << endl;
         polyMesh masterMesh
         (
             IOobject
@@ -439,7 +513,7 @@ int main(int argc, char *argv[])
 
         for (label procI = 0; procI < nProcs; procI++)
         {
-            Pout<< "Reading mesh to add from "
+            Info<< "Reading mesh to add from "
                 << databases[procI].caseName()
                 << " for time = " << databases[procI].timeName()
                 << nl << endl;
@@ -475,7 +549,7 @@ int main(int argc, char *argv[])
 
 
             // Add elements to mesh
-            Pout<< "Adding to master mesh" << nl << endl;
+            Info<< "Adding to master mesh" << nl << endl;
 
             autoPtr<mapAddedPolyMesh> map = polyMeshAdder::add
             (
@@ -503,16 +577,19 @@ int main(int argc, char *argv[])
             renumber(map().addedPointMap(), pointProcAddressing[procI]);
             renumber(map().addedPatchMap(), boundaryProcAddressing[procI]);
 
-            Pout<< endl;
+            Info<< endl;
         }
 
+        // See if any points on the mastermesh have become connected
+        // because of connections through processor meshes.
+        mergeSharedPoints(mergeDist, masterMesh, pointProcAddressing);
 
         // Save some properties on the reconstructed mesh
         masterInternalFaces = masterMesh.nInternalFaces();
         masterOwner = masterMesh.faceOwner();
 
 
-        Pout<< "\nWriting merged mesh to "
+        Info<< "\nWriting merged mesh to "
             << runTime.path()/runTime.timeName()
             << nl << endl;
 
@@ -527,12 +604,12 @@ int main(int argc, char *argv[])
 
     // Write the addressing
 
-    Pout<< "Reconstructing the addressing from the processor meshes"
+    Info<< "Reconstructing the addressing from the processor meshes"
         << " to the newly reconstructed mesh" << nl << endl;
 
     forAll(databases, procI)
     {
-        Pout<< "Reading processor " << procI << " mesh from "
+        Info<< "Reading processor " << procI << " mesh from "
             << databases[procI].caseName() << endl;
 
         polyMesh procMesh
@@ -548,7 +625,7 @@ int main(int argc, char *argv[])
 
         // From processor point to reconstructed mesh point
 
-        Pout<< "Writing pointProcAddressing to "
+        Info<< "Writing pointProcAddressing to "
             << databases[procI].caseName()
               /procMesh.facesInstance()
               /polyMesh::meshSubDir
@@ -572,7 +649,7 @@ int main(int argc, char *argv[])
 
         // From processor face to reconstructed mesh face
 
-        Pout<< "Writing faceProcAddressing to "
+        Info<< "Writing faceProcAddressing to "
             << databases[procI].caseName()
               /procMesh.facesInstance()
               /polyMesh::meshSubDir
@@ -635,7 +712,7 @@ int main(int argc, char *argv[])
 
         // From processor cell to reconstructed mesh cell
 
-        Pout<< "Writing cellProcAddressing to "
+        Info<< "Writing cellProcAddressing to "
             << databases[procI].caseName()
               /procMesh.facesInstance()
               /polyMesh::meshSubDir
@@ -660,7 +737,7 @@ int main(int argc, char *argv[])
 
         // From processor patch to reconstructed mesh patch
 
-        Pout<< "Writing boundaryProcAddressing to "
+        Info<< "Writing boundaryProcAddressing to "
             << databases[procI].caseName()
               /procMesh.facesInstance()
               /polyMesh::meshSubDir
@@ -681,10 +758,10 @@ int main(int argc, char *argv[])
             boundaryProcAddressing[procI]
         ).write();
 
-        Pout<< endl;
+        Info<< endl;
     }
 
-    Pout<< "End.\n" << endl;
+    Info<< "End.\n" << endl;
 
     return 0;
 }

applications/utilities/postProcessing/miscellaneous/postChannel/channelIndexTemplates.C

@@ -54,9 +54,11 @@ Foam::Field<T> Foam::channelIndex::collapse
 ) const
 {
     // Average and order
+    const Field<T> summedField(regionSum(cellField));
+
     Field<T> regionField
     (
-        regionSum(cellField)
+        summedField
       / regionCount_,
         sortMap_
     );

etc/settings.csh

@@ -112,7 +112,7 @@ case OpenFOAM:
     endif
 
     set compilerBin=$WM_COMPILER_DIR/bin
-    set compilerLib=$WM_COMPILER_DIR/lib$WM_COMPILER_LIB_ARCH:$WM_COMPILER_DIR/lib
+    set compilerLib=$WM_COMPILER_DIR/lib${WM_COMPILER_LIB_ARCH}:$WM_COMPILER_DIR/lib
     breaksw
 endsw
 

src/OpenFOAM/containers/Lists/FixedList/FixedListIO.C

@@ -77,7 +77,7 @@ Foam::Istream& Foam::operator>>(Foam::Istream& is, FixedList<T, Size>& L)
         }
         else
         {
-            // Putback the openning bracket
+            // Putback the opening bracket
             is.putBack(firstToken);
         }
 
@@ -190,8 +190,9 @@ Foam::Ostream& Foam::operator<<(Ostream& os, const FixedList<T, Size>& L)
 
         if (uniform)
         {
-            // Write size of list and start contents delimiter
-            os << token::BEGIN_BLOCK;
+            // Write size of list (so it is valid dictionary entry) and
+            // start contents delimiter
+            os << L.size() << token::BEGIN_BLOCK;
 
             // Write list contents
             os << L[0];
@@ -201,7 +202,7 @@ Foam::Ostream& Foam::operator<<(Ostream& os, const FixedList<T, Size>& L)
         }
         else if (Size < 11 && contiguous<T>())
         {
-            // Write size of list and start contents delimiter
+            // Write start of contents delimiter
             os << token::BEGIN_LIST;
 
             // Write list contents
@@ -216,7 +217,7 @@ Foam::Ostream& Foam::operator<<(Ostream& os, const FixedList<T, Size>& L)
         }
         else
         {
-            // Write size of list and start contents delimiter
+            // Write start of contents delimiter
             os << nl << token::BEGIN_LIST;
 
             // Write list contents

src/OpenFOAM/meshes/MeshObject/MeshObject.C

@@ -65,11 +65,11 @@ const Type& Foam::MeshObject<Mesh, Type>::New
 
 
 template<class Mesh, class Type>
-template<class Data>
+template<class Data1>
 const Type& Foam::MeshObject<Mesh, Type>::New
 (
     const Mesh& mesh,
-    const Data& d
+    const Data1& d
 )
 {
     if (!mesh.db().objectRegistry::foundObject<Type>(Type::typeName))
@@ -83,6 +83,69 @@ const Type& Foam::MeshObject<Mesh, Type>::New
 }
 
 
+template<class Mesh, class Type>
+template<class Data1, class Data2>
+const Type& Foam::MeshObject<Mesh, Type>::New
+(
+    const Mesh& mesh,
+    const Data1& d1,
+    const Data2& d2
+)
+{
+    if (!mesh.db().objectRegistry::foundObject<Type>(Type::typeName))
+    {
+        return store(new Type(mesh, d1, d2));
+    }
+    else
+    {
+        return mesh.db().objectRegistry::lookupObject<Type>(Type::typeName);
+    }
+}
+
+
+template<class Mesh, class Type>
+template<class Data1, class Data2, class Data3>
+const Type& Foam::MeshObject<Mesh, Type>::New
+(
+    const Mesh& mesh,
+    const Data1& d1,
+    const Data2& d2,
+    const Data3& d3
+)
+{
+    if (!mesh.db().objectRegistry::foundObject<Type>(Type::typeName))
+    {
+        return store(new Type(mesh, d1, d2, d3));
+    }
+    else
+    {
+        return mesh.db().objectRegistry::lookupObject<Type>(Type::typeName);
+    }
+}
+
+
+template<class Mesh, class Type>
+template<class Data1, class Data2, class Data3, class Data4>
+const Type& Foam::MeshObject<Mesh, Type>::New
+(
+    const Mesh& mesh,
+    const Data1& d1,
+    const Data2& d2,
+    const Data3& d3,
+    const Data4& d4
+)
+{
+    if (!mesh.db().objectRegistry::foundObject<Type>(Type::typeName))
+    {
+        return store(new Type(mesh, d3, d4));
+    }
+    else
+    {
+        return mesh.db().objectRegistry::lookupObject<Type>(Type::typeName);
+    }
+}
+
+
 // * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * //
 
 template<class Mesh, class Type>

src/OpenFOAM/meshes/MeshObject/MeshObject.H

@@ -69,8 +69,39 @@ public:
 
         static const Type& New(const Mesh& mesh);
 
-        template<class Data>
-        static const Type& New(const Mesh& mesh, const Data& d);
+        template<class Data1>
+        static const Type& New
+        (
+            const Mesh& mesh,
+            const Data1& d
+        );
+
+        template<class Data1, class Data2>
+        static const Type& New
+        (
+            const Mesh& mesh,
+            const Data1&,
+            const Data2&
+        );
+
+        template<class Data1, class Data2, class Data3>
+        static const Type& New
+        (
+            const Mesh& mesh,
+            const Data1&,
+            const Data2&,
+            const Data3&
+        );
+
+        template<class Data1, class Data2, class Data3, class Data4>
+        static const Type& New
+        (
+            const Mesh& mesh,
+            const Data1&,
+            const Data2&,
+            const Data3&,
+            const Data4&
+        );
 
 
     // Destructor

src/OpenFOAM/meshes/meshTools/matchPoints.C

@@ -45,9 +45,19 @@ bool Foam::matchPoints
 
     bool fullMatch = true;
 
-    SortableList<scalar> pts0MagSqr(magSqr(pts0 - origin));
+    point compareOrigin = origin;
 
-    SortableList<scalar> pts1MagSqr(magSqr(pts1 - origin));
+    if (origin == point(VGREAT, VGREAT, VGREAT))
+    {
+        if (pts1.size() > 0)
+        {
+            compareOrigin = sum(pts1)/pts1.size();
+        }
+    }
+
+    SortableList<scalar> pts0MagSqr(magSqr(pts0 - compareOrigin));
+
+    SortableList<scalar> pts1MagSqr(magSqr(pts1 - compareOrigin));
 
     forAll(pts0MagSqr, i)
     {

src/OpenFOAM/meshes/meshTools/mergePoints.C

@@ -40,6 +40,16 @@ bool Foam::mergePoints
     const point& origin
 )
 {
+    point compareOrigin = origin;
+
+    if (origin == point(VGREAT, VGREAT, VGREAT))
+    {
+        if (points.size() > 0)
+        {
+            compareOrigin = sum(points)/points.size();
+        }
+    }
+
     // Create a old to new point mapping array
     pointMap.setSize(points.size());
     pointMap = -1;
@@ -56,7 +66,7 @@ bool Foam::mergePoints
     const scalar mergeTolSqr = sqr(mergeTol);
 
     // Sort points by magSqr
-    SortableList<scalar> sortedMagSqr(magSqr(points - origin));
+    SortableList<scalar> sortedMagSqr(magSqr(points - compareOrigin));
 
     bool hasMerged = false;
 

src/OpenFOAM/meshes/polyMesh/mapPolyMesh/mapDistribute/mapDistribute.C

@@ -271,4 +271,144 @@ Foam::mapDistribute::mapDistribute
 }
 
 
+// * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //
+
+void Foam::mapDistribute::compact(const boolList& elemIsUsed)
+{
+    // 1. send back to sender. Have him delete the corresponding element
+    //    from the submap and do the same to the constructMap locally
+    //    (and in same order).
+
+    // Send elemIsUsed field to neighbour. Use nonblocking code from
+    // mapDistribute but in reverse order.
+    {
+        List<boolList> sendFields(Pstream::nProcs());
+
+        for (label domain = 0; domain < Pstream::nProcs(); domain++)
+        {
+            const labelList& map = constructMap_[domain];
+
+            if (domain != Pstream::myProcNo() && map.size() > 0)
+            {
+                boolList& subField = sendFields[domain];
+                subField.setSize(map.size());
+                forAll(map, i)
+                {
+                    subField[i] = elemIsUsed[map[i]];
+                }
+
+                OPstream::write
+                (
+                    Pstream::nonBlocking,
+                    domain,
+                    reinterpret_cast<const char*>(subField.begin()),
+                    subField.size()*sizeof(bool)
+                );
+            }
+        }
+
+        // Set up receives from neighbours
+
+        List<boolList> recvFields(Pstream::nProcs());
+
+        for (label domain = 0; domain < Pstream::nProcs(); domain++)
+        {
+            const labelList& map = subMap_[domain];
+
+            if (domain != Pstream::myProcNo() && map.size() > 0)
+            {
+                recvFields[domain].setSize(map.size());
+                IPstream::read
+                (
+                    Pstream::nonBlocking,
+                    domain,
+                    reinterpret_cast<char*>(recvFields[domain].begin()),
+                    recvFields[domain].size()*sizeof(bool)
+                );
+            }
+        }
+
+
+        // Set up 'send' to myself - write directly into recvFields
+
+        {