Merge branch 'master' of ssh://dm/home/dm4/OpenFOAM/OpenFOAM-dev

applications/solvers/heatTransfer/buoyantSimpleFoam/buoyantSimpleFoam.C

@@ -22,7 +22,7 @@ License
     along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
 
 Application
-    buoyantSimpleRadiationFoam
+    buoyantSimpleFoam
 
 Description
     Steady-state solver for buoyant, turbulent flow of compressible fluids,

applications/utilities/mesh/generation/snappyHexMesh/snappyHexMeshDict

@@ -337,55 +337,75 @@ addLayersControls
 
     // Advanced settings
 
-    // When not to extrude surface. 0 is flat surface, 90 is when two faces
-    // are perpendicular
-    featureAngle 60;
 
-    // At non-patched sides allow mesh to slip if extrusion direction makes
-    // angle larger than slipFeatureAngle.
-    slipFeatureAngle 30;
+    // Static analysis of starting mesh
 
-    // Maximum number of snapping relaxation iterations. Should stop
-    // before upon reaching a correct mesh.
-    nRelaxIter 5;
+        // When not to extrude surface. 0 is flat surface, 90 is when two faces
+        // are perpendicular
+        featureAngle 130;
+
+        // Stop layer growth on highly warped cells
+        maxFaceThicknessRatio 0.5;
+
+
+    // Patch displacement
+
+        // Number of smoothing iterations of surface normals
+        nSmoothSurfaceNormals 1;
+
+        // Smooth layer thickness over surface patches
+        nSmoothThickness 10;
+
+
+
+    // Medial axis analysis
+
+        // Angle used to pick up medial axis points
+        // Note: changed(corrected) w.r.t 17x! 90 degrees corresponds to 130
+        // in 17x.
+        minMedianAxisAngle 90;
+
+        // Reduce layer growth where ratio thickness to medial
+        // distance is large
+        maxThicknessToMedialRatio 0.3;
 
-    // Number of smoothing iterations of surface normals
-    nSmoothSurfaceNormals 1;
+        // Number of smoothing iterations of interior mesh movement direction
+        nSmoothNormals 3;
 
-    // Number of smoothing iterations of interior mesh movement direction
-    nSmoothNormals 3;
+        // Optional: smooth displacement after medial axis determination.
+        // default is 0.
+        nSmoothDisplacement 90;
 
-    // Smooth layer thickness over surface patches
-    nSmoothThickness 10;
 
-    // Stop layer growth on highly warped cells
-    maxFaceThicknessRatio 0.5;
+    // Mesh shrinking
 
-    // Reduce layer growth where ratio thickness to medial
-    // distance is large
-    maxThicknessToMedialRatio 0.3;
+        // Optional: at non-patched sides allow mesh to slip if extrusion
+        // direction makes angle larger than slipFeatureAngle. Default is
+        // 0.5*featureAngle.
+        slipFeatureAngle 30;
 
-    // Angle used to pick up medial axis points
-    // Note: changed(corrected) w.r.t 17x! 90 degrees corresponds to 130 in 17x.
-    minMedianAxisAngle 90;
+        // Maximum number of snapping relaxation iterations. Should stop
+        // before upon reaching a correct mesh.
+        nRelaxIter 5;
 
-    // Create buffer region for new layer terminations
-    nBufferCellsNoExtrude 0;
+        // Create buffer region for new layer terminations
+        nBufferCellsNoExtrude 0;
 
-    // Overall max number of layer addition iterations. The mesher will exit
-    // if it reaches this number of iterations; possibly with an illegal
-    // mesh.
-    nLayerIter 50;
+        // Overall max number of layer addition iterations. The mesher will
+        // exit if it reaches this number of iterations; possibly with an
+        // illegal mesh.
+        nLayerIter 50;
 
-    // Max number of iterations after which relaxed meshQuality controls
-    // get used. Up to nRelaxIter it uses the settings in meshQualityControls,
-    // after nRelaxIter it uses the values in meshQualityControls::relaxed.
-    nRelaxedIter 20;
+        // Max number of iterations after which relaxed meshQuality controls
+        // get used. Up to nRelaxIter it uses the settings in
+        // meshQualityControls,
+        // after nRelaxIter it uses the values in meshQualityControls::relaxed.
+        nRelaxedIter 20;
 
-    // Additional reporting: if there are just a few faces where there
-    // are mesh errors (after adding the layers) print their face centres.
-    // This helps in tracking down problematic mesh areas.
-    //additionalReporting true;
+        // Additional reporting: if there are just a few faces where there
+        // are mesh errors (after adding the layers) print their face centres.
+        // This helps in tracking down problematic mesh areas.
+        //additionalReporting true;
 }
 
 // Generic mesh quality settings. At any undoable phase these determine

applications/utilities/mesh/manipulation/createBaffles/faceSelection/searchableSurfaceSelection.C

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2012 OpenFOAM Foundation
+    \\  /    A nd           | Copyright (C) 2012-2013 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -97,7 +97,7 @@ void Foam::faceSelections::searchableSurfaceSelection::select
 
     // Boundary faces
     vectorField neighbourCellCentres;
-    syncTools::swapBoundaryCellList
+    syncTools::swapBoundaryCellPositions
     (
         mesh_,
         mesh_.cellCentres(),

applications/utilities/mesh/manipulation/renumberMesh/renumberMesh.C

@@ -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 anispulation  |
 -------------------------------------------------------------------------------
 License
@@ -494,7 +494,13 @@ autoPtr<mapPolyMesh> reorderMesh
                     newFlipMap[i] = fZone.flipMap()[i];
                 }
             }
-            fZone.resetAddressing(newAddressing, newFlipMap);
+            labelList newToOld;
+            sortedOrder(newAddressing, newToOld);
+            fZone.resetAddressing
+            (
+                UIndirectList<label>(newAddressing, newToOld)(),
+                UIndirectList<bool>(newFlipMap, newToOld)()
+            );
         }
     }
     // Re-do the cellZones
@@ -508,6 +514,7 @@ autoPtr<mapPolyMesh> reorderMesh
                 reverseCellOrder,
                 cellZones[zoneI]
             )();
+            Foam::sort(cellZones[zoneI]);
         }
     }
 

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

@@ -1404,6 +1404,7 @@ int main(int argc, char *argv[])
     (
         "splits mesh into multiple regions (detected by walking across faces)"
     );
+#   include "addRegionOption.H"
     #include "addOverwriteOption.H"
     argList::addBoolOption
     (
@@ -1467,7 +1468,7 @@ int main(int argc, char *argv[])
     #include "setRootCase.H"
     #include "createTime.H"
     runTime.functionObjects().off();
-    #include "createMesh.H"
+    #include "createNamedMesh.H"
     const word oldInstance = mesh.pointsInstance();
 
     word blockedFacesName;

applications/utilities/postProcessing/wall/wallHeatFlux/Make/options

@@ -9,6 +9,9 @@ EXE_INC = \
 
 EXE_LIBS = \
     -lcompressibleTurbulenceModel \
+    -lcompressibleRASModels \
+    -lcompressibleLESModels \
+    -lLESdeltas \
     -lreactionThermophysicalModels \
     -lfiniteVolume \
     -lgenericPatchFields \

applications/utilities/preProcessing/createExternalCoupledPatchGeometry/Make/files

+createExternalCoupledPatchGeometry.C
+
+EXE = $(FOAM_APPBIN)/createExternalCoupledPatchGeometry

applications/utilities/preProcessing/createExternalCoupledPatchGeometry/Make/options

+EXE_INC = \
+    -I$(LIB_SRC)/finiteVolume/lnInclude
+
+EXE_LIBS = \
+    -lfiniteVolume \
+    -lcompressibleTurbulenceModel

applications/utilities/preProcessing/createExternalCoupledPatchGeometry/createExternalCoupledPatchGeometry.C

+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 2013 OpenFOAM Foundation
+     \\/     M anipulation  |
+-------------------------------------------------------------------------------
+License
+    This file is part of OpenFOAM.
+
+    OpenFOAM is free software: you can redistribute it and/or modify it
+    under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
+    ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+    FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
+    for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
+
+Application
+    createExternalCoupledPatchGeometry.
+
+Description
+    Application to generate the patch geometry (points and faces) for use
+    with the externalCoupled boundary condition.
+
+    Usage:
+
+        createExternalCoupledPatchGeometry <fieldName>
+
+    On execution, the field <fieldName> is read, and its boundary conditions
+    interrogated for the presence of an \c externalCoupled type.  If found,
+    the patch geometry (points and faces) for the coupled patches are output
+    to the communications folder.
+
+Note:
+    The addressing is patch-local, i.e. point indices for each patch point
+    used for face addressing starts at index 0.
+
+SeeAlso
+    externalCoupledMixedFvPatchField
+
+\*---------------------------------------------------------------------------*/
+
+#include "fvCFD.H"
+#include "createExternalCoupledPatchGeometryTemplates.H"
+#include "IOobjectList.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+int main(int argc, char *argv[])
+{
+    #include "addRegionOption.H"
+    argList::validArgs.append("fieldName");
+    #include "setRootCase.H"
+    #include "createTime.H"
+    #include "createNamedMesh.H"
+
+    // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+    const word fieldName = args[1];
+
+    IOobjectList objects(IOobjectList(mesh, mesh.time().timeName()));
+
+    label processed = -1;
+    processField<scalar>(mesh, objects, fieldName, processed);
+    processField<vector>(mesh, objects, fieldName, processed);
+    processField<sphericalTensor>(mesh, objects, fieldName, processed);
+    processField<symmTensor>(mesh, objects, fieldName, processed);
+    processField<tensor>(mesh, objects, fieldName, processed);
+
+    if (processed == -1)
+    {
+        Info<< "Field " << fieldName << " not found" << endl;
+    }
+
+    Info<< "\nEnd\n" << endl;
+
+    return 0;
+}
+
+
+// ************************************************************************* //

applications/utilities/preProcessing/createExternalCoupledPatchGeometry/createExternalCoupledPatchGeometryTemplates.C

+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 2013 OpenFOAM Foundation
+     \\/     M anipulation  |
+-------------------------------------------------------------------------------
+License
+    This file is part of OpenFOAM.
+
+    OpenFOAM is free software: you can redistribute it and/or modify it
+    under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
+    ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+    FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
+    for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
+
+\*---------------------------------------------------------------------------*/
+
+#include "createExternalCoupledPatchGeometryTemplates.H"
+#include "externalCoupledMixedFvPatchField.H"
+#include "IOobjectList.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+template<class Type>
+void processField
+(
+    const fvMesh& mesh,
+    const IOobjectList& objects,
+    const word& fieldName,
+    label& processed
+)
+{
+    if (processed != -1)
+    {
+        return;
+    }
+
+    typedef GeometricField<Type, fvPatchField, volMesh> fieldType;
+
+    const word timeName(mesh.time().timeName());
+
+    IOobjectList fieldObjbjects(objects.lookupClass(fieldType::typeName));
+
+    if (fieldObjbjects.lookup(fieldName) != NULL)
+    {
+        fieldType vtf(*fieldObjbjects.lookup(fieldName), mesh);
+        const typename fieldType::GeometricBoundaryField& bf =
+            vtf.boundaryField();
+
+        forAll(bf, patchI)
+        {
+            if (isA<externalCoupledMixedFvPatchField<Type> >(bf[patchI]))
+            {
+                Info<< "Generating external coupled geometry for field "
+                    << fieldName << endl;
+
+                const externalCoupledMixedFvPatchField<Type>& pf =
+                    refCast<const externalCoupledMixedFvPatchField<Type> >
+                    (
+                        bf[patchI]
+                    );
+
+                pf.writeGeometry();
+                processed = 1;
+
+                break;
+            }
+        }
+
+        if (processed != 1)
+        {
+            processed = 0;
+
+            Info<< "Field " << fieldName << " found, but does not have any "
+                << externalCoupledMixedFvPatchField<Type>::typeName
+                << " boundary conditions" << endl;
+        }
+    }
+}
+
+
+// ************************************************************************* //

applications/utilities/preProcessing/createExternalCoupledPatchGeometry/createExternalCoupledPatchGeometryTemplates.H

+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 2013 OpenFOAM Foundation
+     \\/     M anipulation  |
+-------------------------------------------------------------------------------
+License
+    This file is part of OpenFOAM.
+
+    OpenFOAM is free software: you can redistribute it and/or modify it
+    under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
+    ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+    FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
+    for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef createExternalCoupledPatchGeometryTemplates_H
+#define createExternalCoupledPatchGeometryTemplates_H
+
+#include "word.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+    template<class Type>
+    void processField(bool& processed, const word& fieldName);
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#ifdef NoRepository
+#   include "createExternalCoupledPatchGeometryTemplates.C"
+#endif
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#endif
+
+// ************************************************************************* //

src/OpenFOAM/db/IOobjectList/IOobjectList.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
@@ -148,6 +148,27 @@ Foam::IOobject* Foam::IOobjectList::lookup(const word& name) const
 }
 
 
+Foam::IOobjectList Foam::IOobjectList::lookupRe(const wordRe& name) const
+{
+    IOobjectList objectsOfName(size());
+
+    forAllConstIter(HashPtrTable<IOobject>, *this, iter)
+    {
+        if (name.match(iter()->name()))
+        {
+            if (IOobject::debug)
+            {
+                Info<< "IOobjectList::lookupRe : found " << iter.key() << endl;
+            }
+
+            objectsOfName.insert(iter.key(), new IOobject(*iter()));
+        }
+    }
+
+    return objectsOfName;
+}
+
+
 Foam::IOobjectList Foam::IOobjectList::lookupClass(const word& ClassName) const
 {
     IOobjectList objectsOfClass(size());

src/OpenFOAM/db/IOobjectList/IOobjectList.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
@@ -44,7 +44,7 @@ namespace Foam
 {
 
 /*---------------------------------------------------------------------------*\
-                           Class IOobjectList Declaration
+                        Class IOobjectList Declaration
 \*---------------------------------------------------------------------------*/
 
 class IOobjectList
@@ -91,6 +91,9 @@ public:
         //- Lookup a given name and return IOobject ptr if found else NULL
         IOobject* lookup(const word& name) const;
 
+        //- Return the list for all IOobects whose name matches name
+        IOobjectList lookupRe(const wordRe& name) const;
+
         //- Return the list for all IOobjects of a given class
         IOobjectList lookupClass(const word& className) const;
 

src/OpenFOAM/db/objectRegistry/objectRegistry.H

@@ -163,6 +163,10 @@ public:
             template<class Type>
             HashTable<Type*> lookupClass(const bool strict = false);
 
+            //- Return the list of objects whose name matches the input regExp
+            template<class Type>
+            wordList foundObjectRe(const wordRe& name) const;
+
             //- Is the named Type found?
             template<class Type>
             bool foundObject(const word& name) const;

src/OpenFOAM/db/objectRegistry/objectRegistryTemplates.C

@@ -127,6 +127,31 @@ bool Foam::objectRegistry::foundObject(const word& name) const
 }
 
 
+template<class Type>
+Foam::wordList Foam::objectRegistry::foundObjectRe(const wordRe& name) const
+{
+    wordList objectNames(size());
+
+    label count = 0;
+    forAllConstIter(HashTable<regIOobject*>, *this, iter)
+    {
+        if (isA<Type>(*iter()))
+        {
+            const word& objectName = iter()->name();
+
+            if (name.match(objectName))
+            {
+                objectNames[count++] = objectName;
+            }
+        }
+    }
+
+    objectNames.setSize(count);
+
+    return objectNames;
+}
+
+
 template<class Type>
 const Type& Foam::objectRegistry::lookupObject(const word& name) const
 {

src/OpenFOAM/meshes/primitiveMesh/PatchTools/PatchTools.H

@@ -254,8 +254,8 @@ public:
     );
 
 
-    //- Gather points and faces onto master and merge (geometrically) into
-    //  single patch.
+    //- Gather points and faces onto master and merge into single patch.
+    //  Note: uses faces/points, not localFaces/localPoints.
     template
     <
         class Face,

src/OpenFOAM/meshes/primitiveMesh/PatchTools/PatchToolsGatherAndMerge.C

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2012 OpenFOAM Foundation
+    \\  /    A nd           | Copyright (C) 2012-2013 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -52,7 +52,8 @@ void Foam::PatchTools::gatherAndMerge
     labelList pointSizes;
     {
         List<Field<PointType> > gatheredPoints(Pstream::nProcs());
-        gatheredPoints[Pstream::myProcNo()] = p.localPoints();
+        gatheredPoints[Pstream::myProcNo()] = p.points();
+
         Pstream::gatherList(gatheredPoints);
 
         if (Pstream::master())
@@ -75,7 +76,7 @@ void Foam::PatchTools::gatherAndMerge
     // gathered points
     {
         List<List<Face> > gatheredFaces(Pstream::nProcs());