Merge branch 'develop' into 'master'

Final content for 1806 release

Closes #4

See merge request !4

Allwclean

 #!/bin/sh
-# Compile mesh library
-wclean libso meshLibrary
+cd ${0%/*} || exit 1                        # Run from this directory
 
-# Compile executables
-wclean all executables
+#------------------------------------------------------------------------------
 
-# Compile utilities
+wclean libso meshLibrary
+wclean all executables
 wclean all utilities
+
+#------------------------------------------------------------------------------

Allwmake

 #!/bin/sh
+cd ${0%/*} || exit 1                        # Run from this directory
 
 # Parse arguments for library compilation
 if [ -f $WM_PROJECT_DIR/wmake/scripts/AllwmakeParseArguments ]
@@ -13,13 +14,8 @@ echo "  $WM_COMPILER $WM_COMPILER_TYPE compiler"
 echo "  ${WM_OPTIONS}, with ${WM_MPLIB} ${FOAM_MPI}"
 echo
 
-# Compile mesh library
 wmake libso meshLibrary
-
-# Compile executables
 wmake all executables
-
-# Compile utilities
 wmake all utilities
 
 # Some summary information

executables/cartesianMesh/cartesianMesh.C

@@ -36,8 +36,6 @@ using namespace Foam;
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-// Main program:
-
 int main(int argc, char *argv[])
 {
     #include "setRootCase.H"
@@ -45,11 +43,10 @@ int main(int argc, char *argv[])
 
     Module::cartesianMeshGenerator cmg(runTime);
 
-    Info<< "ExecutionTime = " << runTime.elapsedCpuTime() << " s\n"
-        << "ClockTime = " << runTime.elapsedClockTime() << " s" << endl;
-
     cmg.writeMesh();
 
+    runTime.printExecutionTime(Info);
+
     Info<< "End\n" << endl;
     return 0;
 }

executables/pMesh/pMesh.C

@@ -46,11 +46,10 @@ int main(int argc, char *argv[])
 
     Module::voronoiMeshGenerator pmg(runTime);
 
-    Info<< "ExecutionTime = " << runTime.elapsedCpuTime() << " s\n"
-        << "ClockTime = " << runTime.elapsedClockTime() << endl;
-
     pmg.writeMesh();
 
+    runTime.printExecutionTime(Info);
+
     Info<< "End\n" << endl;
     return 0;
 }

executables/tetMesh/tetMesh.C

@@ -36,23 +36,20 @@ using namespace Foam;
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-// Main program:
-
 int main(int argc, char *argv[])
 {
     #include "setRootCase.H"
     #include "createTime.H"
 
-    // tetrahedral mesher cannot be run in parallel yet
+    // Tetrahedral mesher cannot be run in parallel yet
     argList::noParallel();
 
     Module::tetMeshGenerator tmg(runTime);
 
-    Info<< "ExecutionTime = " << runTime.elapsedCpuTime() << " s\n"
-        << "ClockTime = " << runTime.elapsedClockTime() << endl;
-
     tmg.writeMesh();
 
+    runTime.printExecutionTime(Info);
+
     Info<< "End\n" << endl;
     return 0;
 }

meshLibrary/utilities/boundaryLayers/boundaryLayers/boundaryLayersCreateVertices.C

@@ -210,7 +210,7 @@ Foam::point Foam::Module::boundaryLayers::createNewVertex
                 bool found(true);
                 forAll(otherPatches, opI)
                 {
-                    if (!pPatches.contains(bpJ, otherPatches[opI]))
+                    if (!pPatches.found(bpJ, otherPatches[opI]))
                     {
                         found = false;
                         break;
@@ -940,7 +940,7 @@ void Foam::Module::boundaryLayers::createNewEdgeVerticesParallel
                 bool found(true);
                 forAll(otherPatches, opI)
                 {
-                    if (!pPatches.contains(bpJ, otherPatches[opI]))
+                    if (!pPatches.found(bpJ, otherPatches[opI]))
                     {
                         found = false;
                         break;

meshLibrary/utilities/boundaryLayers/extrudeLayer/extrudeLayerI.H

@@ -122,7 +122,7 @@ Foam::Module::extrudeLayer::addressingCalculator::faceSharingEdge
             continue;
         }
 
-        if (pointExtruded_.contains(nextI, currFaceI))
+        if (pointExtruded_.found(nextI, currFaceI))
         {
             if (otherFace != -1)
             {
@@ -152,7 +152,7 @@ inline void Foam::Module::extrudeLayer::addressingCalculator::facesSharingEdge
     {
         const label currFaceI = pointExtruded_(start, pfI);
 
-        if (pointExtruded_.contains(end, currFaceI))
+        if (pointExtruded_.found(end, currFaceI))
         {
             edgeFaces.append(currFaceI);
         }

meshLibrary/utilities/boundaryLayers/refineBoundaryLayers/refineBoundaryLayersFaces.C

@@ -487,7 +487,7 @@ void Foam::Module::refineBoundaryLayers::sortFacePoints
         {
             const label nfI = facesFromFace_(faceI, i);
 
-            if ((numSplitsI == 1) && newFaces_.contains(nfI, f.nextLabel(pos)))
+            if ((numSplitsI == 1) && newFaces_.found(nfI, f.nextLabel(pos)))
             {
                 numSplitsI = i + 1;
                 break;
@@ -584,7 +584,7 @@ void Foam::Module::refineBoundaryLayers::sortFacePoints
         {
             const label nfI = facesFromFace_(faceI, j);
 
-            if ((numSplitsJ == 1) && newFaces_.contains(nfI, f.prevLabel(pos)))
+            if ((numSplitsJ == 1) && newFaces_.found(nfI, f.prevLabel(pos)))
             {
                 numSplitsJ = j + 1;
                 break;
@@ -735,7 +735,7 @@ void Foam::Module::refineBoundaryLayers::sortFaceFaces
         {
             const label nfI = facesFromFace_(faceI, i);
 
-            if ((numSplitsI == 1) && newFaces_.contains(nfI, f.nextLabel(pos)))
+            if ((numSplitsI == 1) && newFaces_.found(nfI, f.nextLabel(pos)))
             {
                 numSplitsI = i + 1;
                 break;
@@ -789,7 +789,7 @@ void Foam::Module::refineBoundaryLayers::sortFaceFaces
         {
             const label nfI = facesFromFace_(faceI, j);
 
-            if ((numSplitsJ == 1) && newFaces_.contains(nfI, f.prevLabel(pos)))
+            if ((numSplitsJ == 1) && newFaces_.found(nfI, f.prevLabel(pos)))
             {
                 numSplitsJ = j + 1;
                 break;

meshLibrary/utilities/containers/DynList/DynList.C

@@ -2,9 +2,12 @@
   =========                 |
   \\      /  F ield         | cfMesh: A library for mesh generation
    \\    /   O peration     |
-    \\  /    A nd           | Author: Franjo Juretic (franjo.juretic@c-fields.com)
-     \\/     M anipulation  | Copyright (C) Creative Fields, Ltd.
+    \\  /    A nd           | Copyright (C) 2014-2017 Creative Fields, Ltd.
+     \\/     M anipulation  | Copyright (C) 2018 OpenCFD Ltd.
 -------------------------------------------------------------------------------
+Author
+     Franjo Juretic (franjo.juretic@c-fields.com)
+
 License
     This file is part of OpenFOAM.
 
@@ -27,45 +30,53 @@ License
 
 // * * * * * * * * * * * * * * * IOstream Operators  * * * * * * * * * * * * //
 
-template<class T, Foam::label staticSize>
-Foam::Module::DynList<T, staticSize>::DynList(Istream&)
+template<class T, int SizeMin>
+Foam::Module::DynList<T, SizeMin>::DynList(Istream& is)
 :
-    dataPtr_(nullptr),
-    nAllocated_(0),
-    staticData_(),
-    nextFree_(0)
+    UList<T>(),
+    shortList_(),
+    heapList_(),
+    capacity_(0)
 {
-    NotImplemented;
+    is >> *this;
 }
 
 
-template<class T, Foam::label staticSize>
+template<class T, int SizeMin>
 Foam::Ostream& Foam::Module::operator<<
 (
-    Foam::Ostream& os,
-    const Foam::Module::DynList<T, staticSize>& DL
+    Ostream& os,
+    const Foam::Module::DynList<T, SizeMin>& list
 )
 {
-    UList<T> helper(DL.dataPtr_, DL.nextFree_);
-    os << helper;
-
+    os << static_cast<const UList<T>&>(list);
     return os;
 }
 
 
-template<class T, Foam::label staticSize>
+template<class T, int SizeMin>
 Foam::Istream& Foam::Module::operator>>
 (
-    Foam::Istream& is,
-    Foam::Module::DynList<T, staticSize>& DL
+    Istream& is,
+    Foam::Module::DynList<T, SizeMin>& list
 )
 {
-    NotImplemented;
+    list.clearStorage();
+
+    List<T> input(is);
+
+    const label newLen = input.size();
+
+    if (newLen <= SizeMin)
+    {
+        list.shortList_ = input;
+    }
+    else
+    {
+        list.heapList_.transfer(input);
+    }
 
-    UList<T> helper(DL.dataPtr_, DL.nextFree_);
-    //is >> static_cast<List<T>&>(DL);
-    is >> helper;
-    DL.nextFree_ = helper.size();
+    list.setSize(newLen);
 
     return is;
 }

meshLibrary/utilities/containers/FRWGraph/FRWGraph.H

@@ -140,7 +140,6 @@ public:
         inline void setRow(const label rowI, const FixedList<T, width>& l);
 
         //- check if the element is in the given row (takes linear time)
-        inline bool contains(const label rowI, const T& e) const;
         inline bool found(const label rowI, const T& e) const;
         inline label find(const label rowI, const T& e) const;
 

meshLibrary/utilities/containers/FRWGraph/FRWGraphI.H

@@ -155,17 +155,6 @@ inline void Foam::Module::FRWGraph<T, width>::setRow
 }
 
 
-template<class T, Foam::label width>
-inline bool Foam::Module::FRWGraph<T, width>::contains
-(
-    const label rowI,
-    const T& e
-) const
-{
-    return (this->find(rowI, e) >= 0);
-}
-
-
 template<class T, Foam::label width>
 inline bool Foam::Module::FRWGraph<T, width>::found
 (

meshLibrary/utilities/containers/LongList/LongList.H

@@ -178,7 +178,6 @@ public:
         inline void appendIfNotIn(const T& e);
 
         //- check if the element is in the list (takes linear time)
-        inline bool contains(const T& e) const;
         inline bool found(const T& e) const;
         inline label find(const T& e) const;
 

meshLibrary/utilities/containers/LongList/LongListI.H

@@ -296,13 +296,6 @@ inline void Foam::Module::LongList<T, Offset>::appendIfNotIn(const T& e)
 }
 
 
-template<class T, int Offset>
-inline bool Foam::Module::LongList<T, Offset>::contains(const T& e) const
-{
-    return (this->find(e) >= 0);
-}
-
-
 template<class T, int Offset>
 inline bool Foam::Module::LongList<T, Offset>::found(const T& e) const
 {

meshLibrary/utilities/containers/VRWGraph/VRWGraph.H

@@ -261,7 +261,6 @@ public:
         void optimizeMemoryUsage();
 
         //- check if the element is in the given row (takes linear time)
-        inline bool contains(const label rowI, const label e) const;
         inline bool found(const label rowI, const label e) const;
         inline label find(const label rowI, const label e) const;
 

meshLibrary/utilities/containers/VRWGraph/VRWGraphI.H

@@ -574,16 +574,6 @@ inline void Foam::Module::VRWGraph::reverseAddressing
 }
 
 
-inline bool Foam::Module::VRWGraph::contains
-(
-    const label rowI,
-    const label e
-) const
-{
-    return (this->find(rowI, e) >= 0);
-}
-
-
 inline bool Foam::Module::VRWGraph::found
 (
     const label rowI,

meshLibrary/utilities/containers/graphRow/graphConstRow.H

@@ -101,7 +101,6 @@ public:
     // Member Operators
 
         //- check if the element is in the given row (takes linear time)
-        inline bool contains(const label e) const;
         inline bool found(const label e) const;
         inline label find(const label e) const;
 

meshLibrary/utilities/containers/graphRow/graphConstRowI.H

@@ -70,16 +70,6 @@ inline Foam::label Foam::Module::graphConstRow<graphType>::size() const
 }
 
 
-template<class graphType>
-inline bool Foam::Module::graphConstRow<graphType>::contains
-(
-    const label e
-) const
-{
-    return data_.contains(rowI_, e);
-}
-
-
 template<class graphType>
 inline bool Foam::Module::graphConstRow<graphType>::found(const label e) const
 {

meshLibrary/utilities/containers/graphRow/graphRow.H

@@ -105,7 +105,6 @@ public:
         inline void appendIfNotIn(const label);
 
         //- check if the element is in the given row (takes linear time)
-        inline bool contains(const label e) const;
         inline bool found(const label e) const;
         inline label find(const label e) const;
 

meshLibrary/utilities/containers/graphRow/graphRowI.H

@@ -83,13 +83,6 @@ inline void Foam::Module::graphRow<graphType>::appendIfNotIn(const label el)
 }
 
 
-template<class graphType>
-inline bool Foam::Module::graphRow<graphType>::contains(const label e) const
-{
-    return data_.contains(rowI_, e);
-}
-
-
 template<class graphType>
 inline bool Foam::Module::graphRow<graphType>::found(const label e) const
 {

meshLibrary/utilities/containers/subGraph/subGraph.H

@@ -112,7 +112,6 @@ public:
         inline void appendIfNotIn(const label rowI, const label);
 
         //- check if the element is in the given row (takes linear time)
-        inline bool contains(const label rowI, const label e) const;
         inline bool found(const label rowI, const label e) const;
         inline label find(const label rowI, const label e) const;
 

meshLibrary/utilities/containers/subGraph/subGraphI.H

@@ -105,17 +105,6 @@ inline void Foam::Module::subGraph<graphType>::appendIfNotIn
 }
 
 
-template<class graphType>
-inline bool Foam::Module::subGraph<graphType>::contains
-(
-    const label rowI,
-    const label e
-) const
-{
-    return data_.contains(start_ + rowI, e);
-}
-
-
 template<class graphType>
 inline bool Foam::Module::subGraph<graphType>::found
 (

meshLibrary/utilities/decomposeCells/decomposeCellsPyramids.C

@@ -248,7 +248,7 @@ void Foam::Module::decomposeCells::decomposeCellIntoPyramids(const label cellI)
             {
                 const edge e(f[eI], f[(eI + 1)%f.size()]);
 
-                const label pos = cEdges.contains(e);
+                const label pos = cEdges.find(e);
 
                 if (pos < 0)
                 {

meshLibrary/utilities/meshes/polyMeshGen/polyMeshGenCellsI.H

@@ -75,7 +75,7 @@ inline void Foam::Module::polyMeshGenCells::cellInSubsets
 
     forAllConstIters(cellSubsets_, it)
     {
-        if (it->second.contains(cellI))
+        if (it->second.found(cellI))
         {
             cellSubsets.append(it->first);
         }

meshLibrary/utilities/meshes/polyMeshGen/polyMeshGenFaces.C

@@ -29,7 +29,7 @@ License
 #include "IOobjectList.H"
 #include "faceSet.H"
 #include "demandDrivenData.H"
-#include "stringListOps.H"
+#include "ListOps.H"
 
 // * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * * //
 
@@ -268,17 +268,15 @@ Foam::labelList Foam::Module::polyMeshGenFaces::findPatches
     const word& patchName
 ) const
 {
-    wordList allPatches = patchNames();
+    const labelList ids = findIndices(patchNames(), patchName);
 
-    labelList patchIDs = findStrings(patchName, allPatches);
-
-    if (patchIDs.empty())
+    if (ids.empty())
     {
         WarningInFunction
             << "Cannot find any patch names matching " << patchName << endl;
     }
 
-    return patchIDs;
+    return ids;
 }
 
 

meshLibrary/utilities/meshes/polyMeshGen/polyMeshGenFacesI.H

@@ -153,7 +153,7 @@ inline void Foam::Module::polyMeshGenFaces::faceInSubsets
 
     forAllConstIters(faceSubsets_, it)
     {
-        if (it->second.contains(faceI))
+        if (it->second.found(faceI))
         {
             faceSubsets.append(it->first);
         }

meshLibrary/utilities/meshes/polyMeshGen/polyMeshGenPointsI.H

@@ -93,7 +93,7 @@ inline void Foam::Module::polyMeshGenPoints::pointInSubsets
 
     forAllConstIters(pointSubsets_, it)
     {
-        if (it->second.contains(pointI))
+        if (it->second.found(pointI))
         {
             pointSubsets.append(it->first);
         }

meshLibrary/utilities/meshes/polyMeshGenAddressing/polyMeshGenAddressingParallelAddressing.C

@@ -164,7 +164,7 @@ void Foam::Module::polyMeshGenAddressing::calcGlobalPointLabels() const
                 for (label i = 0; i < nProcs; ++i)
                 {
                     const label neiProc = receivedData[counter++];
-                    if (!pProcs.contains(f[pI], neiProc))
+                    if (!pProcs.found(f[pI], neiProc))
                     {
                         pProcs.append(f[pI], neiProc);
                         finished = false;
@@ -618,7 +618,7 @@ void Foam::Module::polyMeshGenAddressing::calcGlobalEdgeLabels() const
                 for (label i = 0; i < nProcs; ++i)
                 {
                     const label neiProc = receivedData[counter++];
-                    if (!eProcs.contains(edgeI, neiProc))
+                    if (!eProcs.found(edgeI, neiProc))
                     {
                         eProcs.append(edgeI, neiProc);
                         finished = false;

meshLibrary/utilities/meshes/primitives/meshSubsets/meshSubset.H

@@ -152,7 +152,7 @@ public:
         // Searches
 
             //- find if the element exists in the subset
-            inline bool contains(const label) const;
+            inline bool found(const label) const;
 
 
     // operators

meshLibrary/utilities/meshes/primitives/meshSubsets/meshSubsetI.H

@@ -162,7 +162,7 @@ inline void Foam::Module::meshSubset::updateSubset(const VRWGraph& newLabels)
 }
 
 
-inline bool Foam::Module::meshSubset::contains(const label elmt) const
+inline bool Foam::Module::meshSubset::found(const label elmt) const
 {
     return (data_.find(elmt) != data_.end());
 }

meshLibrary/utilities/meshes/triSurf/triSurfFacets.C

@@ -27,7 +27,7 @@ License
 #include "pointIOField.H"
 #include "IOobjectList.H"
 #include "pointSet.H"
-#include "stringListOps.H"
+#include "ListOps.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
@@ -89,19 +89,17 @@ Foam::labelList Foam::Module::triSurfFacets::findPatches
     const word& patchName
 ) const
 {
-    const wordList allPatches = patchNames();
-
-    const labelList patchIDs = findStrings(patchName, allPatches);
+    const labelList ids = findIndices(patchNames(), patchName);
 
     # ifdef DEBUGtriSurf
-    if (patchIDs.empty())
+    if (ids.empty())
     {
         WarningInFunction
             << "Cannot find any patch names matching " << patchName << endl;
     }
     # endif
 
-    return patchIDs;
+    return ids;
 }
 
 

meshLibrary/utilities/meshes/triSurf/triSurfFacetsI.H

@@ -100,7 +100,7 @@ inline void Foam::Module::triSurfFacets::facetInSubsets
 
     forAllConstIters(facetSubsets_, it)
     {
-        if (it().contains(triI))
+        if (it().found(triI))
         {
             facetSubsets.append(it.key());
         }

meshLibrary/utilities/meshes/triSurf/triSurfFeatureEdgesI.H

@@ -91,7 +91,7 @@ inline void Foam::Module::triSurfFeatureEdges::edgeInSubsets
 
     forAllConstIters(featureEdgeSubsets_, it)
     {
-        if (it().contains(eI))
+        if (it().found(eI))
         {
             edgeSubsets.append(it.key());
         }

meshLibrary/utilities/meshes/triSurf/triSurfPointsI.H

@@ -87,7 +87,7 @@ inline void Foam::Module::triSurfPoints::pointInSubsets
 
     forAllConstIters(pointSubsets_, it)
     {
-        if (it().contains(pointI))
+        if (it().found(pointI))
         {
             pointSubsets.append(it.key());
         }

meshLibrary/utilities/octrees/meshOctree/meshOctreeAddressing/meshOctreeAddressingParallelAddressing.C

@@ -668,7 +668,7 @@ void Foam::Module::meshOctreeAddressing::calcGlobalLeafLabels() const
                 continue;
             }
 
-            if (!leafAtProcs.contains(leafI, it->first))
+            if (!leafAtProcs.found(leafI, it->first))
             {
                 FatalError << "Problem!!" << leafI
                     << " does not contain processor " << it->first

meshLibrary/utilities/smoothers/geometry/meshOptimizer/meshOptimizerOptimizePointParallel.C

@@ -83,7 +83,7 @@ void Foam::Module::meshOptimizer::laplaceSmoother::laplacianParallel
                 forAllRow(pointAtProcs, nei, procI)
                 {
                     const label procJ = pointAtProcs(nei, procI);
-                    if ((procJ < pMin) && pointAtProcs.contains(pointI, procJ))
+                    if ((procJ < pMin) && pointAtProcs.found(pointI, procJ))
                         pMin = procJ;
                 }