Merge branch 'master' of ssh://hunt/home/hunt2/OpenFOAM/OpenFOAM-dev

applications/solvers/Lagrangian/kinematicParcelFoam/Make/files

 kinematicParcelFoam.C
 
-EXE = $(FOAM_USER_APPBIN)/kinematicParcelFoam
+EXE = $(FOAM_APPBIN)/kinematicParcelFoam

applications/solvers/Lagrangian/kinematicParcelFoam/kinematicParcelFoam.C

@@ -26,7 +26,8 @@ Application
     kinematicParcelFoam
 
 Description
-    Transient solver a single kinematicCloud.
+    Transient solver for a single kinematicCloud. Uses precalculated velocity
+    field to evolve a cloud.
 
 \*---------------------------------------------------------------------------*/
 

applications/utilities/mesh/conversion/fluent3DMeshToFoam/fluent3DMeshToFoam.L

@@ -697,7 +697,7 @@ endOfSection               {space}")"{space}
 
  /* ------              Ignore remaining space and \n s.             ------  */
 
-<*>{some_space}|\n {
+<*>{some_space}|\n|\r {
     }
 
 

applications/utilities/postProcessing/dataConversion/foamToVTK/writeSurfFields.C

@@ -28,7 +28,7 @@ License
 #include "OFstream.H"
 #include "floatScalar.H"
 #include "writeFuns.H"
-#include "emptyFvPatchFields.H"
+#include "emptyFvsPatchFields.H"
 #include "fvsPatchFields.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
@@ -100,7 +100,7 @@ void writeSurfFields
 
             const fvPatch& pp = mesh.boundary()[patchI];
 
-            if (isA<emptyFvPatchVectorField>(pf))
+            if (isA<emptyFvsPatchVectorField>(pf))
             {
                 // Note: loop over polypatch size, not fvpatch size.
                 forAll(pp.patch(), i)

applications/utilities/surface/surfaceSubset/surfaceSubset.C

@@ -248,7 +248,7 @@ int main(int argc, char *argv[])
         indexedOctree<treeDataTriSurface> selectTree
         (
             treeDataTriSurface(selectSurf),
-            bb.extend(rndGen, 1E-3),    // slightly randomize bb
+            bb.extend(rndGen, 1E-4),    // slightly randomize bb
             8,      // maxLevel
             10,     // leafsize
             3.0     // duplicity

etc/apps/paraview3/bashrc

@@ -45,9 +45,9 @@ export ParaView_INST_DIR=$WM_THIRD_PARTY_DIR/ParaView$ParaView_VERSION
 export ParaView_DIR=$ParaView_INST_DIR/platforms/$WM_ARCH$WM_COMPILER
 
 if [ "$PYTHONPATH" ]; then
-    export PYTHONPATH=$PYTHONPATH:$ParaView_DIR/Utilities/VTKPythonWrapping
+    export PYTHONPATH=$PYTHONPATH:$ParaView_DIR/Utilities/VTKPythonWrapping:$ParaView_DIR/lib/paraview-3.3
 else
-    export PYTHONPATH=$ParaView_DIR/Utilities/VTKPythonWrapping
+    export PYTHONPATH=$ParaView_DIR/Utilities/VTKPythonWrapping:$ParaView_DIR/lib/paraview-3.3
 fi
 
 

etc/apps/paraview3/cshrc

@@ -45,9 +45,9 @@ setenv ParaView_INST_DIR $WM_THIRD_PARTY_DIR/ParaView$ParaView_VERSION
 setenv ParaView_DIR $ParaView_INST_DIR/platforms/$WM_ARCH$WM_COMPILER
 
 if ($?PYTHONPATH) then
-    setenv PYTHONPATH ${PYTHONPATH}:$ParaView_DIR/bin:$ParaView_DIR/Utilities/VTKPythonWrapping
+    setenv PYTHONPATH ${PYTHONPATH}:$ParaView_DIR/Utilities/VTKPythonWrapping:$ParaView_DIR/lib/paraview-3.3
 else
-    setenv PYTHONPATH $ParaView_DIR/bin:$ParaView_DIR/Utilities/VTKPythonWrapping
+    setenv PYTHONPATH $ParaView_DIR/Utilities/VTKPythonWrapping:$ParaView_DIR/lib/paraview-3.3
 endif
 
 if ( -r $ParaView_INST_DIR ) then

src/OpenFOAM/db/Time/TimeIO.C

@@ -86,13 +86,6 @@ void Foam::Time::readDict()
 
             purgeWrite_ = 0;
         }
-
-        if (writeControl_ != wcTimeStep && purgeWrite_ > 0)
-        {
-            FatalIOErrorIn("Time::readDict()", controlDict_)
-                << "writeControl must be set to timeStep for purgeWrite "
-                << exit(FatalIOError);
-        }
     }
 
     if (controlDict_.found("timeFormat"))

src/OpenFOAM/meshes/boundBox/boundBox.C

@@ -87,9 +87,47 @@ boundBox::boundBox(Istream& is)
 
 // * * * * * * * * * * * * * * * Ostream Operator  * * * * * * * * * * * * * //
 
-Ostream& operator<<(Ostream& os, const boundBox& b)
+Ostream& operator<<(Ostream& os, const boundBox& bb)
 {
-    return os << b.min() << token::SPACE << b.max();
+    if (os.format() == IOstream::ASCII)
+    {
+        os << bb.min_ << token::SPACE << bb.max_;
+    }
+    else
+    {
+        os.write
+        (
+            reinterpret_cast<const char*>(&bb.min_),
+            sizeof(boundBox)
+        );
+    }
+
+    // Check state of Ostream
+    os.check("Ostream& operator<<(Ostream&, const boundBox&)");
+
+    return os;
+}
+
+
+Istream& operator>>(Istream& is, boundBox& bb)
+{
+    if (is.format() == IOstream::ASCII)
+    {
+        return is >> bb.min_ >>  bb.max_;
+    }
+    else
+    {
+        is.read
+        (
+            reinterpret_cast<char*>(&bb.min_),
+            sizeof(boundBox)
+        );
+    }
+
+    // Check state of Istream
+    is.check("Istream& operator>>(Istream&, boundBox&)");
+
+    return is;
 }
 
 

src/OpenFOAM/meshes/boundBox/boundBox.H

@@ -153,12 +153,31 @@ public:
             }
 
 
-    // Ostream operator
+    // Friend Operators
 
-        friend Ostream& operator<<(Ostream& os, const boundBox& b);
+        friend bool operator==(const boundBox& a, const boundBox& b)
+        {
+            return (a.min_ == b.min_) && (a.max_ == b.max_);
+        }
+
+        friend bool operator!=(const boundBox& a, const boundBox& b)
+        {
+            return !(a == b);
+        }
+
+
+    // IOstream operator
+
+        friend Istream& operator>>(Istream& is, boundBox&);
+        friend Ostream& operator<<(Ostream& os, const boundBox&);
 };
 
 
+//- Specify data associated with boundBox type is contiguous
+template<>
+inline bool contiguous<boundBox>() {return contiguous<point>();}
+
+
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
 } // End namespace Foam

src/autoMesh/autoHexMesh/shellSurfaces/shellSurfaces.C

@@ -30,6 +30,7 @@ License
 #include "triSurfaceMesh.H"
 #include "refinementSurfaces.H"
 #include "searchableSurfaces.H"
+#include "orientedSurface.H"
 #include "pointIndexHit.H"
 
 // * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
@@ -211,7 +212,27 @@ void Foam::shellSurfaces::orient()
                     refCast<const triSurfaceMesh>(s)
                 );
 
-                refinementSurfaces::orientSurface(outsidePt, shell);
+                // Flip surface so outsidePt is outside.
+                bool anyFlipped = orientedSurface::orient
+                (
+                    shell,
+                    outsidePt,
+                    true
+                );
+
+                if (anyFlipped)
+                {
+                    // orientedSurface will have done a clearOut of the surface.
+                    // we could do a clearout of the triSurfaceMeshes::trees()
+                    // but these aren't affected by orientation
+                    // (except for cached
+                    // sideness which should not be set at this point.
+                    // !!Should check!)
+
+                    Info<< "shellSurfaces : Flipped orientation of surface "
+                        << s.name()
+                        << " so point " << outsidePt << " is outside." << endl;
+                }
             }
         }
     }

src/dynamicMesh/polyMeshAdder/faceCoupleInfo.C

@@ -29,8 +29,8 @@ License
 #include "matchPoints.H"
 #include "indirectPrimitivePatch.H"
 #include "meshTools.H"
-#include "octreeDataFace.H"
-#include "octree.H"
+#include "treeDataFace.H"
+#include "indexedOctree.H"
 #include "OFstream.H"
 #include "IndirectList.H"
 
@@ -1011,20 +1011,30 @@ void Foam::faceCoupleInfo::findSlavesCoveringMaster
 )
 {
     // Construct octree from all mesh0 boundary faces
-    octreeDataFace shapes(mesh0);
+    labelList bndFaces(mesh0.nFaces()-mesh0.nInternalFaces());
+    forAll(bndFaces, i)
+    {
+        bndFaces[i] = mesh0.nInternalFaces() + i;
+    }
 
     treeBoundBox overallBb(mesh0.points());
 
-    octree<octreeDataFace> tree
+    Random rndGen(123456);
+
+    indexedOctree<treeDataFace> tree
     (
-        overallBb,  // overall search domain
-        shapes,     // all information needed to do checks on cells
-        1,          // min levels
-        20.0,       // maximum ratio of cubes v.s. cells
-        10.0
+        treeDataFace    // all information needed to search faces
+        (
+            false,                      // do not cache bb
+            mesh0,
+            bndFaces                    // boundary faces only
+        ),
+        overallBb.extend(rndGen, 1E-4), // overall search domain
+        8,                              // maxLevel
+        10,                             // leafsize
+        3.0                             // duplicity
     );
 
-
     if (debug)
     {
         Pout<< "findSlavesCoveringMaster :"
@@ -1048,17 +1058,11 @@ void Foam::faceCoupleInfo::findSlavesCoveringMaster
         // Generate face centre (prevent cellCentres() reconstruction)
         point fc(f1.centre(mesh1.points()));
 
-        // Search in bounding box of face only.
-        treeBoundBox tightest(static_cast<const pointField&>(f1.points(mesh1.points())));
-
-        scalar tightestDist = GREAT;
-
-        label index = tree.findNearest(fc, tightest, tightestDist);
-
+        pointIndexHit nearInfo = tree.findNearest(fc, Foam::sqr(absTol));
 
-        if (index != -1)
+        if (nearInfo.hit())
         {
-            label mesh0FaceI = shapes.meshFaces()[index];
+            label mesh0FaceI = tree.shapes().faceLabels()[nearInfo.index()];
 
             // Check if points of f1 actually lie on top of mesh0 face
             // This is the bit that might fail since if f0 is severely warped

src/dynamicMesh/polyTopoChange/polyTopoChange/hexRef8.H

@@ -174,9 +174,12 @@ class hexRef8
         label findMaxLevel(const labelList& f) const;
         //- Count number of vertices <= anchorLevel
         label countAnchors(const labelList&, const label) const;
+        //- Debugging: dump cell as .obj file
+        void dumpCell(const label cellI) const;
         //- Find index of point with wantedLevel, starting from fp.
         label findLevel
         (
+            const label faceI,
             const face& f,
             const label startFp,
             const bool searchForward,

src/dynamicMesh/polyTopoChange/polyTopoChange/removeFaces.C

@@ -807,7 +807,7 @@ void Foam::removeFaces::setRefinement
     // Edges to remove
     labelHashSet edgesToRemove(faceLabels.size());
 
-    // Per face the region it is. -1 for removed faces, -2 for regions
+    // Per face the region it is in. -1 for removed faces, -2 for regions
     // consisting of single face only.
     labelList faceRegion(mesh_.nFaces(), -1);
 
@@ -1258,10 +1258,15 @@ void Foam::removeFaces::setRefinement
     // are only used by 2 unremoved edges.
     {
         // Usage of points by non-removed edges.
-        labelList nEdgesPerPoint(mesh_.nPoints(), labelMax);
+        labelList nEdgesPerPoint(mesh_.nPoints());
 
         const labelListList& pointEdges = mesh_.pointEdges();
 
+        forAll(pointEdges, pointI)
+        {
+            nEdgesPerPoint[pointI] = pointEdges[pointI].size();
+        }
+
         forAllConstIter(labelHashSet, edgesToRemove, iter)
         {
             // Edge will get removed.
@@ -1269,16 +1274,7 @@ void Foam::removeFaces::setRefinement
 
             forAll(e, i)
             {
-                label pointI = e[i];
-
-                if (nEdgesPerPoint[pointI] == labelMax)
-                {
-                    nEdgesPerPoint[pointI] = pointEdges[pointI].size()-1;
-                }
-                else
-                {
-                    nEdgesPerPoint[pointI]--;
-                }
+                nEdgesPerPoint[e[i]]--;
             }
         }
 

src/finiteVolume/fields/fvPatchFields/derived/directMappedFixedValue/directMappedFixedValueFvPatchField.C

@@ -159,7 +159,7 @@ void directMappedFixedValueFvPatchField<Type>::updateCoeffs()
 
     // Get the scheduling information
     const List<labelPair>& schedule = mpp.schedule();
-    const labelListList& sendCellLabels = mpp.sendCellLabels();
+    const labelListList& sendLabels = mpp.sendLabels();
     const labelListList& receiveFaceLabels = mpp.receiveFaceLabels();
 
 
@@ -177,7 +177,7 @@ void directMappedFixedValueFvPatchField<Type>::updateCoeffs()
             toProc<< IndirectList<Type>
             (
                 this->internalField(),
-                sendCellLabels[recvProc]
+                sendLabels[recvProc]
             )();
         }
         else
@@ -204,7 +204,7 @@ void directMappedFixedValueFvPatchField<Type>::updateCoeffs()
         IndirectList<Type> fromFld
         (
             this->internalField(),
-            sendCellLabels[Pstream::myProcNo()]
+            sendLabels[Pstream::myProcNo()]
         );
     
         // Destination faces

src/lagrangian/basic/Cloud/CloudIO.C

@@ -118,7 +118,8 @@ void Foam::Cloud<ParticleType>::checkFieldIOobject
             "void Cloud<ParticleType>::checkFieldIOobject"
             "(Cloud<ParticleType>, IOField<DataType>)"
         )   << "Size of " << data.name()
-            << " field does not match the number of particles"
+            << " field " << data.size()
+            << " does not match the number of particles " << c.size()
             << abort(FatalError);
     }
 }

src/meshTools/Make/options

@@ -3,5 +3,5 @@ EXE_INC = \
     -I$(LIB_SRC)/lagrangian/basic/lnInclude
 
 LIB_LIBS = \
-   -ltriSurface \
-   -llagrangian
+    -ltriSurface \
+    -llagrangian

src/meshTools/directMapped/directMappedPolyPatch/directMappedPolyPatch.C

@@ -40,6 +40,18 @@ namespace Foam
 
     addToRunTimeSelectionTable(polyPatch, directMappedPolyPatch, word);
     addToRunTimeSelectionTable(polyPatch, directMappedPolyPatch, dictionary);
+
+
+    template<>
+    const char* NamedEnum<directMappedPolyPatch::sampleMode, 3>::names[] =
+    {
+        "nearestCell",
+        "nearestPatchFace",
+        "nearestFace"
+    };
+
+    const NamedEnum<directMappedPolyPatch::sampleMode, 3>
+        directMappedPolyPatch::sampleModeNames_;
 }
 
 
@@ -113,107 +125,236 @@ void Foam::directMappedPolyPatch::collectSamples
 void Foam::directMappedPolyPatch::findSamples
 (
     const pointField& samples,
-    labelList& sampleCellProcs,
-    labelList& sampleCells,
-    pointField& sampleCc
+    labelList& sampleProcs,
+    labelList& sampleIndices,
+    pointField& sampleLocations
 ) const
 {
-    sampleCellProcs.setSize(samples.size());
-    sampleCells.setSize(samples.size());
-    sampleCc.setSize(samples.size());
-    sampleCc = point(-GREAT, -GREAT, -GREAT);
+    const polyMesh& mesh = boundaryMesh().mesh();
 
+    // All the info for nearest. Construct to miss
+    List<nearInfo> nearest(samples.size());
+
+    switch (mode_)
     {
-        // Octree based search engine
-        meshSearch meshSearchEngine(boundaryMesh().mesh(), false);
+        case NEARESTCELL:
+        {
+            if (samplePatch_.size() != 0 && samplePatch_ != "none")
+            {
+                FatalErrorIn
+                (
+                    "directMappedPolyPatch::findSamples(const pointField&,"
+                    " labelList&, labelList&, pointField&) const"
+                )   << "No need to supply a patch name when in "
+                    << sampleModeNames_[mode_] << " mode." << exit(FatalError);
+            }
+
+            // Octree based search engine
+            meshSearch meshSearchEngine(mesh, false);
+
+            forAll(samples, sampleI)
+            {
+                const point& sample = samples[sampleI];
+
+                label cellI = meshSearchEngine.findCell(sample);
+
+                if (cellI == -1)
+                {
+                    nearest[sampleI].second().first() = Foam::sqr(GREAT);
+                    nearest[sampleI].second().second() = Pstream::myProcNo();
+                }
+                else
+                {
+                    const point& cc = mesh.cellCentres()[cellI];
+
+                    nearest[sampleI].first() = pointIndexHit
+                    (
+                        true,
+                        cc,
+                        cellI
+                    );
+                    nearest[sampleI].second().first() = magSqr(cc-sample);
+                    nearest[sampleI].second().second() = Pstream::myProcNo();
+                }
+            }
+            break;
+        }
 
-        forAll(samples, sampleI)
+        case NEARESTPATCHFACE:
         {
-            sampleCells[sampleI] = meshSearchEngine.findCell(samples[sampleI]);
+            label patchI = boundaryMesh().findPatchID(samplePatch_);
 
-            if (sampleCells[sampleI] == -1)
+            if (patchI == -1)
             {
-                sampleCellProcs[sampleI] = -1;
+                FatalErrorIn("directMappedPolyPatch::findSamples(..)")
+                    << "Cannot find patch " << samplePatch_ << endl
+                    << "Valid patches are " << boundaryMesh().names()
+                    << exit(FatalError);
             }
-            else
+
+            Random rndGen(123456);
+
+            const polyPatch& pp = boundaryMesh()[patchI];
+
+            // patch faces
+            const labelList patchFaces(identity(pp.size()) + pp.start());
+
+            const treeBoundBox patchBb
+            (
+                treeBoundBox(pp.points(), pp.meshPoints()).extend
+                (
+                    rndGen,
+                    1E-4
+                )
+            );
+
+            autoPtr<indexedOctree<treeDataFace> > boundaryTree
+            (
+                new indexedOctree<treeDataFace>
+                (
+                    treeDataFace    // all information needed to search faces
+                    (
+                        false,                      // do not cache bb
+                        mesh,
+                        patchFaces                  // boundary faces only
+                    ),
+                    patchBb,   // overall search domain
+                    8,                              // maxLevel
+                    10,                             // leafsize
+                    3.0                             // duplicity
+                )
+            );
+
+            forAll(samples, sampleI)
             {
-                sampleCellProcs[sampleI] = Pstream::myProcNo();
-                sampleCc[sampleI] =
-                    boundaryMesh().mesh().cellCentres()[sampleCells[sampleI]];
+                const point& sample = samples[sampleI];
+
+                pointIndexHit& nearInfo = nearest[sampleI].first();
+                nearInfo = boundaryTree().findNearest
+                (
+                    sample,
+                    magSqr(patchBb.max()-patchBb.min())
+                );
+
+                if (!nearInfo.hit())
+                {
+                    nearest[sampleI].second().first() = Foam::sqr(GREAT);
+                    nearest[sampleI].second().second() = Pstream::myProcNo();
+                }
+                else
+                {
+                    point fc(pp[nearInfo.index()].centre(pp.points()));
+                    nearInfo.setPoint(fc);
+                    nearest[sampleI].second().first() = magSqr(fc-sample);
+                    nearest[sampleI].second().second() = Pstream::myProcNo();
+                }
             }
+            break;
         }
-    }
 
-    // Use only that processor that contains the sample
-    Pstream::listCombineGather(sampleCells, maxEqOp<label>());
-    Pstream::listCombineScatter(sampleCells);
+        case NEARESTFACE:
+        {
+            if (samplePatch_.size() != 0 && samplePatch_ != "none")
+            {
+                FatalErrorIn
+                (
+                    "directMappedPolyPatch::findSamples(const pointField&,"
+                    " labelList&, labelList&, pointField&) const"
+                )   << "No need to supply a patch name when in "
+                    << sampleModeNames_[mode_] << " mode." << exit(FatalError);
+            }
 
-    labelList minSampleCellProcs(sampleCellProcs);
-    Pstream::listCombineGather(sampleCellProcs, maxEqOp<label>());
-    Pstream::listCombineScatter(sampleCellProcs);
+            // Octree based search engine
+            meshSearch meshSearchEngine(mesh, false);
 
-    Pstream::listCombineGather(sampleCc, maxEqOp<point>());
-    Pstream::listCombineScatter(sampleCc);
+            forAll(samples, sampleI)
+            {
+                const point& sample = samples[sampleI];
+
+                label faceI = meshSearchEngine.findNearestFace(sample);
+
+                if (faceI == -1)
+                {