Merge branch 'master' of /home/dm4/OpenFOAM/OpenFOAM-dev

applications/solvers/heatTransfer/thermoFoam/thermoFoam.C

@@ -25,7 +25,7 @@ Application
     thermoFoam
 
 Description
-    Evolves the thermodynamics on a forzen flow field
+    Evolves the thermodynamics on a frozen flow field
 
 \*---------------------------------------------------------------------------*/
 

applications/utilities/mesh/generation/snappyHexMesh/snappyHexMesh.C

@@ -614,11 +614,6 @@ int main(int argc, char *argv[])
         "boundBox",
         "simplify the surface using snappyHexMesh starting from a boundBox"
     );
-    Foam::argList::addBoolOption
-    (
-        "writeLevel",
-        "write pointLevel and cellLevel postprocessing files"
-    );
     Foam::argList::addOption
     (
         "patches",
@@ -640,7 +635,6 @@ int main(int argc, char *argv[])
     const bool overwrite = args.optionFound("overwrite");
     const bool checkGeometry = args.optionFound("checkGeometry");
     const bool surfaceSimplify = args.optionFound("surfaceSimplify");
-    const bool writeLevel = args.optionFound("writeLevel");
 
     autoPtr<fvMesh> meshPtr;
 
@@ -852,6 +846,8 @@ int main(int argc, char *argv[])
         autoLayerDriver::debug  = debug;
     }
 
+    const bool writeLevel = meshDict.lookupOrDefault<bool>("writeLevel", false);
+
 
     // Read geometry
     // ~~~~~~~~~~~~~

applications/utilities/miscellaneous/foamHelp/helpTypes/doxygenXmlParser/doxygenXmlParser.C

@@ -213,25 +213,21 @@ void Foam::doxygenXmlParser::skipForward
 ) const
 {
     // recurse to move forward in 'is' until come across <blockName>
-
-    // fast-forward until we reach a '<'
-    char c;
-    while (is.get(c) && c != '<')
-    {}
-    
     string entryName = "";
-    while (is.get(c) && c  != '>')
-    {
-        entryName = entryName + c;
-    }
+    char c;
 
-    if (entryName == blockName)
-    {
-        return;
-    }
-    else
+    while (is.good() && (entryName != blockName))
     {
-        skipForward(is, blockName);
+        entryName = "";
+
+        // fast-forward until we reach a '<'
+        while (is.get(c) && c != '<')
+        {}
+
+        while (is.get(c) && c  != '>')
+        {
+            entryName = entryName + c;
+        }
     }
 }
 

applications/utilities/postProcessing/dataConversion/foamToEnsight/ensightField.C

@@ -39,6 +39,31 @@ using namespace Foam;
 
 // * * * * * * * * * * * * * * * Global Functions  * * * * * * * * * * * * * //
 
+template<class Type>
+tmp<GeometricField<Type, fvPatchField, volMesh> >
+volField
+(
+    const fvMeshSubset& meshSubsetter,
+    const GeometricField<Type, fvPatchField, volMesh>& vf
+)
+{
+    if (meshSubsetter.hasSubMesh())
+    {
+        tmp<GeometricField<Type, fvPatchField, volMesh> > tfld
+        (
+            meshSubsetter.interpolate(vf)
+        );
+        tfld().checkOut();
+        tfld().rename(vf.name());
+        return tfld;
+    }
+    else
+    {
+        return vf;
+    }
+}
+
+
 template<class Type>
 Field<Type> map
 (
@@ -680,7 +705,7 @@ void ensightPointField
 template<class Type>
 void ensightField
 (
-    const IOobject& fieldObject,
+    const GeometricField<Type, fvPatchField, volMesh>& vf,
     const ensightMesh& eMesh,
     const fileName& postProcPath,
     const word& prepend,
@@ -690,14 +715,11 @@ void ensightField
     Ostream& ensightCaseFile
 )
 {
-    // Read field
-    GeometricField<Type, fvPatchField, volMesh> vf(fieldObject, eMesh.mesh());
-
     if (nodeValues)
     {
         tmp<GeometricField<Type, pointPatchField, pointMesh> > pfld
         (
-            volPointInterpolation::New(eMesh.mesh()).interpolate(vf)
+            volPointInterpolation::New(vf.mesh()).interpolate(vf)
         );
         pfld().rename(vf.name());
 

applications/utilities/postProcessing/dataConversion/foamToEnsight/ensightField.H

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2011 OpenFOAM Foundation
+    \\  /    A nd           | Copyright (C) 2011-2013 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -35,13 +35,24 @@ SourceFiles
 #define ensightField_H
 
 #include "ensightMesh.H"
+#include "fvMeshSubset.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
+//- Wrapper to get hold of the field or the subsetted field
+template<class Type>
+Foam::tmp<Foam::GeometricField<Type, Foam::fvPatchField, Foam::volMesh> >
+volField
+(
+    const Foam::fvMeshSubset&,
+    const Foam::GeometricField<Type, Foam::fvPatchField, Foam::volMesh>& vf
+);
+
+
 template<class Type>
 void ensightField
 (
-    const Foam::IOobject& fieldObject,
+    const Foam::GeometricField<Type, Foam::fvPatchField, Foam::volMesh>& vf,
     const Foam::ensightMesh& eMesh,
     const Foam::fileName& postProcPath,
     const Foam::word& prepend,

applications/utilities/postProcessing/dataConversion/foamToEnsight/ensightMesh.C

@@ -57,14 +57,6 @@ void Foam::ensightMesh::correct()
     nFaceZonePrims_ = 0;
     boundaryFaceToBeIncluded_.clear();
 
-    const cellShapeList& cellShapes = mesh_.cellShapes();
-
-    const cellModel& tet = *(cellModeller::lookup("tet"));
-    const cellModel& pyr = *(cellModeller::lookup("pyr"));
-    const cellModel& prism = *(cellModeller::lookup("prism"));
-    const cellModel& wedge = *(cellModeller::lookup("wedge"));
-    const cellModel& hex = *(cellModeller::lookup("hex"));
-
     if (!noPatches_)
     {
         // Patches are output. Check that they're synced.
@@ -111,6 +103,16 @@ void Foam::ensightMesh::correct()
     }
     else
     {
+        const cellShapeList& cellShapes = mesh_.cellShapes();
+
+        const cellModel& tet = *(cellModeller::lookup("tet"));
+        const cellModel& pyr = *(cellModeller::lookup("pyr"));
+        const cellModel& prism = *(cellModeller::lookup("prism"));
+        const cellModel& wedge = *(cellModeller::lookup("wedge"));
+        const cellModel& hex = *(cellModeller::lookup("hex"));
+
+
+
         // Count the shapes
         labelList& tets = meshCellSets_.tets;
         labelList& pyrs = meshCellSets_.pyrs;
@@ -926,8 +928,10 @@ void Foam::ensightMesh::writeAllNSided
 }
 
 
-void Foam::ensightMesh::writeAllInternalPoints
+void Foam::ensightMesh::writeAllPoints
 (
+    const label ensightPartI,
+    const word& ensightPartName,
     const pointField& uniquePoints,
     const label nPoints,
     ensightStream& ensightGeometryFile
@@ -937,49 +941,8 @@ void Foam::ensightMesh::writeAllInternalPoints
 
     if (Pstream::master())
     {
-        ensightGeometryFile.writePartHeader(1);
-        ensightGeometryFile.write("internalMesh");
-        ensightGeometryFile.write("coordinates");
-        ensightGeometryFile.write(nPoints);
-
-        for (direction d=0; d<vector::nComponents; d++)
-        {
-            ensightGeometryFile.write(uniquePoints.component(d));
-
-            for (int slave=1; slave<Pstream::nProcs(); slave++)
-            {
-                IPstream fromSlave(Pstream::scheduled, slave);
-                scalarField pointsComponent(fromSlave);
-                ensightGeometryFile.write(pointsComponent);
-            }
-        }
-    }
-    else
-    {
-        for (direction d=0; d<vector::nComponents; d++)
-        {
-            OPstream toMaster(Pstream::scheduled, Pstream::masterNo());
-            toMaster<< uniquePoints.component(d);
-        }
-    }
-}
-
-
-void Foam::ensightMesh::writeAllPatchPoints
-(
-    const label ensightPatchI,
-    const word& patchName,
-    const pointField& uniquePoints,
-    const label nPoints,
-    ensightStream& ensightGeometryFile
-) const
-{
-    barrier();
-
-    if (Pstream::master())
-    {
-        ensightGeometryFile.writePartHeader(ensightPatchI);
-        ensightGeometryFile.write(patchName.c_str());
+        ensightGeometryFile.writePartHeader(ensightPartI);
+        ensightGeometryFile.write(ensightPartName.c_str());
         ensightGeometryFile.write("coordinates");
         ensightGeometryFile.write(nPoints);
 
@@ -998,11 +961,7 @@ void Foam::ensightMesh::writeAllPatchPoints
     {
         for (direction d=0; d<vector::nComponents; d++)
         {
-            OPstream toMaster
-            (
-                Pstream::scheduled,
-                Pstream::masterNo()
-            );
+            OPstream toMaster(Pstream::scheduled, Pstream::masterNo());
             toMaster<< uniquePoints.component(d);
         }
     }
@@ -1076,8 +1035,10 @@ void Foam::ensightMesh::write
 
         const pointField uniquePoints(mesh_.points(), uniquePointMap_);
 
-        writeAllInternalPoints
+        writeAllPoints
         (
+            1,
+            "internalMesh",
             uniquePoints,
             nPoints,
             ensightGeometryFile
@@ -1166,7 +1127,7 @@ void Foam::ensightMesh::write
                     inplaceRenumber(pointToGlobal, patchFaces[i]);
                 }
 
-                writeAllPatchPoints
+                writeAllPoints
                 (
                     ensightPatchI++,
                     patchName,
@@ -1271,7 +1232,7 @@ void Foam::ensightMesh::write
                 inplaceRenumber(pointToGlobal, faceZoneMasterFaces[i]);
             }
 
-            writeAllPatchPoints
+            writeAllPoints
             (
                 ensightPatchI++,
                 faceZoneName,

applications/utilities/postProcessing/dataConversion/foamToEnsight/ensightMesh.H

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2011-2012 OpenFOAM Foundation
+    \\  /    A nd           | Copyright (C) 2011-2013 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -244,17 +244,10 @@ private:
             ensightStream& ensightGeometryFile
         ) const;
 
-        void writeAllInternalPoints
+        void writeAllPoints
         (
-            const pointField& uniquePoints,
-            const label nPoints,
-            ensightStream& ensightGeometryFile
-        ) const;
-
-        void writeAllPatchPoints
-        (
-            label ensightPatchI,
-            const word& patchName,
+            const label ensightPartI,
+            const word& ensightPartName,
             const pointField& uniquePoints,
             const label nPoints,
             ensightStream& ensightGeometryFile

applications/utilities/postProcessing/dataConversion/foamToEnsight/foamToEnsight.C

@@ -46,6 +46,9 @@ Usage
     \param -faceZones zoneList \n
     Specify faceZones to write, with wildcards
 
+    \param -cellZone zoneName \n
+    Specify single cellZone to write (not lagrangian)
+
 Note
     Parallel support for cloud data is not supported
     - writes to \a EnSight directory to avoid collisions with foamToEnsightParts
@@ -72,6 +75,9 @@ Note
 
 #include "fvc.H"
 
+#include "cellSet.H"
+#include "fvMeshSubset.H"
+
 using namespace Foam;
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
@@ -128,6 +134,12 @@ int main(int argc, char *argv[])
         "wordReList",
         "specify faceZones to write - eg '( slice \"mfp-.*\" )'."
     );
+    argList::addOption
+    (
+        "cellZone",
+        "word",
+        "specify cellZone to write"
+    );
 
     #include "setRootCase.H"
 
@@ -212,9 +224,28 @@ int main(int argc, char *argv[])
         zonePatterns = wordReList(args.optionLookup("faceZones")());
     }
 
+    word cellZoneName;
+    const bool doCellZone = args.optionReadIfPresent("cellZone", cellZoneName);
+
+    fvMeshSubset meshSubsetter(mesh);
+    if (doCellZone)
+    {
+        Info<< "Converting cellZone " << cellZoneName
+            << " only (puts outside faces into patch "
+            << mesh.boundaryMesh()[0].name()
+            << ")" << endl;
+        const cellZone& cz = mesh.cellZones()[cellZoneName];
+        cellSet c0(mesh, "c0", labelHashSet(cz));
+        meshSubsetter.setLargeCellSubset(c0, 0);
+    }
+
     ensightMesh eMesh
     (
-        mesh,
+        (
+            meshSubsetter.hasSubMesh()
+          ? meshSubsetter.subMesh()
+          : meshSubsetter.baseMesh()
+        ),
         args.optionFound("noPatches"),
         selectedPatches,
         patchPatterns,
@@ -349,6 +380,17 @@ int main(int argc, char *argv[])
         Info<< "Translating time = " << runTime.timeName() << nl;
 
         polyMesh::readUpdateState meshState = mesh.readUpdate();
+        if (timeIndex != 0 && meshSubsetter.hasSubMesh())
+        {
+            Info<< "Converting cellZone " << cellZoneName
+                << " only (puts outside faces into patch "
+                << mesh.boundaryMesh()[0].name()
+                << ")" << endl;
+            const cellZone& cz = mesh.cellZones()[cellZoneName];
+            cellSet c0(mesh, "c0", labelHashSet(cz));
+            meshSubsetter.setLargeCellSubset(c0, 0);
+        }
+
 
         if (meshState != polyMesh::UNCHANGED)
         {
@@ -406,9 +448,10 @@ int main(int argc, char *argv[])
 
                 if (volFieldTypes[i] == volScalarField::typeName)
                 {
+                    volScalarField vf(fieldObject, mesh);
                     ensightField<scalar>
                     (
-                        fieldObject,
+                        volField(meshSubsetter, vf),
                         eMesh,
                         ensightDir,
                         prepend,
@@ -420,9 +463,10 @@ int main(int argc, char *argv[])
                 }
                 else if (volFieldTypes[i] == volVectorField::typeName)
                 {
+                    volVectorField vf(fieldObject, mesh);
                     ensightField<vector>
                     (
-                        fieldObject,
+                        volField(meshSubsetter, vf),
                         eMesh,
                         ensightDir,
                         prepend,
@@ -434,9 +478,10 @@ int main(int argc, char *argv[])
                 }
                 else if (volFieldTypes[i] == volSphericalTensorField::typeName)
                 {
+                    volSphericalTensorField vf(fieldObject, mesh);
                     ensightField<sphericalTensor>
                     (
-                        fieldObject,
+                        volField(meshSubsetter, vf),
                         eMesh,
                         ensightDir,
                         prepend,
@@ -448,9 +493,10 @@ int main(int argc, char *argv[])
                 }
                 else if (volFieldTypes[i] == volSymmTensorField::typeName)
                 {
+                    volSymmTensorField vf(fieldObject, mesh);
                     ensightField<symmTensor>
                     (
-                        fieldObject,
+                        volField(meshSubsetter, vf),
                         eMesh,
                         ensightDir,
                         prepend,
@@ -462,9 +508,10 @@ int main(int argc, char *argv[])
                 }
                 else if (volFieldTypes[i] == volTensorField::typeName)
                 {
+                    volTensorField vf(fieldObject, mesh);
                     ensightField<tensor>
                     (
-                        fieldObject,
+                        volField(meshSubsetter, vf),
                         eMesh,
                         ensightDir,
                         prepend,

applications/utilities/surface/surfaceFeatureExtract/surfaceFeatureExtract.C

@@ -952,8 +952,20 @@ int main(int argc, char *argv[])
 
     forAllConstIter(dictionary, dict, iter)
     {
+        if (!iter().isDict())
+        {
+            continue;
+        }
+
         const dictionary& surfaceDict = iter().dict();
 
+        if (!surfaceDict.found("extractionMethod"))
+        {
+            continue;
+        }
+
+        const word extractionMethod = surfaceDict.lookup("extractionMethod");
+
         const fileName surfFileName = iter().keyword();
         const fileName sFeatFileName = surfFileName.lessExt().name();
 
@@ -971,8 +983,6 @@ int main(int argc, char *argv[])
         const Switch closeness =
             surfaceDict.lookupOrDefault<Switch>("closeness", "off");
 
-        const word extractionMethod = surfaceDict.lookup("extractionMethod");
-
 
         Info<< nl << "Feature line extraction is only valid on closed manifold "
             << "surfaces." << endl;

etc/config/README

@@ -30,6 +30,9 @@ sh/csh variants:
 * scotch.sh
   application settings for compiling against scotch
 
+* metis.sh
+  application settings for compiling against metis 5
+
 ---
 
 The config/example directory contains various example configuration files

src/OpenFOAM/db/dictionary/entry/entryIO.C

@@ -146,7 +146,7 @@ bool Foam::entry::New(dictionary& parentDict, Istream& is)
                 if (ePtr)
                 {
                     // Read as primitiveEntry
-                    const word newKeyword(ePtr->stream());
+                    const keyType newKeyword(ePtr->stream());
 
                     return parentDict.add
                     (

src/OpenFOAM/db/dictionary/functionEntries/calcEntry/calcEntry.C

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2011 OpenFOAM Foundation
+    \\  /    A nd           | Copyright (C) 2011-2013 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -37,6 +37,14 @@ namespace functionEntries
 {
     defineTypeNameAndDebug(calcEntry, 0);
 
+    addToMemberFunctionSelectionTable
+    (
+        functionEntry,
+        calcEntry,
+        execute,
+        dictionaryIstream
+    );
+
     addToMemberFunctionSelectionTable
     (
         functionEntry,
@@ -96,4 +104,48 @@ bool Foam::functionEntries::calcEntry::execute
 }
 
 
+bool Foam::functionEntries::calcEntry::execute
+(
+    dictionary& parentDict,
+    Istream& is
+)
+{
+    Info<< "Using #calcEntry at line " << is.lineNumber()
+        << " in file " <<  parentDict.name() << endl;
+
+    dynamicCode::checkSecurity
+    (
+        "functionEntries::calcEntry::execute(..)",
+        parentDict
+    );
+
+    // Read string
+    string s(is);
+    // Make sure we stop this entry
+    //is.putBack(token(token::END_STATEMENT, is.lineNumber()));
+
+    // Construct codeDict for codeStream
+    // must reference parent for stringOps::expand to work nicely.
+    dictionary codeSubDict;
+    codeSubDict.add("code", "os << (" + s + ");");
+    dictionary codeDict(parentDict, codeSubDict);
+
+    codeStream::streamingFunctionType function = codeStream::getFunction
+    (
+        parentDict,
+        codeDict
+    );
+
+    // use function to write stream
+    OStringStream os(is.format());
+    (*function)(os, parentDict);
+
+    // get the entry from this stream
+    IStringStream resultStream(os.str());
+    parentDict.read(resultStream);
+