Initial autoMesh merge

applications/utilities/mesh/conversion/plot3dToFoam/hexBlock.C

@@ -87,7 +87,7 @@ void hexBlock::setHandedness()
 
     if (blockHandedness_ == noPoints)
     {
-        WarningIn("hexBlock::readPoints(const bool, Istream&)")
+        WarningIn("hexBlock::hexBlock::setHandedness()")
             << "Cannot determine orientation of block."
             << " Continuing as if right handed." << endl;
         blockHandedness_ = right;
@@ -105,35 +105,67 @@ hexBlock::hexBlock(const label nx, const label ny, const label nz)
     zDim_(nz - 1),
     blockHandedness_(noPoints),
     points_((xDim_ + 1)*(yDim_ + 1)*(zDim_ + 1))
-{
-    Pout<< "xDim:" << nx << " yDim:" << ny << " zDim:" << nz << endl;
-}
+{}
 
 
 // * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
 
-void hexBlock::readPoints(const bool readBlank, Istream& is)
+void hexBlock::readPoints
+(
+    const bool readBlank,
+    const scalar twoDThicknes,
+    Istream& is
+)
 {
     scalar iBlank;
 
-    forAll (points_, i)
+    label nPoints = points_.size();
+
+    if (twoDThicknes > 0)
+    {
+        nPoints /= 2;
+    }
+
+    Info<< "Reading " << nPoints << " x coordinates..." << endl;
+    for (label i=0; i < nPoints; i++)
     {
         is >> points_[i].x();
     }
 
-    forAll (points_, i)
+    Info<< "Reading " << nPoints << " y coordinates..." << endl;
+    for (label i=0; i < nPoints; i++)
     {
         is >> points_[i].y();
     }
 
-    forAll (points_, i)
+    if (twoDThicknes > 0)
+    {
+        Info<< "Extruding " << nPoints << " points in z direction..." << endl;
+        // Duplicate points
+        for (label i=0; i < nPoints; i++)
+        {
+            points_[i+nPoints] = points_[i];
+        }
+        for (label i=0; i < nPoints; i++)
+        {
+            points_[i].z() = 0;
+            points_[i+nPoints].z() = twoDThicknes;
+        }
+    }
+    else
     {
-        is >> points_[i].z();
+        Info<< "Reading " << nPoints << " z coordinates..." << endl;
+        for (label i=0; i < nPoints; i++)
+        {
+            is >> points_[i].z();
+        }
     }
 
+
     if (readBlank)
     {
-        forAll (points_, i)
+        Info<< "Reading " << nPoints << " blanks..." << endl;
+        for (label i=0; i < nPoints; i++)
         {
             is >> iBlank;
         }

applications/utilities/mesh/conversion/plot3dToFoam/hexBlock.H

@@ -145,7 +145,14 @@ public:
 
 
         //- Read block points either with or without blanking after every block.
-        void readPoints(const bool readBlank, Istream&);
+        //  If twoDThickness > 0 reads (half) the points and extrudes the
+        //  points in z direction.
+        void readPoints
+        (
+            const bool readBlank,
+            const scalar twoDThicknes,
+            Istream&
+        );
 };
 
 

applications/utilities/mesh/conversion/plot3dToFoam/plot3dToFoam.C

@@ -23,11 +23,12 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Description
-    Plot3d mesh (ascii format) converter.
+    Plot3d mesh (ascii/formatted format) converter.
 
     Work in progress! Handles ascii multiblock (and optionally singleBlock)
     format.
     By default expects blanking. Use -noBlank if none.
+    Use -2D <thickness> if 2D.
     Niklas Nordin has experienced a problem with lefthandedness of the blocks.
     The code should detect this automatically - see hexBlock::readPoints but
     if this goes wrong just set the blockHandedness_ variable to 'right'
@@ -59,6 +60,7 @@ int main(int argc, char *argv[])
     argList::validOptions.insert("scale", "scale factor");
     argList::validOptions.insert("noBlank", "");
     argList::validOptions.insert("singleBlock", "");
+    argList::validOptions.insert("2D", "thickness");
 
     argList args(argc, argv);
 
@@ -75,6 +77,13 @@ int main(int argc, char *argv[])
 
     bool readBlank = !args.options().found("noBlank");
     bool singleBlock = args.options().found("singleBlock");
+    scalar twoDThicknes = -1;
+    if (args.options().found("2D"))
+    {
+        twoDThicknes = readScalar(IStringStream(args.options()["2D"])());
+        Info<< "Reading 2D case by extruding points by " << twoDThicknes
+            << " in z direction." << nl << endl;
+    }
 
 
 #   include "createTime.H"
@@ -95,7 +104,7 @@ int main(int argc, char *argv[])
         plot3dFile >> nblock;
     }
 
-    Info << "Reading " << nblock << " blocks" << endl;
+    Info<< "Reading " << nblock << " blocks" << endl;
 
     PtrList<hexBlock> blocks(nblock);
 
@@ -104,20 +113,32 @@ int main(int argc, char *argv[])
 
         forAll (blocks, blockI)
         {
-            plot3dFile >> nx >> ny >> nz;
+            if (twoDThicknes > 0)
+            {
+                // Fake second set of points (done in readPoints below)
+                plot3dFile >> nx >> ny;
+                nz = 2;
+            }
+            else
+            {
+                plot3dFile >> nx >> ny >> nz;
+            }
+
+            Info<< "block " << blockI << " nx:" << nx
+                << " ny:" << ny << " nz:" << nz << endl;
 
             blocks.set(blockI, new hexBlock(nx, ny, nz));
         }
     }
 
-    Info << "Reading block points" << endl;
+    Info<< "Reading block points" << endl;
     label sumPoints(0);
     label nMeshCells(0);
 
     forAll (blocks, blockI)
     {
-        Info << "block " << blockI << ":" << nl;
-        blocks[blockI].readPoints(readBlank, plot3dFile);
+        Info<< "block " << blockI << ":" << nl;
+        blocks[blockI].readPoints(readBlank, twoDThicknes, plot3dFile);
         sumPoints += blocks[blockI].nBlockPoints();
         nMeshCells += blocks[blockI].nBlockCells();
         Info<< nl;
@@ -136,7 +157,6 @@ int main(int argc, char *argv[])
         }
     }
 
-
     // From old to new master point
     labelList oldToNew;
     pointField newPoints;
@@ -151,13 +171,17 @@ int main(int argc, char *argv[])
         newPoints
     );
 
+    Info<< "Merged points within " << SMALL << " distance. Merged from "
+        << oldToNew.size() << " down to " << newPoints.size()
+        << " points." << endl;
+
     // Scale the points
     if (scaleFactor > 1.0 + SMALL || scaleFactor < 1.0 - SMALL)
     {
         newPoints *= scaleFactor;
     }
 
-    Info << "Creating cells" << endl;
+    Info<< "Creating cells" << endl;
 
     cellShapeList cellShapes(nMeshCells);
 
@@ -190,7 +214,7 @@ int main(int argc, char *argv[])
         }
     }
 
-    Info << "Creating boundary patches" << endl;
+    Info<< "Creating boundary patches" << endl;
 
     faceListList boundary(0);
     wordList patchNames(0);
@@ -220,10 +244,10 @@ int main(int argc, char *argv[])
     // Set the precision of the points data to 10
     IOstream::defaultPrecision(10);
 
-    Info << "Writing polyMesh" << endl;
+    Info<< "Writing polyMesh" << endl;
     pShapeMesh.write();
 
-    Info << "End\n" << endl;
+    Info<< "End\n" << endl;
 
     return 0;
 }

applications/utilities/mesh/manipulation/Optional/setSet/setSet.C

@@ -42,6 +42,7 @@ Description
 #include "demandDrivenData.H"
 #include "writePatch.H"
 #include "writePointSet.H"
+#include "IOobjectList.H"
 
 #include <stdio.h>
 
@@ -233,8 +234,10 @@ void writeVTK
 
 void printHelp(Ostream& os)
 {
-    os  << "Please type 'help', 'quit', 'time ddd'"
+    os  << "Please type 'help', 'list', 'quit', 'time ddd'"
         << " or a set command after prompt." << endl
+        << "'list' will show all current cell/face/point sets." << endl
+        << "'time ddd' will change the current time." << endl
         << endl
         << "A set command should be of the following form" << endl
         << endl
@@ -272,6 +275,47 @@ void printHelp(Ostream& os)
 }
 
 
+void printAllSets(const polyMesh& mesh, Ostream& os)
+{
+    IOobjectList objects
+    (
+        mesh,
+        mesh.pointsInstance(),
+        polyMesh::meshSubDir/"sets"
+    );
+    IOobjectList cellSets(objects.lookupClass(cellSet::typeName));
+    if (cellSets.size() > 0)
+    {
+        os  << "cellSets:" << endl;
+        forAllConstIter(IOobjectList, cellSets, iter)
+        {
+            cellSet set(*iter());
+            os  << '\t' << set.name() << "\tsize:" << set.size() << endl;
+        }
+    }
+    IOobjectList faceSets(objects.lookupClass(faceSet::typeName));
+    if (faceSets.size() > 0)
+    {
+        os  << "faceSets:" << endl;
+        forAllConstIter(IOobjectList, faceSets, iter)
+        {
+            faceSet set(*iter());
+            os  << '\t' << set.name() << "\tsize:" << set.size() << endl;
+        }
+    }
+    IOobjectList pointSets(objects.lookupClass(pointSet::typeName));
+    if (pointSets.size() > 0)
+    {
+        os  << "pointSets:" << endl;
+        forAllConstIter(IOobjectList, pointSets, iter)
+        {
+            pointSet set(*iter());
+            os  << '\t' << set.name() << "\tsize:" << set.size() << endl;
+        }
+    }
+    os  << endl;
+}
+
 
 // Read command and execute. Return true if ok, false otherwise.
 bool doCommand
@@ -531,6 +575,12 @@ commandStatus parseType
 
         return INVALID;
     }
+    else if (setType == "list")
+    {
+        printAllSets(mesh, Pout);
+
+        return INVALID;
+    }
     else if (setType == "time")
     {
         scalar time = readScalar(is);
@@ -612,8 +662,9 @@ commandStatus parseType
         (
             "commandStatus parseType(Time&, polyMesh&, const word&"
             ", IStringStream&)"
-        )   << "Illegal set type " << setType << endl
-            << "Should be one of 'cellSet' 'faceSet' 'pointSet'"
+        )   << "Illegal command " << setType << endl
+            << "Should be one of 'help', 'list', 'time' or a set type :"
+            << " 'cellSet', 'faceSet', 'pointSet'"
             << endl;
 
         return INVALID;

applications/utilities/mesh/manipulation/couplePatches/FoamX/couplePatches.cfg

-/*---------------------------------------------------------------------------*\
-| =========                 |                                                 |
-| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.0                                   |
-|   \\  /    A nd           | Web:      http://www.openfoam.org               |
-|    \\/     M anipulation  |                                                 |
-\*---------------------------------------------------------------------------*/
-// couplePatches tool definition
-
-description     "Utility to reorder face numbering for cyclic and processor patches";
-
-couplePatchesDict
-{
-    type            dictionary;
-    description     "couplePatches control dictionary";
-    dictionaryPath  "system";
-
-    entries
-    {
-        arguments
-        {
-            type        rootCaseArguments;
-        }
-    }
-}
-
-// ************************************************************************* //

applications/utilities/mesh/manipulation/couplePatches/Make/files

-couplePatches.C
-
-EXE = $(FOAM_APPBIN)/couplePatches

applications/utilities/mesh/manipulation/couplePatches/Make/options

-EXE_INC = \
-    -I$(LIB_SRC)/dynamicMesh/lnInclude \
-    -I$(LIB_SRC)/meshTools/lnInclude
-
-EXE_LIBS = \
-    -ldynamicMesh \
-    -lmeshTools

src/Allwmake

@@ -41,6 +41,8 @@ wmake libso randomProcesses
 
 ( cd postProcessing && ./Allwmake )
 
+wmake libso autoMesh
+
 wmake libso errorEstimation
 
 

src/OpenFOAM/containers/Lists/ListOps/ListOps.H

+
 /*---------------------------------------------------------------------------*\
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
@@ -26,7 +27,7 @@ InNamspace
     Foam
 
 Description
-    ListOps. Various functions to operate on Lists.
+    Various functions to operate on Lists.
 
 SourceFiles
     ListOps.C
@@ -66,6 +67,17 @@ template<class List>
 void inplaceReorder(const labelList& oldToNew, List&);
 
 
+// Variants to work with iterators and sparse tables. Need to have iterators
+// and insert()
+
+//- Map values. Do not map negative values.
+template<class Container>
+void inplaceMapValue(const labelList& oldToNew, Container&);
+//- Recreate with mapped keys. Remove elements with negative key.
+template<class Container>
+void inplaceMapKey(const labelList& oldToNew, Container&);
+
+
 //- Extract elements of List whose region is certain value. Use e.g.
 //  to extract all selected elements:
 //  subset<boolList, labelList>(selectedElems, true, lst);
@@ -103,11 +115,21 @@ labelList identity(const label len);
 //- Find first occurence of given element and return index,
 //  return -1 if not found. Linear search.
 template<class List>
-label findIndex(const List&, typename List::const_reference);
+label findIndex
+(
+    const List&,
+    typename List::const_reference,
+    const label start=0
+);
 
 //- Find all occurences of given element. Linear search.
 template<class List>
-labelList findIndices(const List&, typename List::const_reference);
+labelList findIndices
+(
+    const List&,
+    typename List::const_reference,
+    const label start=0
+);
 
 //- Opposite of findIndices: set values at indices to given value
 template<class List>
@@ -123,7 +145,7 @@ template<class List>
 List createWithValues
 (
     const label sz,
-    typename List::const_reference initValue,
+    const typename List::const_reference initValue,
     const labelList& indices,
     typename List::const_reference setValue
 );
@@ -131,25 +153,35 @@ List createWithValues
 //- Find index of max element (and larger than given element).
 //  return -1 if not found. Linear search.
 template<class List>
-label findMax(const List&);
+label findMax(const List&, const label start=0);
 
 
 //- Find index of min element (and less than given element).
 //  return -1 if not found. Linear search.
 template<class List>
-label findMin(const List&);
+label findMin(const List&, const label start=0);
 
 
 //- Find first occurence of given element in sorted list and return index,
 //  return -1 if not found. Binary search.
 template<class List>
-label findSortedIndex(const List&, typename List::const_reference);
+label findSortedIndex
+(
+    const List&,
+    typename List::const_reference,
+    const label start=0
+);
 
 
 //- Find last element < given value in sorted list and return index,
 //  return -1 if not found. Binary search.
 template<class List>
-label findLower(const List&, typename List::const_reference);
+label findLower
+(
+    const List&,
+    typename List::const_reference,
+    const label start=0
+);
 
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

src/OpenFOAM/containers/Lists/ListOps/ListOpsTemplates.C

@@ -118,6 +118,54 @@ void Foam::inplaceReorder
 }
 
 
+template<class Container>
+void Foam::inplaceMapValue
+(
+    const labelList& oldToNew,
+    Container& lst
+)
+{
+    for
+    (
+        typename Container::iterator iter = lst.begin();
+        iter != lst.end();
+        ++iter
+    )
+    {
+        if (iter() >= 0)
+        {
+            iter() = oldToNew[iter()];
+        }
+    }
+}
+
+
+template<class Container>
+void Foam::inplaceMapKey
+(
+    const labelList& oldToNew,
+    Container& lst
+)
+{
+    Container newLst(lst);
+
+    for
+    (
+        typename Container::iterator iter = lst.begin();
+        iter != lst.end();
+        ++iter
+    )
+    {
+        if (iter.key() >= 0)
+        {
+            newLst.insert(oldToNew[iter.key()], iter());
+        }
+    }
+    
+    lst.transfer(newLst);
+}
+
+
 template<class T, class List>
 List Foam::subset(const UList<T>& regions, const T& region, const List& lst)
 {
@@ -221,11 +269,16 @@ void Foam::invertManyToMany
 
 
 template<class List>
-Foam::label Foam::findIndex(const List& l, typename List::const_reference t)
+Foam::label Foam::findIndex
+(
+    const List& l,
+    typename List::const_reference t,
+    const label start
+)
 {
     label index = -1;
 
-    forAll(l, i)
+    for (label i = start; i < l.size(); i++)
     {
         if (l[i] == t)
         {
@@ -242,13 +295,14 @@ template<class List>
 Foam::labelList Foam::findIndices
 (
     const List& l,
-    typename List::const_reference t
+    typename List::const_reference t,
+    const label start
 )
 {
     // Count occurrences
     label n = 0;
 
-    forAll(l, i)
+    for (label i = start; i < l.size(); i++)
     {
         if (l[i] == t)
         {
@@ -260,7 +314,7 @@ Foam::labelList Foam::findIndices
     labelList indices(n);
     n = 0;
 
-    forAll(l, i)
+    for (label i = start; i < l.size(); i++)
     {
         if (l[i] == t)
         {
@@ -291,7 +345,7 @@ template<class List>
 List Foam::createWithValues
 (
     const label sz,
-    typename List::const_reference initValue,
+    const typename List::const_reference initValue,
     const labelList& indices,
     typename List::const_reference setValue
 )
@@ -303,16 +357,16 @@ List Foam::createWithValues
 
 
 template<class List>
-Foam::label Foam::findMax(const List& l)
+Foam::label Foam::findMax(const List& l, const label start)
 {
-    if (l.size() == 0)
+    if (start >= l.size())
     {
         return -1;
     }
 
-    label index = 0;
+    label index = start;
 
-    for (label i = 1; i < l.size(); i++)
+    for (label i = start+1; i < l.size(); i++)
     {
         if (l[i] > l[index])