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

applications/utilities/mesh/manipulation/splitMeshRegions/splitMeshRegions.C

@@ -45,7 +45,7 @@ Description
     so cannot have any cells in any other zone.
     - useCellZonesOnly does not do a walk and uses the cellZones only. Use
     this if you don't mind having disconnected domains in a single region.
-    This option requires all cells to be in one (and one only) region.
+    This option requires all cells to be in one (and one only) cellZone.
 
 \*---------------------------------------------------------------------------*/
 

bin/mpirunDebug

@@ -206,6 +206,21 @@ done
 cmd=""
 if [ .$WM_MPLIB = .OPENMPI ]; then
     cmd="mpirun -app $PWD/mpirun.schema </dev/null"
+elif [ .$WM_MPLIB = .MPICH ]; then
+    cmd="mpiexec"
+    for ((proc=0; proc<$nProcs; proc++))
+    do
+        read procCmd
+
+        procXtermCmdFile="$PWD/processor${proc}Xterm.sh"
+        echo "#!/bin/sh" > $procXtermCmdFile
+        echo "$procCmd" >> $procXtermCmdFile
+        chmod +x $procXtermCmdFile
+        if [ $proc -ne 0 ]; then
+            cmd="${cmd} :"
+        fi
+        cmd="${cmd} -n 1 ${procXtermCmdFile}"
+    done < $PWD/mpirun.schema
 fi
 
 echo "Constructed $PWD/mpirun.schema file."

src/OpenFOAM/containers/Lists/UList/UList.H

@@ -184,6 +184,12 @@ public:
         //  an out-of-range element returns false without any ill-effects
         inline const T& operator[](const label) const;
 
+        //- Return last element of UList.
+        inline T& last();
+
+        //- Return last element of UList.
+        inline const T& last() const;
+
         //- Allow cast to a const List<T>&
         inline operator const Foam::List<T>&() const;
 

src/OpenFOAM/containers/Lists/UList/UListI.H

@@ -114,6 +114,20 @@ inline void Foam::UList<T>::checkIndex(const label i) const
 }
 
 
+template<class T>
+inline T& Foam::UList<T>::last()
+{
+    return this->operator[](this->size()-1);
+}
+
+
+template<class T>
+inline const T& Foam::UList<T>::last() const
+{
+    return this->operator[](this->size()-1);
+}
+
+
 template<class T>
 inline const T* Foam::UList<T>::cdata() const
 {

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

@@ -82,9 +82,6 @@ void Foam::PstreamBuffers::finishedSends(labelListList& sizes, const bool block)
 
     if (commsType_ == UPstream::nonBlocking)
     {
-        labelListList sizes;
-        labelListList send,recv;
-
         Pstream::exchange<DynamicList<char>, char>
         (
             sendBuf_,
@@ -96,20 +93,30 @@ void Foam::PstreamBuffers::finishedSends(labelListList& sizes, const bool block)
     }
     else
     {
-        sizes.setSize(UPstream::nProcs());
-        labelList& nsTransPs = sizes[UPstream::myProcNo()];
-        nsTransPs.setSize(UPstream::nProcs());
-
-        forAll(sendBuf_, procI)
-        {
-            nsTransPs[procI] = sendBuf_[procI].size();
-        }
-
-        // Send sizes across.
-        int oldTag = UPstream::msgType();
-        UPstream::msgType() = tag_;
-        combineReduce(sizes, UPstream::listEq());
-        UPstream::msgType() = oldTag;
+        FatalErrorIn
+        (
+            "PstreamBuffers::finishedSends(labelListList&, const bool)"
+        )   << "Obtaining sizes not supported in "
+            << UPstream::commsTypeNames[commsType_] << endl
+            << " since transfers already in progress. Use non-blocking instead."
+            << exit(FatalError);
+
+        // Note: possible only if using different tag from write started
+        // by ~UOPstream. Needs some work.
+        //sizes.setSize(UPstream::nProcs());
+        //labelList& nsTransPs = sizes[UPstream::myProcNo()];
+        //nsTransPs.setSize(UPstream::nProcs());
+        //
+        //forAll(sendBuf_, procI)
+        //{
+        //    nsTransPs[procI] = sendBuf_[procI].size();
+        //}
+        //
+        //// Send sizes across.
+        //int oldTag = UPstream::msgType();
+        //UPstream::msgType() = tag_;
+        //combineReduce(sizes, UPstream::listEq());
+        //UPstream::msgType() = oldTag;
     }
 }
 

src/OpenFOAM/db/IOstreams/Pstreams/PstreamBuffers.H

@@ -138,7 +138,8 @@ public:
         void finishedSends(const bool block = true);
 
         //- Mark all sends as having been done. Same as above but also returns
-        //  sizes (bytes) transferred.
+        //  sizes (bytes) transferred. Note:currently only valid for
+        //  non-blocking.
         void finishedSends(labelListList& sizes, const bool block = true);
 
 };

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

@@ -50,43 +50,42 @@ void Pstream::exchange
     const bool block
 )
 {
-    if (UPstream::parRun())
+    if (!contiguous<T>())
     {
-        if (!contiguous<T>())
-        {
-            FatalErrorIn
-            (
-                "Pstream::exchange(..)"
-            )   << "Continuous data only." << Foam::abort(FatalError);
-        }
-
-        if (sendBufs.size() != UPstream::nProcs())
-        {
-            FatalErrorIn
-            (
-                "Pstream::exchange(..)"
-            )   << "Size of list:" << sendBufs.size()
-                << " does not equal the number of processors:"
-                << UPstream::nProcs()
-                << Foam::abort(FatalError);
-        }
+        FatalErrorIn
+        (
+            "Pstream::exchange(..)"
+        )   << "Continuous data only." << Foam::abort(FatalError);
+    }
 
-        sizes.setSize(UPstream::nProcs());
-        labelList& nsTransPs = sizes[UPstream::myProcNo()];
-        nsTransPs.setSize(UPstream::nProcs());
+    if (sendBufs.size() != UPstream::nProcs())
+    {
+        FatalErrorIn
+        (
+            "Pstream::exchange(..)"
+        )   << "Size of list:" << sendBufs.size()
+            << " does not equal the number of processors:"
+            << UPstream::nProcs()
+            << Foam::abort(FatalError);
+    }
 
-        forAll(sendBufs, procI)
-        {
-            nsTransPs[procI] = sendBufs[procI].size();
-        }
+    sizes.setSize(UPstream::nProcs());
+    labelList& nsTransPs = sizes[UPstream::myProcNo()];
+    nsTransPs.setSize(UPstream::nProcs());
 
-        // Send sizes across.
-        int oldTag = UPstream::msgType();
-        UPstream::msgType() = tag;
-        combineReduce(sizes, UPstream::listEq());
-        UPstream::msgType() = oldTag;
+    forAll(sendBufs, procI)
+    {
+        nsTransPs[procI] = sendBufs[procI].size();
+    }
 
+    // Send sizes across.
+    int oldTag = UPstream::msgType();
+    UPstream::msgType() = tag;
+    combineReduce(sizes, UPstream::listEq());
+    UPstream::msgType() = oldTag;
 
+    if (Pstream::parRun())
+    {
         // Set up receives
         // ~~~~~~~~~~~~~~~
 

src/OpenFOAM/db/functionObjects/OutputFilterFunctionObject/OutputFilterFunctionObject.C

@@ -37,8 +37,43 @@ void Foam::OutputFilterFunctionObject<OutputFilter>::readDict()
     dict_.readIfPresent("region", regionName_);
     dict_.readIfPresent("dictionary", dictName_);
     dict_.readIfPresent("enabled", enabled_);
+    dict_.readIfPresent("storeFilter", storeFilter_);
 }
 
+template<class OutputFilter>
+void Foam::OutputFilterFunctionObject<OutputFilter>::allocateFilter()
+{
+    if (dictName_.size())
+    {
+        ptr_.reset
+        (
+            new IOOutputFilter<OutputFilter>
+            (
+                name(),
+                time_.lookupObject<objectRegistry>(regionName_),
+                dictName_
+            )
+        );
+    }
+    else
+    {
+        ptr_.reset
+        (
+            new OutputFilter
+            (
+                name(),
+                time_.lookupObject<objectRegistry>(regionName_),
+                dict_
+            )
+        );
+    }
+}
+
+template<class OutputFilter>
+void Foam::OutputFilterFunctionObject<OutputFilter>::destroyFilter()
+{
+    ptr_.reset();
+}
 
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
@@ -56,6 +91,7 @@ Foam::OutputFilterFunctionObject<OutputFilter>::OutputFilterFunctionObject
     regionName_(polyMesh::defaultRegion),
     dictName_(),
     enabled_(true),
+    storeFilter_(true),
     outputControl_(t, dict)
 {
     readDict();
@@ -83,32 +119,9 @@ bool Foam::OutputFilterFunctionObject<OutputFilter>::start()
 {
     readDict();
 
-    if (enabled_)
+    if (enabled_&&storeFilter_)
     {
-        if (dictName_.size())
-        {
-            ptr_.reset
-            (
-                new IOOutputFilter<OutputFilter>
-                (
-                    name(),
-                    time_.lookupObject<objectRegistry>(regionName_),
-                    dictName_
-                )
-            );
-        }
-        else
-        {
-            ptr_.reset
-            (
-                new OutputFilter
-                (
-                    name(),
-                    time_.lookupObject<objectRegistry>(regionName_),
-                    dict_
-                )
-            );
-        }
+        allocateFilter();
     }
 
     return true;
@@ -120,12 +133,22 @@ bool Foam::OutputFilterFunctionObject<OutputFilter>::execute()
 {
     if (enabled_)
     {
+        if (!storeFilter_)
+        {
+            allocateFilter();
+        }
+
         ptr_->execute();
 
         if (enabled_ && outputControl_.output())
         {
             ptr_->write();
         }
+
+        if (!storeFilter_)
+        {
+            destroyFilter();
+        }
     }
 
     return true;
@@ -137,12 +160,22 @@ bool Foam::OutputFilterFunctionObject<OutputFilter>::end()
 {
     if (enabled_)
     {
+        if (!storeFilter_)
+        {
+            allocateFilter();
+        }
+
         ptr_->end();
 
         if (enabled_ && outputControl_.output())
         {
             ptr_->write();
         }
+
+        if (!storeFilter_)
+        {
+            destroyFilter();
+        }
     }
 
     return true;

src/OpenFOAM/db/functionObjects/OutputFilterFunctionObject/OutputFilterFunctionObject.H

@@ -78,6 +78,10 @@ class OutputFilterFunctionObject
         //- Switch for the execution of the functionObject
         bool enabled_;
 
+        //- Switch to store filter in between writes or use on-the-fly
+        //  construction
+        bool storeFilter_;
+
         //- Output controls
         outputFilterOutputControl outputControl_;
 
@@ -89,6 +93,12 @@ class OutputFilterFunctionObject
 
         //- Read relevant dictionary entries
         void readDict();
+ 
+        //- Creates most of the data associated with this object.
+        void allocateFilter();
+
+        //- Destroys most of the data associated with this object.
+        void destroyFilter();
 
         //- Disallow default bitwise copy construct
         OutputFilterFunctionObject(const OutputFilterFunctionObject&);

src/OpenFOAM/meshes/pointMesh/pointBoundaryMesh/pointBoundaryMesh.C

@@ -28,6 +28,9 @@ License
 #include "polyBoundaryMesh.H"
 #include "facePointPatch.H"
 #include "globalPointPatch.H"
+#include "PstreamBuffers.H"
+#include "lduSchedule.H"
+#include "globalMeshData.H"
 
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
@@ -58,14 +61,46 @@ Foam::pointBoundaryMesh::pointBoundaryMesh
 
 void Foam::pointBoundaryMesh::calcGeometry()
 {
-    forAll(*this, patchi)
+    PstreamBuffers pBufs(Pstream::defaultCommsType);
+
+    if
+    (
+        Pstream::defaultCommsType == Pstream::blocking
+     || Pstream::defaultCommsType == Pstream::nonBlocking
+    )
     {
-        operator[](patchi).initGeometry();
-    }
+        forAll(*this, patchi)
+        {
+            operator[](patchi).initGeometry(pBufs);
+        }
 
-    forAll(*this, patchi)
+        pBufs.finishedSends();
+
+        forAll(*this, patchi)
+        {
+            operator[](patchi).calcGeometry(pBufs);
+        }
+    }
+    else if (Pstream::defaultCommsType == Pstream::scheduled)
     {
-        operator[](patchi).calcGeometry();
+        const lduSchedule& patchSchedule = mesh().globalData().patchSchedule();
+
+        // Dummy.
+        pBufs.finishedSends();
+
+        forAll(patchSchedule, patchEvali)
+        {
+            label patchi = patchSchedule[patchEvali].patch;
+
+            if (patchSchedule[patchEvali].init)
+            {
+                operator[](patchi).initGeometry(pBufs);
+            }
+            else
+            {
+                operator[](patchi).calcGeometry(pBufs);
+            }
+        }
     }
 }
 
@@ -97,32 +132,92 @@ Foam::pointBoundaryMesh::globalPatch() const
 
 void Foam::pointBoundaryMesh::movePoints(const pointField& p)
 {
-    pointPatchList& patches = *this;
+    PstreamBuffers pBufs(Pstream::defaultCommsType);
 
-    forAll(patches, patchi)
+    if
+    (
+        Pstream::defaultCommsType == Pstream::blocking
+     || Pstream::defaultCommsType == Pstream::nonBlocking
+    )
     {
-        patches[patchi].initMovePoints(p);
-    }
+        forAll(*this, patchi)
+        {
+            operator[](patchi).initMovePoints(pBufs, p);
+        }
 
-    forAll(patches, patchi)
+        pBufs.finishedSends();
+
+        forAll(*this, patchi)
+        {
+            operator[](patchi).movePoints(pBufs, p);
+        }
+    }
+    else if (Pstream::defaultCommsType == Pstream::scheduled)
     {
-        patches[patchi].movePoints(p);
+        const lduSchedule& patchSchedule = mesh().globalData().patchSchedule();
+
+        // Dummy.
+        pBufs.finishedSends();
+
+        forAll(patchSchedule, patchEvali)
+        {
+            label patchi = patchSchedule[patchEvali].patch;
+
+            if (patchSchedule[patchEvali].init)
+            {
+                operator[](patchi).initMovePoints(pBufs, p);
+            }
+            else
+            {
+                operator[](patchi).movePoints(pBufs, p);
+            }
+        }
     }
 }
 
 
 void Foam::pointBoundaryMesh::updateMesh()
 {
-    pointPatchList& patches = *this;
+    PstreamBuffers pBufs(Pstream::defaultCommsType);
 
-    forAll(patches, patchi)
+    if
+    (
+        Pstream::defaultCommsType == Pstream::blocking
+     || Pstream::defaultCommsType == Pstream::nonBlocking
+    )
     {
-        patches[patchi].initUpdateMesh();
-    }
+        forAll(*this, patchi)
+        {
+            operator[](patchi).initUpdateMesh(pBufs);
+        }
+
+        pBufs.finishedSends();
 
-    forAll(patches, patchi)
+        forAll(*this, patchi)
+        {
+            operator[](patchi).updateMesh(pBufs);
+        }
+    }
+    else if (Pstream::defaultCommsType == Pstream::scheduled)
     {
-        patches[patchi].updateMesh();
+        const lduSchedule& patchSchedule = mesh().globalData().patchSchedule();
+
+        // Dummy.
+        pBufs.finishedSends();
+
+        forAll(patchSchedule, patchEvali)
+        {
+            label patchi = patchSchedule[patchEvali].patch;
+
+            if (patchSchedule[patchEvali].init)
+            {
+                operator[](patchi).initUpdateMesh(pBufs);
+            }
+            else
+            {
+                operator[](patchi).updateMesh(pBufs);
+            }
+        }
     }
 }
 

src/OpenFOAM/meshes/pointMesh/pointPatches/basic/coupled/coupledPointPatch.H

@@ -66,22 +66,22 @@ protected:
     // Protected Member Functions
 
         //- Initialise the calculation of the patch geometry
-        virtual void initGeometry() = 0;
+        virtual void initGeometry(PstreamBuffers&) = 0;
 
         //- Calculate the patch geometry
-        virtual void calcGeometry() = 0;
+        virtual void calcGeometry(PstreamBuffers&) = 0;
 
         //- Initialise the patches for moving points
-        virtual void initMovePoints(const pointField&) = 0;
+        virtual void initMovePoints(PstreamBuffers&, const pointField&) = 0;
 
         //- Correct patches after moving points
-        virtual void movePoints(const pointField&) = 0;
+        virtual void movePoints(PstreamBuffers&, const pointField&) = 0;
 
         //- Initialise the update of the patch topology
-        virtual void initUpdateMesh() = 0;
+        virtual void initUpdateMesh(PstreamBuffers&) = 0;
 
         //- Update of the patch topology
-        virtual void updateMesh() = 0;
+        virtual void updateMesh(PstreamBuffers&) = 0;
 
 
 public:

src/OpenFOAM/meshes/pointMesh/pointPatches/constraint/cyclic/cyclicPointPatch.C

@@ -50,13 +50,13 @@ addToRunTimeSelectionTable
 
 // * * * * * * * * * * * * * Protected Member Functions  * * * * * * * * * * //
 
-void Foam::cyclicPointPatch::initGeometry()
+void Foam::cyclicPointPatch::initGeometry(PstreamBuffers&)
 {
     transformPairs_.setSize(0);
 }
 
 
-void Foam::cyclicPointPatch::calcGeometry()
+void Foam::cyclicPointPatch::calcGeometry(PstreamBuffers&)
 {
     const edgeList& cp = cyclicPolyPatch_.coupledPoints();
     const labelList& mp = cyclicPolyPatch_.meshPoints();
@@ -128,16 +128,20 @@ void Foam::cyclicPointPatch::calcGeometry()
             }
             else if (pointMap[cp[i][0]] == -1 && pointMap[cp[i][1]] != -1)
             {
-                FatalErrorIn("cyclicPointPatch::calcGeometry() const")
-                    << "Point " << cp[i][0] << "of point-pair " << i
+                FatalErrorIn
+                (
+                    "cyclicPointPatch::calcGeometry(PstreamBuffers&) const"
+                )   << "Point " << cp[i][0] << "of point-pair " << i
                     << " is a global point but the other point "
                     << cp[i][1] << " is not"
                     << exit(FatalError);
             }
             else if (pointMap[cp[i][0]] != -1 && pointMap[cp[i][1]] == -1)
             {