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

applications/test/readCHEMKINIII/readCHEMKINIII.C

@@ -57,7 +57,7 @@ int main(int argc, char *argv[])
     //Info<< ck.specieThermo() << endl;
     //Info<< ck.reactions() << endl;
 
-    PtrList<chemkinReader::reaction> reactions = ck.reactions();
+    const SLPtrList<gasReaction>& reactions = ck.reactions();
 
     {
         OFstream reactionStream("reactions");
@@ -70,17 +70,17 @@ int main(int argc, char *argv[])
         label nReactions(readLabel(reactionStream));
         reactionStream.readBeginList(args.executable().c_str());
 
-        PtrList<chemkinReader::reaction> testReactions(nReactions);
+        PtrList<gasReaction> testReactions(nReactions);
 
         forAll (testReactions, i)
         {
             testReactions.set
             (
                 i,
-                chemkinReader::reaction::New
+                gasReaction::New
                 (
                     ck.species(),
-                    ck.specieThermo(),
+                    ck.speciesThermo(),
                     reactionStream
                 )
             );

applications/utilities/mesh/conversion/ansysToFoam/ansysToFoam.L

@@ -39,6 +39,8 @@ Description
  \* ------------------------------------------------------------------------- */
 
 #include <sstream>
+// For EOF only
+#include <cstdio>
 
 #include "scalar.H"
 #include "IStringStream.H"

applications/utilities/mesh/conversion/gambitToFoam/gambitToFoam.L

@@ -41,6 +41,9 @@ Description
 #include "scalarList.H"
 #include "IStringStream.H"
 
+// For EOF only
+#include <cstdio>
+
 using namespace Foam;
 
 #include "argList.H"

applications/utilities/surface/surfaceRedistributePar/surfaceRedistributePar.C

@@ -62,7 +62,7 @@ void writeProcStats
     // Determine surface bounding boxes, faces, points
     List<treeBoundBox> surfBb(Pstream::nProcs());
     {
-        surfBb[Pstream::myProcNo()] = boundBox(s.points(), false);
+        surfBb[Pstream::myProcNo()] = treeBoundBox(s.points());
         Pstream::gatherList(surfBb);
         Pstream::scatterList(surfBb);
     }

src/OpenFOAM/containers/Lists/CompactListList/CompactListList.H

@@ -61,8 +61,16 @@ namespace Foam
 
 template<class T, class Container> class CompactListList;
 
-template<class T, class Container> Istream& operator>>(Istream&, CompactListList<T, Container>&);
-template<class T, class Container> Ostream& operator<<(Ostream&, const CompactListList<T, Container>&);
+template<class T, class Container> Istream& operator>>
+(
+    Istream&,
+    CompactListList<T, Container>&
+);
+template<class T, class Container> Ostream& operator<<
+(
+    Ostream&,
+    const CompactListList<T, Container>&
+);
 
 
 /*---------------------------------------------------------------------------*\

src/OpenFOAM/fields/GeometricFields/GeometricField/GeometricField.C

@@ -52,20 +52,11 @@ Foam::tmp
     typename Foam::GeometricField<Type, PatchField, GeoMesh>::
     GeometricBoundaryField
 >
-Foam::GeometricField<Type, PatchField, GeoMesh>::readField(Istream& is)
+Foam::GeometricField<Type, PatchField, GeoMesh>::readField
+(
+    const dictionary& fieldDict
+)
 {
-    if (is.version() < 2.0)
-    {
-        FatalIOErrorIn
-        (
-            "GeometricField<Type, PatchField, GeoMesh>::readField(Istream&)",
-            is
-        )   << "IO versions < 2.0 are not supported."
-            << exit(FatalIOError);
-    }
-
-    dictionary fieldDict(is);
-
     DimensionedField<Type, GeoMesh>::readField(fieldDict, "internalField");
 
     tmp<GeometricBoundaryField> tboundaryField
@@ -96,6 +87,28 @@ Foam::GeometricField<Type, PatchField, GeoMesh>::readField(Istream& is)
 }
 
 
+template<class Type, template<class> class PatchField, class GeoMesh>
+Foam::tmp
+<
+    typename Foam::GeometricField<Type, PatchField, GeoMesh>::
+    GeometricBoundaryField
+>
+Foam::GeometricField<Type, PatchField, GeoMesh>::readField(Istream& is)
+{
+    if (is.version() < 2.0)
+    {
+        FatalIOErrorIn
+        (
+            "GeometricField<Type, PatchField, GeoMesh>::readField(Istream&)",
+            is
+        )   << "IO versions < 2.0 are not supported."
+            << exit(FatalIOError);
+    }
+
+    return readField(dictionary(is));
+}
+
+
 template<class Type, template<class> class PatchField, class GeoMesh>
 bool Foam::GeometricField<Type, PatchField, GeoMesh>::readIfPresent()
 {
@@ -404,6 +417,44 @@ Foam::GeometricField<Type, PatchField, GeoMesh>::GeometricField
 }
 
 
+template<class Type, template<class> class PatchField, class GeoMesh>
+Foam::GeometricField<Type, PatchField, GeoMesh>::GeometricField
+(
+    const IOobject& io,
+    const Mesh& mesh,
+    const dictionary& dict
+)
+:
+    DimensionedField<Type, GeoMesh>(io, mesh, dimless),
+    timeIndex_(this->time().timeIndex()),
+    field0Ptr_(NULL),
+    fieldPrevIterPtr_(NULL),
+    boundaryField_(*this, readField(dict))
+{
+    // Check compatibility between field and mesh
+
+    if (this->size() != GeoMesh::size(this->mesh()))
+    {
+        FatalErrorIn
+        (
+            "GeometricField<Type, PatchField, GeoMesh>::GeometricField"
+            "(const IOobject&, const Mesh&, const dictionary&)"
+        )   << "   number of field elements = " << this->size()
+            << " number of mesh elements = " << GeoMesh::size(this->mesh())
+            << exit(FatalIOError);
+    }
+
+    readOldTimeIfPresent();
+
+    if (debug)
+    {
+        Info<< "Finishing dictionary-construct of "
+               "GeometricField<Type, PatchField, GeoMesh>"
+            << endl << this->info() << endl;
+    }
+}
+
+
 // construct as copy
 template<class Type, template<class> class PatchField, class GeoMesh>
 Foam::GeometricField<Type, PatchField, GeoMesh>::GeometricField

src/OpenFOAM/fields/GeometricFields/GeometricField/GeometricField.H

@@ -240,6 +240,9 @@ private:
 
     // Private member functions
 
+        //- Read the field from the dictionary
+        tmp<GeometricBoundaryField> readField(const dictionary&);
+
         //- Read the field from the given stream
         tmp<GeometricBoundaryField> readField(Istream& is);
 
@@ -327,6 +330,14 @@ public:
             Istream&
         );
 
+        //- Construct from dictionary
+        GeometricField
+        (
+            const IOobject&,
+            const Mesh&,
+            const dictionary&
+        );
+
         //- Construct as copy
         GeometricField
         (

src/Pstream/mpi/UIPread.C

@@ -66,6 +66,14 @@ Foam::UIPstream::UIPstream
 
         label wantedSize = externalBuf_.capacity();
 
+        if (debug)
+        {
+            Pout<< "UIPstream::UIPstream : read from:" << fromProcNo
+                << " tag:" << tag << " wanted size:" << wantedSize
+                << Foam::endl;
+        }
+
+
         // If the buffer size is not specified, probe the incomming message
         // and set it
         if (!wantedSize)
@@ -75,6 +83,12 @@ Foam::UIPstream::UIPstream
 
             externalBuf_.setCapacity(messageSize_);
             wantedSize = messageSize_;
+
+            if (debug)
+            {
+                Pout<< "UIPstream::UIPstream : probed size:" << wantedSize
+                    << Foam::endl;
+            }
         }
 
         messageSize_ = UIPstream::read
@@ -127,6 +141,7 @@ Foam::UIPstream::UIPstream(const int fromProcNo, PstreamBuffers& buffers)
     if (commsType() == UPstream::nonBlocking)
     {
         // Message is already received into externalBuf
+        messageSize_ = buffers.recvBuf_[fromProcNo].size();
     }
     else
     {
@@ -134,6 +149,14 @@ Foam::UIPstream::UIPstream(const int fromProcNo, PstreamBuffers& buffers)
 
         label wantedSize = externalBuf_.capacity();
 
+        if (debug)
+        {
+            Pout<< "UIPstream::UIPstream PstreamBuffers :"
+                << " read from:" << fromProcNo
+                << " tag:" << tag_ << " wanted size:" << wantedSize
+                << Foam::endl;
+        }
+
         // If the buffer size is not specified, probe the incomming message
         // and set it
         if (!wantedSize)
@@ -143,6 +166,12 @@ Foam::UIPstream::UIPstream(const int fromProcNo, PstreamBuffers& buffers)
 
             externalBuf_.setCapacity(messageSize_);
             wantedSize = messageSize_;
+
+            if (debug)
+            {
+                Pout<< "UIPstream::UIPstream PstreamBuffers : probed size:"
+                    << wantedSize << Foam::endl;
+            }
         }
 
         messageSize_ = UIPstream::read
@@ -180,6 +209,14 @@ Foam::label Foam::UIPstream::read
     const int tag
 )
 {
+    if (debug)
+    {
+        Pout<< "UIPstream::read : starting read from:" << fromProcNo
+            << " tag:" << tag << " wanted size:" << label(bufSize)
+            << " commsType:" << UPstream::commsTypeNames[commsType]
+            << Foam::endl;
+    }
+
     if (commsType == blocking || commsType == scheduled)
     {
         MPI_Status status;
@@ -214,6 +251,14 @@ Foam::label Foam::UIPstream::read
         label messageSize;
         MPI_Get_count(&status, MPI_BYTE, &messageSize);
 
+        if (debug)
+        {
+            Pout<< "UIPstream::read : finished read from:" << fromProcNo
+                << " tag:" << tag << " read size:" << label(bufSize)
+                << " commsType:" << UPstream::commsTypeNames[commsType]
+                << Foam::endl;
+        }
+
         if (messageSize > bufSize)
         {
             FatalErrorIn
@@ -256,6 +301,15 @@ Foam::label Foam::UIPstream::read
             return 0;
         }
 
+        if (debug)
+        {
+            Pout<< "UIPstream::read : started read from:" << fromProcNo
+                << " tag:" << tag << " read size:" << label(bufSize)
+                << " commsType:" << UPstream::commsTypeNames[commsType]
+                << " request:" << PstreamGlobals::outstandingRequests_.size()
+                << Foam::endl;
+        }
+
         PstreamGlobals::outstandingRequests_.append(request);
 
         // Assume the message is completely received.
@@ -267,7 +321,8 @@ Foam::label Foam::UIPstream::read
         (
             "UIPstream::read"
             "(const int fromProcNo, char* buf, std::streamsize bufSize)"
-        )   << "Unsupported communications type " << commsType
+        )   << "Unsupported communications type "
+            << commsType
             << Foam::abort(FatalError);
 
         return 0;

src/Pstream/mpi/UOPwrite.C

@@ -43,6 +43,14 @@ bool Foam::UOPstream::write
     const int tag
 )
 {
+    if (debug)
+    {
+        Pout<< "UIPstream::write : starting write to:" << toProcNo
+            << " tag:" << tag << " size:" << label(bufSize)
+            << " commsType:" << UPstream::commsTypeNames[commsType]
+            << Foam::endl;
+    }
+
     bool transferFailed = true;
 
     if (commsType == blocking)
@@ -56,6 +64,14 @@ bool Foam::UOPstream::write
             tag,
             MPI_COMM_WORLD
         );
+
+        if (debug)
+        {
+            Pout<< "UIPstream::write : finished write to:" << toProcNo
+                << " tag:" << tag << " size:" << label(bufSize)
+                << " commsType:" << UPstream::commsTypeNames[commsType]
+                << Foam::endl;
+        }
     }
     else if (commsType == scheduled)
     {
@@ -68,6 +84,14 @@ bool Foam::UOPstream::write
             tag,
             MPI_COMM_WORLD
         );
+
+        if (debug)
+        {
+            Pout<< "UIPstream::write : finished write to:" << toProcNo
+                << " tag:" << tag << " size:" << label(bufSize)
+                << " commsType:" << UPstream::commsTypeNames[commsType]
+                << Foam::endl;
+        }
     }
     else if (commsType == nonBlocking)
     {
@@ -84,6 +108,15 @@ bool Foam::UOPstream::write
             &request
         );
 
+        if (debug)
+        {
+            Pout<< "UIPstream::write : started write to:" << toProcNo
+                << " tag:" << tag << " size:" << label(bufSize)
+                << " commsType:" << UPstream::commsTypeNames[commsType]
+                << " request:" << PstreamGlobals::outstandingRequests_.size()
+                << Foam::endl;
+        }
+
         PstreamGlobals::outstandingRequests_.append(request);
     }
     else
@@ -93,7 +126,8 @@ bool Foam::UOPstream::write
             "UOPstream::write"
             "(const int fromProcNo, char* buf, std::streamsize bufSize"
             ", const int)"
-        )   << "Unsupported communications type " << commsType
+        )   << "Unsupported communications type "
+            << UPstream::commsTypeNames[commsType]
             << Foam::abort(FatalError);
     }
 

src/Pstream/mpi/UPstream.C

@@ -70,6 +70,12 @@ bool Foam::UPstream::init(int& argc, char**& argv)
     MPI_Comm_size(MPI_COMM_WORLD, &numprocs);
     MPI_Comm_rank(MPI_COMM_WORLD, &myProcNo_);
 
+    if (debug)
+    {
+        Pout<< "UPstream::init : initialised with numProcs:" << numprocs
+            << " myProcNo:" << myProcNo_ << endl;
+    }
+
     if (numprocs <= 1)
     {
         FatalErrorIn("UPstream::init(int& argc, char**& argv)")
@@ -124,6 +130,11 @@ bool Foam::UPstream::init(int& argc, char**& argv)
 
 void Foam::UPstream::exit(int errnum)
 {
+    if (debug)
+    {
+        Pout<< "UPstream::exit." << endl;
+    }
+
 #   ifndef SGIMPI
     int size;
     char* buff;
@@ -164,6 +175,11 @@ void Foam::UPstream::abort()
 
 void Foam::reduce(scalar& Value, const sumOp<scalar>& bop)
 {
+    if (Pstream::debug)
+    {
+        Pout<< "UPstream::reduce : value:" << Value << endl;
+    }
+
     if (!UPstream::parRun())
     {
         return;
@@ -433,11 +449,23 @@ void Foam::reduce(scalar& Value, const sumOp<scalar>& bop)
         }
         */
     }
+
+    if (Pstream::debug)
+    {
+        Pout<< "UPstream::reduce : reduced value:" << Value << endl;
+    }
 }
 
 
 void Foam::UPstream::waitRequests()
 {
+    if (debug)
+    {
+        Pout<< "UPstream::waitRequests : starting wait for "
+            << PstreamGlobals::outstandingRequests_.size()
+            << " outstanding requests." << endl;
+    }
+
     if (PstreamGlobals::outstandingRequests_.size())
     {
         if
@@ -458,11 +486,22 @@ void Foam::UPstream::waitRequests()
 
         PstreamGlobals::outstandingRequests_.clear();
     }
+
+    if (debug)
+    {
+        Pout<< "UPstream::waitRequests : finished wait." << endl;
+    }
 }
 
 
 bool Foam::UPstream::finishedRequest(const label i)
 {
+    if (debug)
+    {
+        Pout<< "UPstream::waitRequests : starting wait for request:" << i
+            << endl;
+    }
+
     if (i >= PstreamGlobals::outstandingRequests_.size())
     {
         FatalErrorIn
@@ -483,6 +522,12 @@ bool Foam::UPstream::finishedRequest(const label i)
         MPI_STATUS_IGNORE
     );
 
+    if (debug)
+    {
+        Pout<< "UPstream::waitRequests : finished wait for request:" << i
+            << endl;
+    }
+
     return flag != 0;
 }
 

src/dynamicMesh/fvMeshAdder/fvMeshAdderTemplates.C

@@ -330,8 +330,6 @@ void Foam::fvMeshAdder::MapVolFields
 
         if (fieldsToAdd.found(fld.name()))
         {
-            Pout<< "Mapping field " << fld.name() << endl;
-
             const GeometricField<Type, fvPatchField, volMesh>& fldToAdd =
                 *fieldsToAdd[fld.name()];
 
@@ -339,7 +337,7 @@ void Foam::fvMeshAdder::MapVolFields
         }
         else
         {
-            WarningIn("fvMeshAdder::MapVolFields")
+            WarningIn("fvMeshAdder::MapVolFields(..)")
                 << "Not mapping field " << fld.name()
                 << " since not present on mesh to add"
                 << endl;
@@ -642,15 +640,13 @@ void Foam::fvMeshAdder::MapSurfaceFields
 
         if (fieldsToAdd.found(fld.name()))
         {
-            Pout<< "Mapping field " << fld.name() << endl;
-
             const fldType& fldToAdd = *fieldsToAdd[fld.name()];
 
             MapSurfaceField<Type>(meshMap, fld, fldToAdd);
         }
         else
         {
-            WarningIn("fvMeshAdder::MapSurfaceFields")
+            WarningIn("fvMeshAdder::MapSurfaceFields(..)")
                 << "Not mapping field " << fld.name()
                 << " since not present on mesh to add"
                 << endl;

src/dynamicMesh/fvMeshDistribute/fvMeshDistribute.H

@@ -82,38 +82,8 @@ class fvMeshDistribute
         const scalar mergeTol_;
 
 
-    // Private classes
-
-        //- Check words are the same. Used in patch type checking of similarly
-        //  named patches.
-        class checkEqualType
-        {
-        public:
-
-            void operator()(word& x, const word& y) const
-            {
-                if (x != y)
-                {
-                    FatalErrorIn("checkEqualType()(word&, const word&) const")
-                        << "Patch type " << x << " possibly on processor "
-                        << Pstream::myProcNo()
-                        << " does not equal patch type " << y
-                        << " on some other processor." << nl
-                        << "Please check similarly named patches for"
-                        << " having exactly the same type."
-                        << abort(FatalError);
-                }
-            }
-        };
-
-
     // Private Member Functions
 
-        //- Given distribution work out a communication schedule. Is list
-        //  of pairs. First element of pair is send processor, second is
-        //  receive processor.
-        //static List<labelPair> getSchedule(const labelList&);
-
         //- Find indices with value
         static labelList select
         (
@@ -123,7 +93,7 @@ class fvMeshDistribute
         );
 
         //- Check all procs have same names and in exactly same order.
-        static void checkEqualWordList(const wordList&);
+        static void checkEqualWordList(const string&, const wordList&);
 
         //- Merge wordlists over all processors
         static wordList mergeWordList(const wordList&);
@@ -288,7 +258,8 @@ class fvMeshDistribute
                 const wordList& cellZoneNames,
                 const labelList& sourceFace,
                 const labelList& sourceProc,
-                const labelList& sourceNewProc
+                const labelList& sourceNewProc,
+                UOPstream& toDomain
             );
             //- Send subset of fields
             template<class GeoField>
@@ -296,7 +267,8 @@ class fvMeshDistribute
             (
                 const label domain,
                 const wordList& fieldNames,
-                const fvMeshSubset&
+                const fvMeshSubset&,
+                UOPstream& toNbr
             );
 
             //- Receive mesh. Opposite of sendMesh
@@ -309,7 +281,8 @@ class fvMeshDistribute
                 const Time& runTime,
                 labelList& domainSourceFace,
                 labelList& domainSourceProc,
-                labelList& domainSourceNewProc
+                labelList& domainSourceNewProc,
+                UIPstream& fromNbr
             );
 
             //- Receive fields. Opposite of sendFields
@@ -319,7 +292,8 @@ class fvMeshDistribute
                 const label domain,
                 const wordList& fieldNames,
                 fvMesh&,
-                PtrList<GeoField>&
+                PtrList<GeoField>&,
+                const dictionary& fieldDicts
             );
 
             //- Disallow default bitwise copy construct

src/dynamicMesh/fvMeshDistribute/fvMeshDistributeTemplates.C

@@ -184,7 +184,7 @@ void Foam::fvMeshDistribute::mapBoundaryFields
 
     if (flds.size() != oldBflds.size())
     {
-        FatalErrorIn("fvMeshDistribute::mapBoundaryFields") << "problem"
+        FatalErrorIn("fvMeshDistribute::mapBoundaryFields(..)") << "problem"
             << abort(FatalError);
     }