Merge commit 'bundle/home' into olesenm

applications/test/DynamicList/DynamicListTest.C

@@ -43,9 +43,14 @@ int main(int argc, char *argv[])
     ldl[0](3) = 3;
     ldl[0](1) = 1;
 
-    ldl[0].setSize(5);     // increase allocated size
-    ldl[1].setSize(10);    // increase allocated size
-    ldl[1](2) = 2;
+    ldl[0].allocSize(5);   // increase allocated size
+    ldl[1].allocSize(10);  // increase allocated size
+    ldl[0].reserve(15);    // should increase allocated size
+    ldl[1].reserve(5);     // should not decrease allocated size
+    ldl[1](3) = 2;         // allocates space and sets value
+
+    // this works without a segfault, but doesn't change the list size
+    ldl[0][4] = 4;
 
     ldl[1] = 3;
 
@@ -78,7 +83,7 @@ int main(int argc, char *argv[])
     {
         dlA.append(i);
     }
-    dlA.setSize(10);
+    dlA.allocSize(10);
 
     Info<< "<dlA>" << dlA << "</dlA>" << nl << "sizes: "
         << " " << dlA.size() << "/" << dlA.allocSize() << endl;
@@ -95,6 +100,14 @@ int main(int argc, char *argv[])
     Info<< "<dlB>" << dlB << "</dlB>" << nl << "sizes: "
         << " " << dlB.size() << "/" << dlB.allocSize() << endl;
 
+    // try with a normal list:
+    List<label> lstA;
+    lstA.transfer(dlB);
+    Info<< "Transferred to normal list" << endl;
+    Info<< "<lstA>" << lstA << "</lstA>" << nl << "sizes: "
+        << " " << lstA.size() << endl;
+    Info<< "<dlB>" << dlB << "</dlB>" << nl << "sizes: "
+        << " " << dlB.size() << "/" << dlB.allocSize() << endl;
 
     return 0;
 }

applications/test/sort/sortListTest.C

@@ -70,6 +70,13 @@ int main(int argc, char *argv[])
     Info << "sorted:   " << b << endl;
     Info << "indices:  " << b.indices() << endl;
 
+    labelList flatten;
+    flatten.transfer(b);
+    
+    Info << "flatten:  " << flatten << endl;
+    Info << "sorted:   " << b << endl;
+    Info << "indices:  " << b.indices() << endl;
+
     Info << "End\n" << endl;
 
     return 0;

applications/utilities/mesh/manipulation/checkMesh/checkTopology.C

@@ -109,7 +109,7 @@ Foam::label Foam::checkTopology
         {
             Info<< "    Number of regions: " << rs.nRegions() << " (OK)."
                 << endl;
-        
+
         }
         else
         {
@@ -214,7 +214,7 @@ Foam::label Foam::checkTopology
                 const pointField& pts = pp.points();
                 const labelList& mp = pp.meshPoints();
 
-                boundBox bb(vector::zero, vector::zero);
+                boundBox bb;   // zero-sized
                 if (returnReduce(mp.size(), sumOp<label>()) > 0)
                 {
                     bb.min() = pts[mp[0]];

applications/utilities/parallelProcessing/reconstructParMesh/reconstructParMesh.C

@@ -273,7 +273,7 @@ autoPtr<mapPolyMesh> mergeSharedPoints
         }
     }
 
-    return map;    
+    return map;
 }
 
 
@@ -418,11 +418,7 @@ int main(int argc, char *argv[])
     // Read point on individual processors to determine merge tolerance
     // (otherwise single cell domains might give problems)
 
-    boundBox bb
-    (
-        point(GREAT, GREAT, GREAT),
-        point(-GREAT, -GREAT, -GREAT)
-    );
+    boundBox bb = boundBox::invertedBox;
 
     for (label procI = 0; procI < nProcs; procI++)
     {

applications/utilities/surface/surfaceCoordinateSystemTransform/surfaceCoordinateSystemTransform.C

@@ -199,7 +199,6 @@ int main(int argc, char *argv[])
         if (args.options().found("clean"))
         {
             surf.cleanup(true);
-            surf.checkOrientation(true);
         }
 
         if (fromCsys.valid())

applications/utilities/surface/surfaceMeshConvert/surfaceMeshConvert.C

@@ -104,13 +104,19 @@ int main(int argc, char *argv[])
     {
         triSurface surf(importName);
 
+        Info<< "Read surface:" << endl;
+        surf.writeStats(Info);
+        Info<< endl;
+
         if (args.options().found("clean"))
         {
+            Info<< "Cleaning up surface" << endl;
             surf.cleanup(true);
-            surf.checkOrientation(true);
+            surf.writeStats(Info);
+            Info<< endl;
         }
 
-        Info << "writing " << exportName;
+        Info<< "writing " << exportName;
         if (scaleFactor <= 0)
         {
             Info<< " without scaling" << endl;
@@ -119,6 +125,8 @@ int main(int argc, char *argv[])
         {
             Info<< " with scaling " << scaleFactor << endl;
             surf.scalePoints(scaleFactor);
+            surf.writeStats(Info);
+            Info<< endl;
         }
 
         // write sorted by region
@@ -128,13 +136,19 @@ int main(int argc, char *argv[])
     {
         UnsortedMeshedSurface<face> surf(importName);
 
+        Info<< "Read surface:" << endl;
+        surf.writeStats(Info);
+        Info<< endl;
+
         if (args.options().found("clean"))
         {
+            Info<< "Cleaning up surface" << endl;
             surf.cleanup(true);
-            surf.checkOrientation(true);
+            surf.writeStats(Info);
+            Info<< endl;
         }
 
-        Info << "writing " << exportName;
+        Info<< "writing " << exportName;
         if (scaleFactor <= 0)
         {
             Info<< " without scaling" << endl;
@@ -143,8 +157,9 @@ int main(int argc, char *argv[])
         {
             Info<< " with scaling " << scaleFactor << endl;
             surf.scalePoints(scaleFactor);
+            surf.writeStats(Info);
+            Info<< endl;
         }
-
         surf.write(exportName);
     }
 #if 1
@@ -152,10 +167,16 @@ int main(int argc, char *argv[])
     {
         MeshedSurface<triFace> surf(importName);
 
+        Info<< "Read surface:" << endl;
+        surf.writeStats(Info);
+        Info<< endl;
+
         if (args.options().found("clean"))
         {
+            Info<< "Cleaning up surface" << endl;
             surf.cleanup(true);
-            surf.checkOrientation(true);
+            surf.writeStats(Info);
+            Info<< endl;
         }
 
         Info<< "writing " << exportName;
@@ -167,6 +188,8 @@ int main(int argc, char *argv[])
         {
             Info<< " with scaling " << scaleFactor << endl;
             surf.scalePoints(scaleFactor);
+            surf.writeStats(Info);
+            Info<< endl;
         }
         surf.write(exportName);
     }
@@ -175,10 +198,16 @@ int main(int argc, char *argv[])
     {
         MeshedSurface<face> surf(importName);
 
+        Info<< "Read surface:" << endl;
+        surf.writeStats(Info);
+        Info<< endl;
+
         if (args.options().found("clean"))
         {
+            Info<< "Cleaning up surface" << endl;
             surf.cleanup(true);
-            surf.checkOrientation(true);
+            surf.writeStats(Info);
+            Info<< endl;
         }
 
         Info<< "writing " << exportName;
@@ -190,6 +219,8 @@ int main(int argc, char *argv[])
         {
             Info<< " with scaling " << scaleFactor << endl;
             surf.scalePoints(scaleFactor);
+            surf.writeStats(Info);
+            Info<< endl;
         }
         surf.write(exportName);
     }

src/OpenFOAM/containers/Lists/DynamicList/DynamicList.H

@@ -118,18 +118,30 @@ public:
         //- Size of the underlying storage.
         inline label allocSize() const;
 
-
         // Edit
 
-        //- Alter the list size.
-        //  When the new size is greater than the addressed list size, the
+        //- Alter the size of the underlying storage.
+        //  The addressed size will be truncated if needed to fit, but will
+        //  otherwise remain untouched.
+        inline void allocSize(const label);
+
+        // CURRENT BEHAVIOUR
+        //- When the new size is greater than the addressed list size, the
         //  allocated list sizes is adjusted and the
         //  addressed size does not change.
         //  Otherwise the addressed list size is just reduced and the
         //  allocated size does not change.
+        //
+        // PROPOSED BEHAVIOUR
+        //- Alter the addressed list size.
+        //  New space will be allocated if required.
         inline void setSize(const label);
 
-        //- Clear the list, i.e. set the size to zero.
+        //- Reserve allocation space for at least this size.
+        //  Never shrinks the allocated size, use allocSize() for that.
+        inline void reserve(const label);
+
+        //- Clear the addressed list, i.e. set the size to zero.
         //  Allocated size does not change
         inline void clear();
 

src/OpenFOAM/containers/Lists/DynamicList/DynamicListI.H

@@ -70,12 +70,61 @@ const
 }
 
 
+template<class T, unsigned SizeInc, unsigned SizeMult, unsigned SizeDiv>
+inline void Foam::DynamicList<T, SizeInc, SizeMult, SizeDiv>::allocSize
+(
+    const label s
+)
+{
+    label nextFree = List<T>::size();
+    allocSize_ = s;
+
+    // truncate addressed size too?
+    if (nextFree > allocSize_)
+    {
+        nextFree = allocSize_;
+    }
+
+    // adjust allocated size, and addressed size if necessary
+    List<T>::setSize(allocSize_);
+    List<T>::size(nextFree);
+}
+
+
+template<class T, unsigned SizeInc, unsigned SizeMult, unsigned SizeDiv>
+inline void Foam::DynamicList<T, SizeInc, SizeMult, SizeDiv>::reserve
+(
+    const label s
+)
+{
+    if (s > allocSize_)
+    {
+        allocSize_ = max
+        (
+            s,
+            label(SizeMult*allocSize_/SizeDiv + SizeInc)
+        );
+
+        // adjust allocated size, leave addressed size untouched
+        label nextFree = List<T>::size();
+        List<T>::setSize(allocSize_);
+        List<T>::size(nextFree);
+    }
+}
+
+
 template<class T, unsigned SizeInc, unsigned SizeMult, unsigned SizeDiv>
 inline void Foam::DynamicList<T, SizeInc, SizeMult, SizeDiv>::setSize
 (
     const label s
 )
 {
+#if 1
+    // CURRENT BEHAVIOUR:
+    // slightly ambiguous about what size the list will actually get
+    // cannot increase the size of the addressed list (for compatibility
+    // with List), without automatically adjusting the allocated space!
+
     label nextFree = List<T>::size();
     if (s <= nextFree)
     {
@@ -89,6 +138,22 @@ inline void Foam::DynamicList<T, SizeInc, SizeMult, SizeDiv>::setSize
         List<T>::setSize(allocSize_);
     }
     List<T>::size(nextFree);
+#else
+    // allocate more space?
+    if (s > allocSize_)
+    {
+        allocSize_ = max
+        (
+            s,
+            label(SizeMult*allocSize_/SizeDiv + SizeInc)
+        );
+
+        List<T>::setSize(allocSize_);
+    }
+
+    // adjust addressed size
+    List<T>::size(s);
+#endif
 }
 
 
@@ -153,21 +218,10 @@ inline void Foam::DynamicList<T, SizeInc, SizeMult, SizeDiv>::append(const T& e)
     // Work on copy free index since gets overwritten by setSize
     label nextFree = List<T>::size();
 
-    nextFree++;
+    reserve(nextFree+1);
+    List<T>::size(nextFree+1);
 
-    if (nextFree > allocSize_)
-    {
-        allocSize_ = max
-        (
-            nextFree,
-            label(SizeMult*allocSize_/SizeDiv + SizeInc)
-        );
-        List<T>::setSize(allocSize_);
-    }
-
-    List<T>::size(nextFree);
-
-    this->operator[](nextFree - 1) = e;
+    this->operator[](nextFree) = e;
 }
 
 
@@ -201,19 +255,9 @@ inline T& Foam::DynamicList<T, SizeInc, SizeMult, SizeDiv>::operator()
 )
 {
     label nextFree = List<T>::size();
-
     nextFree = max(nextFree, i + 1);
 
-    if (nextFree > allocSize_)
-    {
-        allocSize_ = max
-        (
-            nextFree,
-            label(SizeMult*allocSize_/SizeDiv + SizeInc)
-        );
-        List<T>::setSize(allocSize_);
-    }
-
+    reserve(nextFree);
     List<T>::size(nextFree);
 
     return this->operator[](i);

src/OpenFOAM/containers/Lists/List/List.C

@@ -432,14 +432,20 @@ void Foam::List<T>::transfer(DynamicList<T, SizeInc, SizeMult, SizeDiv>& a)
 {
     // shrink the allocated space to the number of elements used
     a.shrink();
+    a.allocSize_ = 0;
 
-    if (this->v_) delete[] this->v_;
-    this->size_ = a.size_;
-    this->v_ = a.v_;
+    transfer(static_cast<List<T>&>(a));
+}
 
-    a.size_ = 0;
-    a.v_ = 0;
-    a.allocSize_ = 0;
+
+// Transfer the contents of the argument SortableList into this List
+// and anull the argument list
+template<class T>
+void Foam::List<T>::transfer(SortableList<T>& a)
+{
+    // shrink away the sort indices
+    a.shrink();
+    transfer(static_cast<List<T>&>(a));
 }
 
 

src/OpenFOAM/containers/Lists/List/List.H

@@ -63,7 +63,8 @@ template<class T, label Size> class FixedList;
 template<class T> class PtrList;
 template<class T> class SLList;
 template<class T, unsigned SizeInc, unsigned SizeMult, unsigned SizeDiv>
- class DynamicList;
+    class DynamicList;
+template<class T> class SortableList;
 template<class T> class IndirectList;
 template<class T> class BiIndirectList;
 
@@ -173,6 +174,10 @@ public:
             template<unsigned SizeInc, unsigned SizeMult, unsigned SizeDiv>
             void transfer(DynamicList<T, SizeInc, SizeMult, SizeDiv>&);
 
+            //- Transfer the contents of the argument List into this List
+            //  and annull the argument list.
+            void transfer(SortableList<T>&);
+
             //- Return subscript-checked element of UList.
             inline T& newElmt(const label);
 

src/OpenFOAM/meshes/boundBox/boundBox.C

@@ -27,18 +27,34 @@ License
 #include "boundBox.H"
 #include "PstreamReduceOps.H"
 
+// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
+
+const Foam::boundBox Foam::boundBox::greatBox
+(
+    point(-VGREAT, -VGREAT, -VGREAT),
+    point(VGREAT, VGREAT, VGREAT)
+);
+
+
+const Foam::boundBox Foam::boundBox::invertedBox
+(
+    point(VGREAT, VGREAT, VGREAT),
+    point(-VGREAT, -VGREAT, -VGREAT)
+);
+
+
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
 Foam::boundBox::boundBox(const pointField& points, const bool doReduce)
 :
-    min_(vector::zero),
-    max_(vector::zero)
+    min_(point::zero),
+    max_(point::zero)
 {
     if (points.size() == 0)
     {
         if (Pstream::parRun() && doReduce)
         {
-            // Use values which get overwritten by reduce minOp,maxOp below
+            // Use values that get overwritten by reduce minOp, maxOp below
             min_ = point(VGREAT, VGREAT, VGREAT);
             max_ = point(-VGREAT, -VGREAT, -VGREAT);
         }
@@ -89,7 +105,6 @@ Foam::Ostream& Foam::operator<<(Ostream& os, const boundBox& bb)
 
     // Check state of Ostream
     os.check("Ostream& operator<<(Ostream&, const boundBox&)");
-
     return os;
 }
 
@@ -111,7 +126,6 @@ Foam::Istream& Foam::operator>>(Istream& is, boundBox& bb)
 
     // Check state of Istream
     is.check("Istream& operator>>(Istream&, boundBox&)");
-
     return is;
 }
 

src/OpenFOAM/meshes/boundBox/boundBox.H

@@ -48,7 +48,7 @@ Ostream& operator<<(Ostream& os, const boundBox& b);
 
 
 /*---------------------------------------------------------------------------*\
-                           Class boundBox Declaration
+                         Class boundBox Declaration
 \*---------------------------------------------------------------------------*/
 
 class boundBox
@@ -61,13 +61,22 @@ class boundBox
 
 public:
 
+    // Static data members
+
+        //- A very large boundBox: min/max == -/+ VGREAT
+        static const boundBox greatBox;
+
+        //- A very large inverted boundBox: min/max == +/- VGREAT
+        static const boundBox invertedBox;
+
+
     // Constructors
 
-        //- Construct null setting points to zero
+        //- Construct null, setting points to zero
         boundBox()
         :
-            min_(vector::zero),
-            max_(vector::zero)
+            min_(point::zero),
+            max_(point::zero)
         {}
 
         //- Construct from components
@@ -77,8 +86,8 @@ public:
             max_(max)
         {}
 
-        //- Construct as the bounding box of the given pointField. Does
-        //  parallel communication (doReduce = true)
+        //- Construct as the bounding box of the given pointField.
+        //  Does parallel communication (doReduce = true)
         boundBox(const pointField& points, const bool doReduce = true);
 
         //- Construct from Istream
@@ -117,39 +126,26 @@ public:
 
         // Query
 
-            //- Intersects other boundingbox?
+            //- Intersects other boundingBox?
             bool overlaps(const boundBox& bb) const
             {
-                if
+                return
                 (
-                    (min_.x() <= bb.max().x()) &&
-                    (min_.y() <= bb.max().y()) &&
-                    (min_.z() <= bb.max().z()) &&
-
-                    (max_.x() >= bb.min().x()) &&
-                    (max_.y() >= bb.min().y()) &&
-                    (max_.z() >= bb.min().z())
-                )
-                {
-                    return true;
-                }
-                else
-                {
-                    return false;
-                }
+                    min_.x() <= bb.max().x() && max_.x() >= bb.min().x()
+                 && min_.y() <= bb.max().y() && max_.y() >= bb.min().y()
+                 && min_.z() <= bb.max().z() && max_.z() >= bb.min().z()
+                );
             }
 
-
             //- Contains a point?
             bool contains(const point& pt) const
             {
                 return
-                    pt.x() >= min().x()
-                 && pt.y() >= min().y()
-                 && pt.z() >= min().z()
-                 && pt.x() <= max().x()
-                 && pt.y() <= max().y()
-                 && pt.z() <= max().z();
+                (
+                    pt.x() >= min().x() && pt.x() <= max().x()
+                 && pt.y() >= min().y() && pt.y() <= max().y()
+                 && pt.z() >= min().z() && pt.z() <= max().z()
+                );
             }
 
 
@@ -173,7 +169,7 @@ public:
 };
 
 
-//- Specify data associated with boundBox type is contiguous
+//- Specify data associated with boundBox type are contiguous
 template<>
 inline bool contiguous<boundBox>() {return contiguous<point>();}
 

src/OpenFOAM/meshes/meshShapes/face/face.C

@@ -119,7 +119,7 @@ Foam::label Foam::face::mostConcaveAngle
 }
 
 
-void Foam::face::split
+Foam::label Foam::face::split
 (
     const face::splitMode mode,
     const pointField& points,
@@ -129,6 +129,8 @@ void Foam::face::split