Merge branch 'master' of ssh://noisy/home/noisy3/OpenFOAM/OpenFOAM-dev

ReleaseNotes-dev

@@ -35,6 +35,9 @@
 *** Core library
     + Large number of code refinements and consistency improvements to support
       other developments.
+      Parallel : using non-blocking communications wherever possible. This will
+      lead to lower requirements for MPI_BUFFER_SIZE and possibly better
+      start-up performance on larger numbers of processors.
 *** Turbulence modelling
 *** *Updated* thermophysical libraries
     + Now use the more descriptive dictionary input format, e.g. for a single
@@ -102,15 +105,28 @@
     + Parallel aware
 *** *New* ptscotch decomposition method
 *** *Updated* particle tracking algorithm
+    + uses non-blocking parallel transfers
+    + does 'minimum-tet' decomposition of face to work with warped faces (snappyHexMesh!)
+    + reuses tracking state in interpolation - improves consistency and speed
 *** *Updated* split cyclics into two separate patches. See doc/changed/splitCyclics.txt
   * *Updated* interpolation (volPointInterpolation) now works without the
     globalPointPatch. Moving mesh cases can now be run non-parallel and
     continued in parallel and reconstructed without any limitation.
 *** *New* compact binary I/O for faces and cells. This speeds up reading/writing meshes in binary.
 *** *Updated* runTimeModifiable
-    + on linux uses inotify instead of time stamps - more efficient for large
+    + user selectable model to use for checking run-time modifiable
+      dictionaries:
+      + timeStamp : use time stamp as before
+      + inotify : use inotify instead of time stamp
+      + timeStampMaster : only master checks and reads file. Slaves get file
+        contents from master.
+      + inotifyMaster : only master checks and reads file. Slaves get file
+        contents from master.
+    + on linux optionally uses inotify instead of time stamps - more efficient for large
       numbers of monitored files. No more fileModificationSkew needed.
     + single integer reduction instead of one reduction per monitored file.
+    + only files that can be re-read are being checked. Drastic reduction of
+      number of files to check.
 * Solvers
   A number of new solvers have been developed for a range of engineering
   applications.  There has been a set of improvements to certain classes of

applications/utilities/surface/surfaceFeatureExtract/Make/options

 EXE_INC = \
-    -I$(LIB_SRC)/cfdTools/general/lnInclude \
     -I$(LIB_SRC)/meshTools/lnInclude \
+    -I$(LIB_SRC)/edgeMesh/lnInclude \
     -I$(LIB_SRC)/triSurface/lnInclude
 
 EXE_LIBS = \
     -lmeshTools \
+    -ledgeMesh \
     -ltriSurface

applications/utilities/surface/surfaceFeatureExtract/surfaceFeatureExtract.C

@@ -29,10 +29,13 @@ Description
 
 \*---------------------------------------------------------------------------*/
 
+
 #include "triangle.H"
 #include "triSurface.H"
 #include "argList.H"
+#include "Time.H"
 #include "surfaceFeatures.H"
+#include "featureEdgeMesh.H"
 #include "treeBoundBox.H"
 #include "meshTools.H"
 #include "OFstream.H"
@@ -135,7 +138,8 @@ int main(int argc, char *argv[])
         "remove edges within specified bounding box"
     );
 
-    argList args(argc, argv);
+#   include "setRootCase.H"
+#   include "createTime.H"
 
     Info<< "Feature line extraction is only valid on closed manifold surfaces."
         << endl;
@@ -282,7 +286,6 @@ int main(int argc, char *argv[])
     Info<< endl << "Writing edge objs." << endl;
     newSet.writeObj("final");
 
-
     Info<< nl
         << "Final feature set:" << nl
         << "    feature points : " << newSet.featurePoints().size() << nl
@@ -293,6 +296,22 @@ int main(int argc, char *argv[])
         << "        internal edges : " << newSet.nInternalEdges() << nl
         << endl;
 
+    // Extracting and writing a featureEdgeMesh
+
+    Pout<< nl << "Writing featureEdgeMesh to constant/featureEdgeMesh."
+        << endl;
+
+    featureEdgeMesh feMesh
+    (
+        newSet,
+        runTime,
+        surfFileName.lessExt().name() + ".featureEdgeMesh"
+    );
+
+    feMesh.writeObj(surfFileName.lessExt().name());
+
+    feMesh.write();
+
     Info<< "End\n" << endl;
 
     return 0;

src/Allwmake

@@ -38,6 +38,8 @@ wmake libso genericPatchFields
 # Build the proper scotchDecomp, metisDecomp etc.
 parallel/Allwmake
 
+wmake libso conversion
+
 wmake libso sampling
 
 wmake libso dynamicMesh
@@ -53,7 +55,6 @@ turbulenceModels/Allwmake
 wmake libso surfaceFilmModels
 lagrangian/Allwmake
 postProcessing/Allwmake
-conversion/Allwmake
 mesh/Allwmake
 
 wmake libso errorEstimation

src/OpenFOAM/db/IOobjects/IOdictionary/IOdictionary.C

@@ -67,8 +67,16 @@ void Foam::IOdictionary::readFile(const bool masterOnly)
                 slave++
             )
             {
-
-                OPstream toSlave(Pstream::scheduled, slave);
+                // Note: use ASCII for now - binary IO of dictionaries is
+                // not currently supported
+                OPstream toSlave
+                (
+                    Pstream::scheduled,
+                    slave,
+                    0,
+                    UPstream::msgType(),
+                    IOstream::ASCII
+                );
                 IOdictionary::writeData(toSlave);
             }
         }
@@ -79,7 +87,13 @@ void Foam::IOdictionary::readFile(const bool masterOnly)
                 Pout<< "IOdictionary : Reading " << objectPath()
                     << " from master processor " << Pstream::masterNo() << endl;
             }
-            IPstream fromMaster(Pstream::scheduled, Pstream::masterNo());
+            IPstream fromMaster
+            (
+                Pstream::scheduled,
+                Pstream::masterNo(),
+                0,
+                IOstream::ASCII
+            );
             IOdictionary::readData(fromMaster);
         }
     }

src/OpenFOAM/db/IOstreams/Pstreams/UOPstream.C

@@ -213,9 +213,20 @@ Foam::Ostream& Foam::UOPstream::write(const string& str)
 }
 
 
-Foam::Ostream& Foam::UOPstream::writeQuoted(const std::string& str, const bool)
+Foam::Ostream& Foam::UOPstream::writeQuoted
+(
+    const std::string& str,
+    const bool quoted
+)
 {
-    write(char(token::STRING));
+    if (quoted)
+    {
+        write(char(token::STRING));
+    }
+    else
+    {
+        write(char(token::WORD));
+    }
 
     size_t len = str.size();
     writeToBuffer(len);

src/OpenFOAM/db/regIOobject/regIOobjectRead.C

@@ -196,8 +196,16 @@ bool Foam::regIOobject::read()
                 slave++
             )
             {
-
-                OPstream toSlave(Pstream::scheduled, slave);
+                // Note: use ASCII for now - binary IO of dictionaries is
+                // not currently supported
+                OPstream toSlave
+                (
+                    Pstream::scheduled,
+                    slave,
+                    0,
+                    UPstream::msgType(),
+                    IOstream::ASCII
+                );
                 writeData(toSlave);
             }
         }
@@ -210,7 +218,13 @@ bool Foam::regIOobject::read()
                     << " from master processor " << Pstream::masterNo()
                     << endl;
             }
-            IPstream fromMaster(Pstream::scheduled, Pstream::masterNo());
+            IPstream fromMaster
+            (
+                Pstream::scheduled,
+                Pstream::masterNo(),
+                0,
+                IOstream::ASCII
+            );
             ok = readData(fromMaster);
         }
     }

src/OpenFOAM/meshes/polyMesh/polyPatches/constraint/processor/processorPolyPatch.C

@@ -63,8 +63,6 @@ Foam::processorPolyPatch::processorPolyPatch
     neighbFaceCentres_(),
     neighbFaceAreas_(),
     neighbFaceCellCentres_()
-//    neighbPointsPtr_(NULL),
-//    neighbEdgesPtr_(NULL)
 {}
 
 
@@ -82,8 +80,6 @@ Foam::processorPolyPatch::processorPolyPatch
     neighbFaceCentres_(),
     neighbFaceAreas_(),
     neighbFaceCellCentres_()
-//    neighbPointsPtr_(NULL),
-//    neighbEdgesPtr_(NULL)
 {}
 
 
@@ -99,8 +95,6 @@ Foam::processorPolyPatch::processorPolyPatch
     neighbFaceCentres_(),
     neighbFaceAreas_(),
     neighbFaceCellCentres_()
-//    neighbPointsPtr_(NULL),
-//    neighbEdgesPtr_(NULL)
 {}
 
 
@@ -119,8 +113,6 @@ Foam::processorPolyPatch::processorPolyPatch
     neighbFaceCentres_(),
     neighbFaceAreas_(),
     neighbFaceCellCentres_()
-//    neighbPointsPtr_(NULL),
-//    neighbEdgesPtr_(NULL)
 {}
 
 
@@ -139,8 +131,6 @@ Foam::processorPolyPatch::processorPolyPatch
     neighbFaceCentres_(),
     neighbFaceAreas_(),
     neighbFaceCellCentres_()
-//    neighbPointsPtr_(NULL),
-//    neighbEdgesPtr_(NULL)
 {}
 
 
@@ -157,7 +147,6 @@ Foam::processorPolyPatch::~processorPolyPatch()
 
 void Foam::processorPolyPatch::initGeometry(PstreamBuffers& pBufs)
 {
-//Pout<< "**processorPolyPatch::initGeometry()" << endl;
     if (Pstream::parRun())
     {
         UOPstream toNeighbProc(neighbProcNo(), pBufs);
@@ -172,7 +161,6 @@ void Foam::processorPolyPatch::initGeometry(PstreamBuffers& pBufs)
 
 void Foam::processorPolyPatch::calcGeometry(PstreamBuffers& pBufs)
 {
-//Pout<< "processorPolyPatch::calcGeometry() for " << name() << endl;
     if (Pstream::parRun())
     {
         {
@@ -184,8 +172,6 @@ void Foam::processorPolyPatch::calcGeometry(PstreamBuffers& pBufs)
                 >> neighbFaceCellCentres_;
         }
 
-//Pout<< "processorPolyPatch::calcGeometry() : received data for "
-//    << neighbFaceCentres_.size() << " faces." << endl;
 
         // My normals
         vectorField faceNormals(size());
@@ -252,9 +238,6 @@ void Foam::processorPolyPatch::calcGeometry(PstreamBuffers& pBufs)
             nbrFaceNormals,
             calcFaceTol(*this, points(), faceCentres())
         );
-//Pout<< "**neighbFaceCentres_:" << neighbFaceCentres_ << endl;
-//Pout<< "**neighbFaceAreas_:" << neighbFaceAreas_ << endl;
-//Pout<< "**neighbFaceCellCentres_:" << neighbFaceCellCentres_ << endl;
     }
 }
 

src/conversion/Make/files

@@ -4,6 +4,7 @@ ensight/part/ensightPart.C
 ensight/part/ensightPartIO.C
 ensight/part/ensightPartCells.C
 ensight/part/ensightPartFaces.C
+ensight/part/ensightPartNonMeshFaces.C
 ensight/part/ensightParts.C
 
 meshTables/boundaryRegion.C

src/conversion/ensight/part/ensightPart.H

@@ -267,6 +267,12 @@ public:
             matId_ = value;
         }
 
+        //- simple labelList with a name
+        const labelListList& elemLists() const
+        {
+            return elemLists_;
+        }
+
         //- offset for element ids
         label offset() const
         {
@@ -285,8 +291,12 @@ public:
         //- write reconstruction information for the object
         bool writeData(Ostream&) const;
 
-        //- write geometry
-        void writeGeometry(ensightGeoFile&) const;
+        //- Write geometry
+        virtual void writeGeometry(ensightGeoFile&) const
+        {}
+
+        //- Helper: write geometry given the pointField
+        void writeGeometry(ensightGeoFile&, const pointField& points) const;
 
         //- write scalar field
         void writeScalarField

src/conversion/ensight/part/ensightPartCells.C

@@ -427,4 +427,11 @@ void Foam::ensightPartCells::writeConnectivity
 }
 
 
+void Foam::ensightPartCells::writeGeometry(ensightGeoFile& os) const
+{
+    const polyMesh& mesh = *meshPtr_;
+    ensightPart::writeGeometry(os, mesh.points());
+}
+
+
 // ************************************************************************* //

src/conversion/ensight/part/ensightPartCells.H

@@ -74,6 +74,9 @@ class ensightPartCells
             const labelList& pointMap
         ) const;
 
+        //- write geometry
+        virtual void writeGeometry(ensightGeoFile& os) const;
+
 
 protected:
 

src/conversion/ensight/part/ensightPartFaces.C

@@ -47,41 +47,18 @@ Foam::List<Foam::word> Foam::ensightPartFaces::elemTypes_
 );
 
 
-// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+// * * * * * * * * * * * * Protected Member Functions  * * * * * * * * * * * //
 
-Foam::ensightPartFaces::ensightPartFaces
-(
-    label partNumber,
-    const string& partDescription
-)
-:
-    ensightPart(partNumber, partDescription)
+void Foam::ensightPartFaces::binShapes(const faceList& faces)
 {
-    isCellData_ = false;
-}
-
-
-Foam::ensightPartFaces::ensightPartFaces
-(
-    label partNumber,
-    const polyMesh& pMesh,
-    const polyPatch& pPatch
-)
-:
-    ensightPart(partNumber, pPatch.name(), pMesh)
-{
-    isCellData_ = false;
-    offset_ = pPatch.start();
-    size_ = pPatch.size();
-
     // count the shapes
     label nTri  = 0;
     label nQuad = 0;
     label nPoly = 0;
 
-    forAll(pPatch, patchfaceI)
+    forAll(faces, faceI)
     {
-        const face& f = pMesh.faces()[patchfaceI + offset_];
+        const face& f = faces[faceI];
 
         if (f.size() == 3)
         {
@@ -108,21 +85,21 @@ Foam::ensightPartFaces::ensightPartFaces
     nPoly = 0;
 
     // classify the shapes
-    forAll(pPatch, patchfaceI)
+    forAll(faces, faceI)
     {
-        const face& f = pMesh.faces()[patchfaceI + offset_];
+        const face& f = faces[faceI];
 
         if (f.size() == 3)
         {
-            triCells[nTri++] = patchfaceI;
+            triCells[nTri++] = faceI;
         }
         else if (f.size() == 4)
         {
-            quadCells[nQuad++] = patchfaceI;
+            quadCells[nQuad++] = faceI;
         }
         else
         {
-            polygonCells[nPoly++] = patchfaceI;
+            polygonCells[nPoly++] = faceI;
         }
     }
 
@@ -133,10 +110,45 @@ Foam::ensightPartFaces::ensightPartFaces
     elemLists_[tria3Elements].transfer( triCells );
     elemLists_[quad4Elements].transfer( quadCells );
     elemLists_[nsidedElements].transfer( polygonCells );
+
+    size_ = faces.size();
 }
 
 
-Foam::ensightPartFaces::ensightPartFaces(const ensightPartFaces &part)
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+Foam::ensightPartFaces::ensightPartFaces
+(
+    label partNumber,
+    const string& partDescription
+)
+:
+    ensightPart(partNumber, partDescription)
+{
+    isCellData_ = false;
+    offset_ = 0;
+    size_ = 0;
+}
+
+
+Foam::ensightPartFaces::ensightPartFaces
+(
+    label partNumber,
+    const polyMesh& pMesh,
+    const polyPatch& pPatch
+)
+:
+    ensightPart(partNumber, pPatch.name(), pMesh)
+{
+    isCellData_ = false;
+    offset_ = pPatch.start();
+
+    // count the shapes
+    binShapes(pPatch);
+}
+
+
+Foam::ensightPartFaces::ensightPartFaces(const ensightPartFaces& part)
 :
     ensightPart(part)
 {}
@@ -206,6 +218,7 @@ void Foam::ensightPartFaces::writeConnectivity
 (
     ensightGeoFile& os,
     const word& key,
+    const faceList& faces,
     const labelList& idList,
     const labelList& pointMap
 ) const
@@ -214,8 +227,6 @@ void Foam::ensightPartFaces::writeConnectivity
     os.write(idList.size());
     os.newline();
 
-    const faceList& meshFaces = meshPtr_->faces();
-
     // write (polygon) face sizes
     if (key == "nsided")
     {
@@ -223,7 +234,7 @@ void Foam::ensightPartFaces::writeConnectivity
         forAll(idList, i)
         {
             label id = idList[i] + offset_;
-            const face& f = meshFaces[id];
+            const face& f = faces[id];
 
             os.write( f.size() );
             os.newline();
@@ -234,7 +245,7 @@ void Foam::ensightPartFaces::writeConnectivity
     forAll(idList, i)
     {
         label id = idList[i] + offset_;
-        const face& f = meshFaces[id];
+        const face& f = faces[id];
 
         // convert global -> local index
         // (note: Ensight indices start with 1)
@@ -247,4 +258,31 @@ void Foam::ensightPartFaces::writeConnectivity
 }
 
 
+void Foam::ensightPartFaces::writeConnectivity
+(
+    ensightGeoFile& os,
+    const word& key,
+    const labelList& idList,
+    const labelList& pointMap
+) const
+{
+    writeConnectivity
+    (
+        os,
+        key,
+        meshPtr_->faces(),
+        idList,
+        pointMap
+    );
+}
+
+
+void Foam::ensightPartFaces::writeGeometry(ensightGeoFile& os) const
+{
+    const polyMesh& mesh = *meshPtr_;
+    const pointField& points = mesh.points();
+    ensightPart::writeGeometry(os, points);
+}
+
+
 // ************************************************************************* //

src/conversion/ensight/part/ensightPartFaces.H

@@ -67,6 +67,9 @@ class ensightPartFaces
             const labelList& pointMap
         ) const;
 
+        //- write geometry
+        virtual void writeGeometry(ensightGeoFile& os) const;
+
 
 protected:
 
@@ -81,6 +84,19 @@ protected:
     // Static data members
     static List<word> elemTypes_;
 
+    //- Divide the shapes, set elemLists.
+    void binShapes(const faceList& faces);
+
+    //- Helper: write connectivity
+    void writeConnectivity
+    (
+        ensightGeoFile& os,
+        const word& key,
+        const faceList& faces,
+        const labelList& idList,
+        const labelList& pointMap
+    ) const;
+
 
 public:
 

src/conversion/ensight/part/ensightPartIO.C

@@ -118,15 +118,16 @@ bool Foam::ensightPart::writeData(Ostream& os) const
 }
 
 
-void Foam::ensightPart::writeGeometry(ensightGeoFile& os) const
+void Foam::ensightPart::writeGeometry
+(
+    ensightGeoFile& os,
+    const pointField& points
+) const
 {
-    if (size() && meshPtr_)
+    if (size())
     {
-        const polyMesh& mesh = *meshPtr_;
-        const pointField& meshPoints = mesh.points();
-
-        localPoints ptList = calcLocalPoints();
-        labelList& pointMap = ptList.list;
+        const localPoints ptList = calcLocalPoints();
+        const labelList& pointMap = ptList.list;
 
         writeHeader(os, true);
 
@@ -141,7 +142,7 @@ void Foam::ensightPart::writeGeometry(ensightGeoFile& os) const
             {
                 if (pointMap[ptI] > -1)
                 {
-                    os.write( meshPoints[ptI].component(cmpt) );
+                    os.write( points[ptI].component(cmpt) );
                     os.newline();
                 }
             }

src/conversion/ensight/part/ensightPartNonMeshFaces.C

+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2010 OpenCFD Ltd.
+     \\/     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