Merge remote branch 'opencfd/master' into olesenm

ReleaseNotes-dev

@@ -240,11 +240,14 @@
     + =snappyHexMesh=:
       + extrude across multi-processor boundaries
       + preserve faceZones during layering
+      + combining patch faces after snapping
       + *Warning*:
             - minMedianAxisAngle angle fixed w.r.t. 17x. Set to
               90 to get same behaviour as 130 in 17x.
             - nGrow did not work in 17x. Set to 0
               to get same behaviour as 130 in 17x.
+            - nSolveIter reinstated to smooth internal mesh. Set to 0
+              to get same behaviour at 17x.
             - new minTetQuality setting (see tracking). Disable for 17x
               compatibility.
 * Post-processing
@@ -309,3 +312,8 @@
 * Other
   + compilable with =clang=
     In your prefs.sh set the WM_COMPILER to Clang
+  + dlclose error: upon exit of e.g. paraFoam you can get the error
+    Inconsistency detected by ld.so: dl-close.c: 731: _dl_close: Assertion
+    `map->l_init_called' failed!
+    This seems to happen with a mix of system libraries and a thirdParty
+    compiler.

applications/solvers/basic/potentialFoam/createFields.H

@@ -47,4 +47,10 @@
 
     label pRefCell = 0;
     scalar pRefValue = 0.0;
-    setRefCell(p, mesh.solutionDict().subDict("SIMPLE"), pRefCell, pRefValue);
+    setRefCell
+    (
+        p,
+        potentialFlow,
+        pRefCell,
+        pRefValue
+    );

applications/solvers/basic/potentialFoam/potentialFoam.C

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2004-2010 OpenCFD Ltd.
+    \\  /    A nd           | Copyright (C) 2004-2011 OpenCFD Ltd.
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -42,8 +42,8 @@ int main(int argc, char *argv[])
     #include "setRootCase.H"
     #include "createTime.H"
     #include "createMesh.H"
+    #include "readControls.H"
     #include "createFields.H"
-    #include "readSIMPLEControls.H"
 
     // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 

applications/solvers/basic/potentialFoam/readControls.H

@@ -0,0 +1,6 @@
+    const dictionary& potentialFlow =
+        mesh.solutionDict().subDict("potentialFlow");
+
+    const int nNonOrthCorr =
+        potentialFlow.lookupOrDefault<int>("nNonOrthogonalCorrectors", 0);
+

applications/solvers/compressible/rhoPimpleFoam/rhoPorousMRFLTSPimpleFoam/setrDeltaT.H

@@ -19,7 +19,7 @@
         pimple.lookupOrDefault<scalar>("maxDeltaT", GREAT)
     );
 
-    volScalarField rDeltaT0 = rDeltaT;
+    volScalarField rDeltaT0("rDeltaT0", rDeltaT);
 
     // Set the reciprocal time-step from the local Courant number
     rDeltaT.dimensionedInternalField() = max

applications/solvers/compressible/rhoPimpleFoam/rhoPorousMRFPimpleFoam/UEqn.H

@@ -3,7 +3,7 @@
 tmp<fvVectorMatrix> UEqn
 (
     //pZones.ddt(rho, U)
-    fvc::ddt(rho, U)
+    fvm::ddt(rho, U)
   + fvm::div(phi, U)
   + turbulence->divDevRhoReff(U)
 );

applications/solvers/multiphase/interFoam/LTSInterFoam/setrDeltaT.H

@@ -49,7 +49,7 @@
         piso.lookupOrDefault<scalar>("maxDeltaT", GREAT)
     );
 
-    volScalarField rDeltaT0 = rDeltaT;
+    volScalarField rDeltaT0("rDeltaT0", rDeltaT);
 
     // Set the reciprocal time-step from the local Courant number
     rDeltaT.dimensionedInternalField() = max
@@ -64,7 +64,7 @@
         // Further limit the reciprocal time-step
         // in the vicinity of the interface
 
-        volScalarField alpha1Bar = fvc::average(alpha1);
+        volScalarField alpha1Bar(fvc::average(alpha1));
 
         rDeltaT.dimensionedInternalField() = max
         (

applications/solvers/multiphase/interFoam/porousInterFoam/UEqn.H

@@ -11,7 +11,7 @@
     fvVectorMatrix UEqn
     (
         //pZones.ddt(rho, U)
-        fvc::ddt(rho, U)
+        fvm::ddt(rho, U)
       + fvm::div(rhoPhi, U)
       - fvm::laplacian(muEff, U)
       - (fvc::grad(U) & fvc::grad(muEff))

applications/test/Hashing/hashingTests

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.6                                   |
+|  \\    /   O peration     | Version:  dev                                   |
 |   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

applications/test/dictionary/testDictRegex

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.6                                   |
+|  \\    /   O peration     | Version:  dev                                   |
 |   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

applications/test/regex/testRegexps

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.6                                   |
+|  \\    /   O peration     | Version:  dev                                   |
 |   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

applications/test/router/routerDict

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.6                                   |
+|  \\    /   O peration     | Version:  dev                                   |
 |   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

applications/test/spline/test-splines

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.6                                   |
+|  \\    /   O peration     | Version:  dev                                   |
 |   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

applications/test/wordRe/testRegexps

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.6                                   |
+|  \\    /   O peration     | Version:  dev                                   |
 |   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

applications/utilities/mesh/advanced/PDRMesh/PDRMeshDict

@@ -2,7 +2,7 @@
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
 |  \\    /   O peration     | Version:  dev                                   |
-|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/
 FoamFile

applications/utilities/mesh/advanced/autoRefineMesh/autoRefineMeshDict

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.6                                   |
+|  \\    /   O peration     | Version:  dev                                   |
 |   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

applications/utilities/mesh/advanced/modifyMesh/modifyMeshDict

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.6                                   |
+|  \\    /   O peration     | Version:  dev                                   |
 |   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

applications/utilities/mesh/advanced/selectCells/selectCells.C

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2004-2010 OpenCFD Ltd.
+    \\  /    A nd           | Copyright (C) 2004-2011 OpenCFD Ltd.
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -268,7 +268,7 @@ label selectOutsideCells
         // Find cell containing point. Linear search.
         label cellI = queryMesh.findCell(outsidePts[outsidePtI], -1, false);
 
-        if (cellType[cellI] == MESH)
+        if (cellI != -1 && cellType[cellI] == MESH)
         {
             Info<< "Marking cell " << cellI << " containing outside point "
                 << outsidePts[outsidePtI] << " with type " << cellType[cellI]
@@ -388,7 +388,8 @@ int main(int argc, char *argv[])
     {
         const point& outsidePoint = outsidePts[outsideI];
 
-        if (queryMesh.findCell(outsidePoint, -1, false) == -1)
+        label cellI = queryMesh.findCell(outsidePoint, -1, false);
+        if (returnReduce(cellI, maxOp<label>()) == -1)
         {
             FatalErrorIn(args.executable())
                 << "outsidePoint " << outsidePoint

applications/utilities/mesh/advanced/selectCells/selectCellsDict

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.6                                   |
+|  \\    /   O peration     | Version:  dev                                   |
 |   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

applications/utilities/mesh/conversion/sammToFoam/readPoints.C

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2004-2010 OpenCFD Ltd.
+    \\  /    A nd           | Copyright (C) 2004-2011 OpenCFD Ltd.
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License

applications/utilities/mesh/conversion/star3ToFoam/readPoints.C

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2004-2010 OpenCFD Ltd.
+    \\  /    A nd           | Copyright (C) 2004-2011 OpenCFD Ltd.
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -86,7 +86,6 @@ void starMesh::readPoints(const scalar scaleFactor)
         if (pointsFile.good())
         {
             label pointLabel;
-            scalar x, y, z;
 
             maxLabel = -1;
             while (pointsFile)
@@ -97,9 +96,9 @@ void starMesh::readPoints(const scalar scaleFactor)
 
                 maxLabel = max(maxLabel, pointLabel);
 
-                x = readVtxCmpt(pointsFile);
+                readVtxCmpt(pointsFile);
-                y = readVtxCmpt(pointsFile);
+                readVtxCmpt(pointsFile);
-                z = readVtxCmpt(pointsFile);
+                readVtxCmpt(pointsFile);
 
                 readToNl(pointsFile);
 

applications/utilities/mesh/conversion/writeMeshObj/writeMeshObj.C

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2004-2010 OpenCFD Ltd.
+    \\  /    A nd           | Copyright (C) 2004-2011 OpenCFD Ltd.
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -44,6 +44,7 @@ Description
 #include "meshTools.H"
 #include "cellSet.H"
 #include "faceSet.H"
+#include "SubField.H"
 
 using namespace Foam;
 

applications/utilities/mesh/generation/extrude/extrudeMesh/extrudeMeshDict

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.6                                   |
+|  \\    /   O peration     | Version:  dev                                   |
 |   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

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

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2004-2010 OpenCFD Ltd.
+    \\  /    A nd           | Copyright (C) 2004-2011 OpenCFD Ltd.
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -37,6 +37,7 @@ Description
 #include "autoLayerDriver.H"
 #include "searchableSurfaces.H"
 #include "refinementSurfaces.H"
+#include "refinementFeatures.H"
 #include "shellSurfaces.H"
 #include "decompositionMethod.H"
 #include "fvMeshDistribute.H"
@@ -250,6 +251,20 @@ int main(int argc, char *argv[])
         << mesh.time().cpuTimeIncrement() << " s" << nl << endl;
 
 
+    // Read feature meshes
+    // ~~~~~~~~~~~~~~~~~~~
+
+    Info<< "Reading features." << endl;
+    refinementFeatures features
+    (
+        mesh,
+        refineDict.lookup("features")
+    );
+    Info<< "Read features in = "
+        << mesh.time().cpuTimeIncrement() << " s" << nl << endl;
+
+
+
     // Refinement engine
     // ~~~~~~~~~~~~~~~~~
 
@@ -265,6 +280,7 @@ int main(int argc, char *argv[])
         mergeDist,          // tolerance used in sorting coordinates
         overwrite,          // overwrite mesh files?
         surfaces,           // for surface intersection refinement
+        features,           // for feature edges/point based refinement
         shells              // for volume (inside/outside) refinement
     );
     Info<< "Calculated surface intersections in = "
@@ -429,13 +445,19 @@ int main(int argc, char *argv[])
 
         // Snap parameters
         snapParameters snapParams(snapDict);
+        // Temporary hack to get access to resolveFeatureAngle
+        scalar curvature;
+        {
+            refinementParameters refineParams(refineDict);
+            curvature = refineParams.curvature();
+        }
 
         if (!overwrite)
         {
             const_cast<Time&>(mesh.time())++;
         }
 
-        snapDriver.doSnap(snapDict, motionDict, snapParams);
+        snapDriver.doSnap(snapDict, motionDict, curvature, snapParams);
 
         writeMesh
         (

applications/utilities/mesh/generation/snappyHexMesh/snappyHexMeshDict

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.7.1                                 |
+|  \\    /   O peration     | Version:  dev                                   |
 |   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/
@@ -217,10 +217,10 @@ snapControls
     //  to surface
     nSmoothPatch 3;
 
-    //- Relative distance for points to be attracted by surface feature point
+    //- Maximum relative distance for points to be attracted by surface.
-    //  or edge. True distance is this factor times local
+    //  True distance is this factor times local maximum edge length.
-    //  maximum edge length.
+    // Note: changed(corrected) w.r.t 17x! (17x used 2* tolerance)
-    tolerance 4.0;
+    tolerance 2.0;
 
     //- Number of mesh displacement relaxation iterations.
     nSolveIter 30;

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

@@ -179,7 +179,7 @@ Foam::label Foam::checkTopology
         if (nTwoCells > 0)
         {
             Info<< "  <<Writing " << nTwoCells
-                << " cells with with single non-boundary face to set "
+                << " cells with with two non-boundary faces to set "
                 << twoCells.name()
                 << endl;
             twoCells.instance() = mesh.pointsInstance();

applications/utilities/mesh/manipulation/createPatch/createPatchDict

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.6                                   |
+|  \\    /   O peration     | Version:  dev                                   |
 |   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

applications/utilities/mesh/manipulation/mirrorMesh/mirrorMeshDict

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.6                                   |
+|  \\    /   O peration     | Version:  dev                                   |
 |   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

applications/utilities/mesh/manipulation/refineMesh/refineMesh.C

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2004-2010 OpenCFD Ltd.
+    \\  /    A nd           | Copyright (C) 2004-2011 OpenCFD Ltd.
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -44,6 +44,7 @@ Description
 #include "labelIOList.H"
 #include "wedgePolyPatch.H"
 #include "plane.H"
+#include "SubField.H"
 
 using namespace Foam;
 

applications/utilities/mesh/manipulation/refineMesh/refineMeshDict

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.6                                   |
+|  \\    /   O peration     | Version:  dev                                   |
 |   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

applications/utilities/mesh/manipulation/topoSet/topoSetDict

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.6                                   |
+|  \\    /   O peration     | Version:  dev                                   |
 |   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

applications/utilities/miscellaneous/foamDebugSwitches/Make/options

@@ -33,7 +33,6 @@ EXE_LIBS = \
     -linterfaceProperties \
     -lIOFunctionObjects \
     -ljobControl \
-    -lkineticTheoryModel \
     -llagrangian \
     -llagrangianIntermediate \
     -llaminarFlameSpeedModels \

applications/utilities/miscellaneous/foamFormatConvert/foamFormatConvert.C

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2004-2010 OpenCFD Ltd.
+    \\  /    A nd           | Copyright (C) 2004-2011 OpenCFD Ltd.
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -148,6 +148,11 @@ int main(int argc, char *argv[])
 #   include "setRootCase.H"
 #   include "createTime.H"
 
+    // Make sure we do not use the master-only reading since we read
+    // fields (different per processor) as dictionaries.
+    regIOobject::fileModificationChecking = regIOobject::timeStamp;
+
+
     fileName meshDir = polyMesh::meshSubDir;
     fileName regionPrefix = "";
     word regionName = polyMesh::defaultRegion;

applications/utilities/parallelProcessing/decomposePar/decomposeParDict

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.6                                   |
+|  \\    /   O peration     | Version:  dev                                   |
 |   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

applications/utilities/postProcessing/dataConversion/foamDataToFluent/foamDataToFluentDict

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.6                                   |
+|  \\    /   O peration     | Version:  dev                                   |
 |   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

applications/utilities/postProcessing/dataConversion/foamToFieldview9/foamToFieldview9.C

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2004-2010 OpenCFD Ltd.
+    \\  /    A nd           | Copyright (C) 2004-2011 OpenCFD Ltd.
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -183,12 +183,14 @@ int main(int argc, char *argv[])
     );
     timeSelector::addOptions(true, false);
 
+#   include "addRegionOption.H"
+
 #   include "setRootCase.H"
 #   include "createTime.H"
 
     instantList timeDirs = timeSelector::select0(runTime, args);
 
-#   include "createMesh.H"
+#   include "createNamedMesh.H"
 
     // Initialize name mapping table
     FieldviewNames.insert("alpha", "aalpha");
@@ -260,10 +262,23 @@ int main(int argc, char *argv[])
     // make a directory called FieldView in the case
     fileName fvPath(runTime.path()/"Fieldview");
 
+    if (regionName != polyMesh::defaultRegion)
+    {
+        fvPath = fvPath/regionName;
+    }
+
     if (isDir(fvPath))
     {
+        if (regionName != polyMesh::defaultRegion)
+        {
+            Info<< "Keeping old FieldView files in " << fvPath << nl << endl;
+        }
+        else
+        {
+            Info<< "Deleting old FieldView files in " << fvPath << nl << endl;
             rmDir(fvPath);
         }
+    }
 
     mkDir(fvPath);
 

applications/utilities/postProcessing/graphics/PV3Readers/PV3FoamReader/vtkPV3Foam/vtkPV3FoamMeshVolume.C

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2004-2010 OpenCFD Ltd.
+    \\  /    A nd           | Copyright (C) 2004-2011 OpenCFD Ltd.
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -383,16 +383,12 @@ vtkUnstructuredGrid* Foam::vtkPV3Foam::volumeVTKMesh
 
                 forAll(quadFcs, quadI)
                 {
-                    label thisCellI;
-
                     if (substituteCell)
                     {
-                        thisCellI = cellI;
                         substituteCell = false;
                     }
                     else
                     {
-                        thisCellI = mesh.nCells() + addCellI;
                         superCells[addCellI++] = cellI;
                     }
 
@@ -430,16 +426,12 @@ vtkUnstructuredGrid* Foam::vtkPV3Foam::volumeVTKMesh
 
                 forAll(triFcs, triI)
                 {
-                    label thisCellI;
-
                     if (substituteCell)
                     {
-                        thisCellI = cellI;
                         substituteCell = false;
                     }
                     else
                     {
-                        thisCellI = mesh.nCells() + addCellI;
                         superCells[addCellI++] = cellI;
                     }
 

applications/utilities/postProcessing/lagrangian/particleTracks/particleTrackProperties

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.6                                   |
+|  \\    /   O peration     | Version:  dev                                   |
 |   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

applications/utilities/postProcessing/lagrangian/steadyParticleTracks/particleTrackDict

@@ -2,7 +2,7 @@
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
 |  \\    /   O peration     | Version:  dev                                   |
-|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
+|   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/
 FoamFile

applications/utilities/postProcessing/miscellaneous/pdfPlot/pdfDict

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.6                                   |
+|  \\    /   O peration     | Version:  dev                                   |
 |   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

applications/utilities/postProcessing/miscellaneous/postChannel/postChannelDict

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.6                                   |
+|  \\    /   O peration     | Version:  dev                                   |
 |   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

applications/utilities/postProcessing/sampling/probeLocations/probesDict

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.6                                   |
+|  \\    /   O peration     | Version:  dev                                   |
 |   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

applications/utilities/postProcessing/sampling/sample/sampleDict

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.7.1                                 |
+|  \\    /   O peration     | Version:  dev                                   |
 |   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/
@@ -150,29 +150,29 @@ surfaces
         interpolate     true;
     }
 
-    movingWall_constant
+    walls_constant
     {
         type            patch;
-        patchName       movingWall;
+        patches         ( ".*Wall.*" );
         // Optional: whether to leave as faces (=default) or triangulate
         // triangulate     false;
     }
 
-    movingWall_interpolated
+    walls_interpolated
     {
         type            patch;
-        patchName       movingWall;
+        patches         ( ".*Wall.*" );
         interpolate     true;
         // Optional: whether to leave as faces (=default) or triangulate
         // triangulate     false;
     }
 
-    movingNearWall_interpolated
+    nearWalls_interpolated
     {
         // Sample cell values off patch. Does not need to be the near-wall
         // cell, can be arbitrarily far away.
         type            patchInternalField;
-        patchName       movingWall;
+        patches         ( ".*Wall.*" );
         distance        0.0001;
         interpolate     true;
         // Optional: whether to leave as faces (=default) or triangulate

applications/utilities/preProcessing/changeDictionary/changeDictionary.C

@@ -305,6 +305,11 @@ int main(int argc, char *argv[])
         instance = args.options()["instance"];
     }
 
+    // Make sure we do not use the master-only reading since we read
+    // fields (different per processor) as dictionaries.
+    regIOobject::fileModificationChecking = regIOobject::timeStamp;
+
+
     // Get the replacement rules from a dictionary
     IOdictionary dict
     (

applications/utilities/preProcessing/changeDictionary/changeDictionaryDict

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.6                                   |
+|  \\    /   O peration     | Version:  dev                                   |
 |   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

applications/utilities/preProcessing/foamUpgradeCyclics/foamUpgradeCyclics.C

@@ -405,6 +405,12 @@ int main(int argc, char *argv[])
 #   include "setRootCase.H"
 #   include "createTime.H"
 
+
+    // Make sure we do not use the master-only reading since we read
+    // fields (different per processor) as dictionaries.
+    regIOobject::fileModificationChecking = regIOobject::timeStamp;
+
+
     instantList timeDirs = timeSelector::select0(runTime, args);
 
     const bool isTestRun = args.optionFound("test");

applications/utilities/preProcessing/mapFields/mapFieldsDict

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.6                                   |
+|  \\    /   O peration     | Version:  dev                                   |
 |   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

applications/utilities/preProcessing/setFields/setFieldsDict

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.6                                   |
+|  \\    /   O peration     | Version:  dev                                   |
 |   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

applications/utilities/preProcessing/wallFunctionTable/wallFunctionDict

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.6                                   |
+|  \\    /   O peration     | Version:  dev                                   |
 |   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

applications/utilities/surface/surfaceFeatureExtract/surfaceFeatureExtract.C

@@ -40,6 +40,7 @@ Description
 #include "treeBoundBox.H"
 #include "meshTools.H"
 #include "OFstream.H"
+#include "unitConversion.H"
 
 using namespace Foam;
 
@@ -90,6 +91,55 @@ void deleteBox
 }
 
 
+// Unmark non-manifold edges if individual triangles are not features
+void unmarkBaffles
+(
+    const triSurface& surf,
+    const scalar includedAngle,
+    List<surfaceFeatures::edgeStatus>& edgeStat
+)
+{
+    scalar minCos = Foam::cos(degToRad(180.0 - includedAngle));
+
+    const labelListList& edgeFaces = surf.edgeFaces();
+
+    forAll(edgeFaces, edgeI)
+    {
+        const labelList& eFaces = edgeFaces[edgeI];
+
+        if (eFaces.size() > 2)
+        {
+            label i0 = eFaces[0];
+            //const labelledTri& f0 = surf[i0];
+            const vector& n0 = surf.faceNormals()[i0];
+
+            //Pout<< "edge:" << edgeI << " n0:" << n0 << endl;
+
+            bool same = true;
+
+            for (label i = 1; i < eFaces.size(); i++)
+            {
+                //const labelledTri& f = surf[i];
+                const vector& n = surf.faceNormals()[eFaces[i]];
+
+                //Pout<< "    mag(n&n0): " << mag(n&n0) << endl;
+
+                if (mag(n&n0) < minCos)
+                {
+                    same = false;
+                    break;
+                }
+            }
+
+            if (same)
+            {
+                edgeStat[edgeI] = surfaceFeatures::NONE;
+            }
+        }
+    }
+}
+
+
 // Main program:
 
 int main(int argc, char *argv[])
@@ -138,6 +188,11 @@ int main(int argc, char *argv[])
         "((x0 y0 z0)(x1 y1 z1))",
         "remove edges within specified bounding box"
     );
+    argList::addBoolOption
+    (
+        "writeObj",
+        "write extendedFeatureEdgeMesh obj files"
+    );
 
 #   include "setRootCase.H"
 #   include "createTime.H"
@@ -145,6 +200,7 @@ int main(int argc, char *argv[])
     Info<< "Feature line extraction is only valid on closed manifold surfaces."
         << endl;
 
+    bool writeObj = args.optionFound("writeObj");
 
     const fileName surfFileName = args[1];
     const fileName outFileName  = args[2];
@@ -153,6 +209,8 @@ int main(int argc, char *argv[])
         << "Output feature set : " << outFileName << nl
         << endl;
 
+    fileName sFeatFileName = surfFileName.lessExt().name();
+
 
     // Read
     // ~~~~
@@ -164,7 +222,6 @@ int main(int argc, char *argv[])
     Info<< endl;
 
 
-
     // Either construct features from surface&featureangle or read set.
     // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -187,9 +244,9 @@ int main(int argc, char *argv[])
 
         set = surfaceFeatures(surf, includedAngle);
 
-        Info<< nl << "Writing initial features" << endl;
+        // Info<< nl << "Writing initial features" << endl;
-        set.write("initial.fSet");
+        // set.write("initial.fSet");
-        set.writeObj("initial");
+        // set.writeObj("initial");
     }
     else
     {
@@ -200,7 +257,6 @@ int main(int argc, char *argv[])
             << exit(FatalError);
     }
 
-
     Info<< nl
         << "Initial feature set:" << nl
         << "    feature points : " << set.featurePoints().size() << nl
@@ -284,8 +340,8 @@ int main(int argc, char *argv[])
     Info<< endl << "Writing trimmed features to " << outFileName << endl;
     newSet.write(outFileName);
 
-    Info<< endl << "Writing edge objs." << endl;
+    // Info<< endl << "Writing edge objs." << endl;
-    newSet.writeObj("final");
+    // newSet.writeObj("final");
 
     Info<< nl
         << "Final feature set:" << nl
@@ -297,20 +353,22 @@ int main(int argc, char *argv[])
         << "        internal edges : " << newSet.nInternalEdges() << nl
         << endl;
 
-    // Extracting and writing a featureEdgeMesh
+    // Extracting and writing a extendedFeatureEdgeMesh
 
     extendedFeatureEdgeMesh feMesh
     (
         newSet,
         runTime,
-        surfFileName.lessExt().name() + ".featureEdgeMesh"
+        sFeatFileName + ".extendedFeatureEdgeMesh"
     );
 
     Info<< nl << "Writing extendedFeatureEdgeMesh to " << feMesh.objectPath()
         << endl;
 
-
+    if (writeObj)
+    {
         feMesh.writeObj(surfFileName.lessExt().name());
+    }
 
     feMesh.write();
 

applications/utilities/surface/surfaceMeshConvert/coordinateSystems

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.6                                   |
+|  \\    /   O peration     | Version:  dev                                   |
 |   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

applications/utilities/surface/surfaceSubset/surfaceSubsetDict

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.6                                   |
+|  \\    /   O peration     | Version:  dev                                   |
 |   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

applications/utilities/thermophysical/adiabaticFlameT/Hydrogen.log

@@ -1,7 +1,7 @@
 /*---------------------------------------------------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.6                                   |
+|  \\    /   O peration     | Version:  dev                                   |
 |   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

applications/utilities/thermophysical/adiabaticFlameT/Methane.log

@@ -1,7 +1,7 @@
 /*---------------------------------------------------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.6                                   |
+|  \\    /   O peration     | Version:  dev                                   |
 |   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

applications/utilities/thermophysical/adiabaticFlameT/Propane.log

@@ -1,7 +1,7 @@
 /*---------------------------------------------------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.6                                   |
+|  \\    /   O peration     | Version:  dev                                   |
 |   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

applications/utilities/thermophysical/adiabaticFlameT/controlDict

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.6                                   |
+|  \\    /   O peration     | Version:  dev                                   |
 |   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

applications/utilities/thermophysical/equilibriumFlameT/Hydrogen.log

@@ -1,7 +1,7 @@
 /*---------------------------------------------------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.6                                   |
+|  \\    /   O peration     | Version:  dev                                   |
 |   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

applications/utilities/thermophysical/equilibriumFlameT/controlDict

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.6                                   |
+|  \\    /   O peration     | Version:  dev                                   |
 |   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

bin/tools/CleanFunctions

@@ -95,6 +95,7 @@ cleanCase()
         > /dev/null 2>&1 \
     )
     rm -rf VTK > /dev/null 2>&1
+    rm -f 0/cellLevel 0/pointLevel
 
     if [ -e constant/polyMesh/blockMeshDict.m4 ]
     then

bin/tools/pre-commit-hook

@@ -39,7 +39,6 @@
 #
 #     Checks for
 #     - illegal code, e.g. <TAB>
-#     - copyright is current, e.g. if present, contains XXX-<current-year>
 #     - columns greater than 80 for *.[CH] files
 #
 # Note
@@ -138,8 +137,8 @@ checkIllegalCode()
 {
     echo "$hookName: check bad strings/characters etc ..." 1>&2
 
-    reBad="(N""abla|"$'\t'")"
+    reBad="("$'\t'")"
-    msgBad="N""abla or <TAB>"
+    msgBad="<TAB>"
 
     scope=$(gitScope $@)
 
@@ -167,40 +166,6 @@ checkIllegalCode()
 }
 
 
-#
-# check that OpenCFD copyright is current
-#
-checkCopyright()
-{
-    year=$(date +%Y)
-    echo "$hookName: check copyright ..." 1>&2
-
-    scope=$(gitScope $@)
-
-    badFiles=$(
-    for f in $fileList
-    do
-        # NB: need to have OpenCFD on a separate line to prevent
-        #     this check being caught by itself!
-        #
-        # parse line numbers from grep output:
-        #        <lineNr>:   contents
-        #
-        lines=$(git grep -F -hn -e Copyright \
-            --and -e OpenCFD \
-            --and --not -e "$year" \
-            $scope"$f" |
-            sed -e 's@:.*@@' |
-            tr '\n' ' '
-        )
-        [ -n "$lines" ] && echo "$Indent$f -- lines: $lines"
-    done
-    )
-
-    dieOnBadFiles "Update copyright year, e.g. XXXX-$year"
-}
-
-
 #
 # limit line length to 80-columns
 #
@@ -308,9 +273,6 @@ bad=$(git diff-index --cached --check $against --) || die "$bad"
 # check for illegal code, e.g. <TAB>, etc
 checkIllegalCode
 
-# ensure OpenCFD copyright contains correct year
-checkCopyright
-
 # ensure code conforms to 80 columns max
 checkLineLengthNonDirective
 

bin/tools/pre-receive-hook

@@ -39,7 +39,6 @@
 #
 #     Checks for
 #     - illegal code, e.g. <TAB>
-#     - copyright is current, e.g. if present, contains XXX-<current-year>
 #     - columns greater than 80 for *.[CH] files
 #
 #------------------------------------------------------------------------------
@@ -101,8 +100,8 @@ checkIllegalCode()
 {
     echo "$hookName: check bad strings/characters etc ..." 1>&2
 
-    reBad="(N""abla|"$'\t'"|"$'\r\n'")"
+    reBad="("$'\t'"|"$'\r\n'")"
-    msgBad="N""abla, <TAB> or DOS-line-endings"
+    msgBad="<TAB> or DOS-line-endings"
 
     scope=$(gitScope $@)
 
@@ -130,40 +129,6 @@ checkIllegalCode()
 }
 
 
-#
-# check that OpenCFD copyright is current
-#
-checkCopyright()
-{
-    year=$(date +%Y)
-    echo "$hookName: check copyright ..." 1>&2
-
-    scope=$(gitScope $@)
-
-    badFiles=$(
-    for f in $fileList
-    do
-        # NB: need to have OpenCFD on a separate line to prevent
-        #     this check being caught by itself!
-        #
-        # parse line numbers from grep output:
-        #        <lineNr>:   contents
-        #
-        lines=$(git grep -F -hn -e Copyright \
-            --and -e OpenCFD \
-            --and --not -e "$year" \
-            $scope"$f" |
-            sed -e 's@:.*@@' |
-            tr '\n' ' '
-        )
-        [ -n "$lines" ] && echo "$Indent$f -- lines: $lines"
-    done
-    )
-
-    dieOnBadFiles "Update copyright year, e.g. XXXX-$year"
-}
-
-
 #
 # limit line length to 80-columns
 #
@@ -297,9 +262,6 @@ do
     # check for illegal code, e.g. <TAB>, etc
     checkIllegalCode $newSHA1
 
-    # ensure OpenCFD copyright contains correct year
-    checkCopyright $newSHA1
-
     # ensure code conforms to 80 columns max
     checkLineLengthNonDirective $newSHA1
 

etc/cellModels

@@ -1,7 +1,7 @@
 /*--------------------------------*- C++ -*----------------------------------*\
 | =========                 |                                                 |
 | \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.7                                   |
+|  \\    /   O peration     | Version:  dev                                   |
 |   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
 |    \\/     M anipulation  |                                                 |
 \*---------------------------------------------------------------------------*/

etc/settings.csh

@@ -388,6 +388,10 @@ case SYSTEMOPENMPI:
     setenv PLIBS "`mpicc --showme:link`"
     set libDir=`echo "$PLIBS" | sed -e 's/.*-L\([^ ]*\).*/\1/'`
 
+    # Bit of a hack: strip off 'lib' and hope this is the path to openmpi
+    # include files and libraries.
+    setenv MPI_ARCH_PATH "${libDir:h}"
+
     if ($?FOAM_VERBOSE && $?prompt) then
         echo "Using system installed MPI:"
         echo "    compile flags : $PINC"

etc/settings.sh

@@ -408,6 +408,10 @@ SYSTEMOPENMPI)
     export PLIBS="`mpicc --showme:link`"
     libDir=`echo "$PLIBS" | sed -e 's/.*-L\([^ ]*\).*/\1/'`
 
+    # Bit of a hack: strip off 'lib' and hope this is the path to openmpi
+    # include files and libraries.
+    export MPI_ARCH_PATH="${libDir%/*}"
+
     if [ "$FOAM_VERBOSE" -a "$PS1" ]
     then
         echo "Using system installed MPI:"

src/OpenFOAM/algorithms/indexedOctree/treeDataCell.C

@@ -126,7 +126,7 @@ Foam::treeDataCell::treeDataCell
 
 // * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
 
-Foam::pointField Foam::treeDataCell::points() const
+Foam::pointField Foam::treeDataCell::shapePoints() const
 {
     pointField cc(cellLabels_.size());
 

src/OpenFOAM/algorithms/indexedOctree/treeDataCell.H

@@ -125,7 +125,7 @@ public:
 
             //- Get representative point cloud for all shapes inside
             //  (one point per shape)
-            pointField points() const;
+            pointField shapePoints() const;
 
 
         // Search

src/OpenFOAM/containers/Lists/PackedList/PackedBoolList.C

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2010-2010 OpenCFD Ltd.
+    \\  /    A nd           | Copyright (C) 2010-2011 OpenCFD Ltd.
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -287,7 +287,7 @@ Foam::Xfer<Foam::labelList> Foam::PackedBoolList::used() const
 // * * * * * * * * * * * * * * Member Operators  * * * * * * * * * * * * * * //
 
 Foam::PackedBoolList&
-Foam::PackedBoolList::operator=(const UList<bool>& lst)
+Foam::PackedBoolList::operator=(const Foam::UList<bool>& lst)
 {
     this->setSize(lst.size());
 

src/OpenFOAM/containers/Lists/PackedList/PackedBoolList.H

@@ -115,7 +115,7 @@ public:
         inline PackedBoolList(const Xfer<PackedList<1> >&);
 
         //- Construct from a list of bools
-        explicit inline PackedBoolList(const UList<bool>&);
+        explicit inline PackedBoolList(const Foam::UList<bool>&);
 
         //- Construct from a list of labels
         //  using the labels as indices to indicate which bits are set

src/OpenFOAM/containers/Lists/PackedList/PackedBoolListI.H

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2010-2010 OpenCFD Ltd.
+    \\  /    A nd           | Copyright (C) 2010-2011 OpenCFD Ltd.
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -73,7 +73,7 @@ inline Foam::PackedBoolList::PackedBoolList(const Xfer<PackedList<1> >& lst)
 {}
 
 
-inline Foam::PackedBoolList::PackedBoolList(const UList<bool>& lst)
+inline Foam::PackedBoolList::PackedBoolList(const Foam::UList<bool>& lst)
 :
     PackedList<1>()
 {

src/OpenFOAM/db/IOobjects/CompactIOField/CompactIOField.H

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2010-2010 OpenCFD Ltd.
+    \\  /    A nd           | Copyright (C) 2010-2011 OpenCFD Ltd.
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -47,9 +47,6 @@ SourceFiles
 namespace Foam
 {
 
-class Istream;
-class Ostream;
-
 // Forward declaration of friend functions and operators
 template<class T, class BaseType> class CompactIOField;
 
@@ -58,6 +55,7 @@ template<class T, class BaseType> Istream& operator>>
     Istream&,
     CompactIOField<T, BaseType>&
 );
+
 template<class T, class BaseType> Ostream& operator<<
 (
     Ostream&,
@@ -122,23 +120,6 @@ public:
         void operator=(const CompactIOField<T, BaseType>&);
 
         void operator=(const Field<T>&);
-
-
-    // IOstream operators
-
-        //- Read Field from Istream, discarding contents of existing Field.
-        friend Istream& operator>> <T, BaseType>
-        (
-            Istream&,
-            CompactIOField<T, BaseType>&
-        );
-
-        // Write Field to Ostream.
-        friend Ostream& operator<< <T, BaseType>
-        (
-            Ostream&,
-            const CompactIOField<T, BaseType>&
-        );
 };
 
 

src/OpenFOAM/db/IOobjects/IOdictionary/IOdictionary.C

@@ -124,16 +124,14 @@ Foam::IOdictionary::IOdictionary(const IOobject& io)
     regIOobject(io)
 {
     // Temporary warning
-    if (io.readOpt() == IOobject::MUST_READ)
+    if (debug && io.readOpt() == IOobject::MUST_READ)
     {
         WarningIn("IOdictionary::IOdictionary(const IOobject&)")
-        //FatalErrorIn("IOdictionary::IOdictionary(const IOobject&)")
             << "Dictionary " << name()
             << " constructed with IOobject::MUST_READ"
             " instead of IOobject::MUST_READ_IF_MODIFIED." << nl
             << "Use MUST_READ_IF_MODIFIED if you need automatic rereading."
             << endl;
-            //<< abort(FatalError);
     }
 
     // Everyone check or just master
@@ -182,7 +180,7 @@ Foam::IOdictionary::IOdictionary(const IOobject& io, const dictionary& dict)
     regIOobject(io)
 {
     // Temporary warning
-    if (io.readOpt() == IOobject::MUST_READ)
+    if (debug && io.readOpt() == IOobject::MUST_READ)
     {
         WarningIn
         (

src/OpenFOAM/db/Time/TimeIO.C

@@ -168,6 +168,12 @@ void Foam::Time::readDict()
 
         Pout.precision(IOstream::defaultPrecision());
         Perr.precision(IOstream::defaultPrecision());
+
+        FatalError().precision(IOstream::defaultPrecision());
+        FatalIOError.error::operator()().precision
+        (
+            IOstream::defaultPrecision()
+        );
     }
 
     if (controlDict_.found("writeCompression"))

src/OpenFOAM/db/dynamicLibrary/dlLibraryTable/dlLibraryTable.C

@@ -55,6 +55,10 @@ Foam::dlLibraryTable::~dlLibraryTable()
 {
     forAllConstIter(dlLibraryTable, *this, iter)
     {
+        // bug in dlclose - does not call static destructors of
+        // loaded library when actually unloading the library.
+        // See https://bugzilla.novell.com/show_bug.cgi?id=680125 and 657627.
+        // Seems related to using a non-system compiler!
         dlClose(iter.key());
     }
 }

src/OpenFOAM/fields/Fields/DynamicField/DynamicField.H

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2009-2010 OpenCFD Ltd.
+    \\  /    A nd           | Copyright (C) 2009-2011 OpenCFD Ltd.
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -55,6 +55,7 @@ Ostream& operator<<
     Ostream&,
     const DynamicField<T, SizeInc, SizeMult, SizeDiv>&
 );
+
 template<class T, unsigned SizeInc, unsigned SizeMult, unsigned SizeDiv>
 Istream& operator>>
 (
@@ -234,23 +235,6 @@ public:
 
             //- Assignment from UList
             inline void operator=(const UList<T>&);
-
-
-        // IOstream operators
-
-            // Write DynamicField to Ostream.
-            friend Ostream& operator<< <T, SizeInc, SizeMult, SizeDiv>
-            (
-                Ostream&,
-                const DynamicField<T, SizeInc, SizeMult, SizeDiv>&
-            );
-
-            //- Read from Istream, discarding contents of existing DynamicField.
-            friend Istream& operator>> <T, SizeInc, SizeMult, SizeDiv>
-            (
-                Istream&,
-                DynamicField<T, SizeInc, SizeMult, SizeDiv>&
-            );
 };
 
 

src/OpenFOAM/include/checkTimeOptions.H

@@ -2,11 +2,11 @@
 // checkTimeOptions.H
 // ~~~~~~~~~~~~~~~~~~
 
-    Foam::label startTime = 0;
+Foam::label startTime = 0;
-    Foam::label endTime = Times.size();
+Foam::label endTime = Times.size();
 
 // unless -constant is present, skip startTime if it is "constant"
-#   include "checkConstantOption.H"
+#include "checkConstantOption.H"
 
 // check -time and -latestTime options
-#   include "checkTimeOption.H"
+#include "checkTimeOption.H"

src/OpenFOAM/meshes/polyMesh/polyMesh.C

@@ -34,6 +34,9 @@ License
 #include "OSspecific.H"
 #include "demandDrivenData.H"
 #include "polyMeshTetDecomposition.H"
+#include "indexedOctree.H"
+#include "treeDataCell.H"
+#include "SubField.H"
 
 #include "pointMesh.H"
 

src/OpenFOAM/meshes/polyMesh/polyMeshTetDecomposition/polyMeshTetDecomposition.C

@@ -55,6 +55,8 @@ Foam::label Foam::polyMeshTetDecomposition::findSharedBasePoint
 
     const point& oCc = pC[oCI];
 
+    List<scalar> tetQualities(2, 0.0);
+
     forAll(f, faceBasePtI)
     {
         scalar thisBaseMinTetQuality = VGREAT;
@@ -66,8 +68,6 @@ Foam::label Foam::polyMeshTetDecomposition::findSharedBasePoint
             label facePtI = (tetPtI + faceBasePtI) % f.size();
             label otherFacePtI = f.fcIndex(facePtI);
 
-            List<scalar> tetQualities(2, 0.0);
-
             {
                 // owner cell tet
                 label ptAI = f[facePtI];

src/OpenFOAM/meshes/polyMesh/polyPatches/constraint/cyclic/cyclicPolyPatch.C

@@ -35,6 +35,7 @@ License
 #include "Time.H"
 #include "diagTensor.H"
 #include "transformField.H"
+#include "SubField.H"
 
 // * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
 

src/OpenFOAM/meshes/polyMesh/syncTools/syncToolsTemplates.C

@@ -31,6 +31,7 @@ License
 #include "contiguous.H"
 #include "transform.H"
 #include "transformList.H"
+#include "SubField.H"
 
 // * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //
 

src/OpenFOAM/meshes/primitiveMesh/primitiveMesh.C

@@ -25,6 +25,8 @@ License
 
 #include "primitiveMesh.H"
 #include "demandDrivenData.H"
+#include "indexedOctree.H"
+#include "treeDataCell.H"
 
 // * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
 

src/OpenFOAM/meshes/primitiveMesh/primitiveMesh.H

@@ -56,8 +56,6 @@ SourceFiles
 #include "DynamicList.H"
 #include "edgeList.H"
 #include "pointField.H"
-#include "SubField.H"
-#include "SubList.H"
 #include "faceList.H"
 #include "cellList.H"
 #include "cellShapeList.H"
@@ -65,16 +63,16 @@ SourceFiles
 #include "boolList.H"
 #include "HashSet.H"
 #include "Map.H"
-#include "EdgeMap.H"
-#include "boundBox.H"
-#include "indexedOctree.H"
-#include "treeDataCell.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
 namespace Foam
 {
 
+// Forward declaration of classes
+class treeDataCell;
+template<class Type> class indexedOctree;
+
 /*---------------------------------------------------------------------------*\
                       Class primitiveMesh Declaration
 \*---------------------------------------------------------------------------*/

src/OpenFOAM/meshes/primitiveMesh/primitiveMeshCheck/primitiveMeshCheck.C

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2004-2010 OpenCFD Ltd.
+    \\  /    A nd           | Copyright (C) 2004-2011 OpenCFD Ltd.
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -29,7 +29,7 @@ License
 #include "ListOps.H"
 #include "unitConversion.H"
 #include "SortableList.H"
-
+#include "EdgeMap.H"
 
 // * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
 

src/OpenFOAM/meshes/primitiveMesh/primitiveMeshClear.C

@@ -24,8 +24,11 @@ License
 \*---------------------------------------------------------------------------*/
 
 #include "primitiveMesh.H"
+#include "indexedOctree.H"
+#include "treeDataCell.H"
 #include "demandDrivenData.H"
-
+#include "indexedOctree.H"
+#include "treeDataCell.H"
 
 // * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
 

src/OpenFOAM/meshes/primitiveMesh/primitiveMeshFindCell.C

@@ -25,6 +25,7 @@ License
 
 #include "primitiveMesh.H"
 #include "cell.H"
+#include "boundBox.H"
 
 // * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
 

src/engine/ignition/ignitionSite.C

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2004-2010 OpenCFD Ltd.
+    \\  /    A nd           | Copyright (C) 2004-2011 OpenCFD Ltd.
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -51,7 +51,6 @@ void Foam::ignitionSite::findIgnitionCells(const fvMesh& mesh)
     cellVolumes_[0] = vols[ignCell];
 
     scalar minDist = GREAT;
-    label nearestCell = 0;
     label nIgnCells = 1;
 
     forAll(centres, celli)
@@ -60,7 +59,6 @@ void Foam::ignitionSite::findIgnitionCells(const fvMesh& mesh)
 
         if (dist < minDist)
         {
-            nearestCell = celli;
             minDist = dist;
         }
 

src/finiteVolume/interpolation/surfaceInterpolation/schemes/pointLinear/pointLinear.C

@@ -39,8 +39,10 @@ correction
 {
     const fvMesh& mesh = this->mesh();
 
-    GeometricField<Type, pointPatchField, pointMesh> pvf =
+    GeometricField<Type, pointPatchField, pointMesh> pvf
-        volPointInterpolation::New(mesh).interpolate(vf);
+    (
+        volPointInterpolation::New(mesh).interpolate(vf)
+    );
 
     tmp<GeometricField<Type, fvsPatchField, surfaceMesh> > tsfCorr =
         linearInterpolate(vf);

src/lagrangian/basic/InteractionLists/InteractionLists.C

@@ -654,8 +654,6 @@ void Foam::InteractionLists<ParticleType>::findExtendedProcBbsInRange
     {
         List<label> permutationIndices(nTrans, 0);
 
-        vector s = vector::zero;
-
         if (nTrans == 0 && procI != Pstream::myProcNo())
         {
             treeBoundBox extendedReferredProcBb = allExtendedProcBbs[procI];

src/lagrangian/basic/particle/particle.C

@@ -32,6 +32,8 @@ Foam::label Foam::particle::particleCount_ = 0;
 
 const Foam::scalar Foam::particle::trackingCorrectionTol = 1e-5;
 
+const Foam::scalar Foam::particle::lambdaDistanceToleranceCoeff = 1e3*SMALL;
+
 namespace Foam
 {
     defineTypeNameAndDebug(particle, 0);

src/lagrangian/basic/particle/particle.H

@@ -164,7 +164,8 @@ protected:
             DynamicList<label>& faceList,
             const tetPointRef& tet,
             const FixedList<vector, 4>& tetAreas,
-            const FixedList<label, 4>& tetPlaneBasePtIs
+            const FixedList<label, 4>& tetPlaneBasePtIs,
+            const scalar tol
         ) const;
 
         //- Find the lambda value for the line to-from across the
@@ -178,7 +179,8 @@ protected:
             const label tetPlaneBasePtI,
             const label cellI,
             const label tetFaceI,
-            const label tetPtI
+            const label tetPtI,
+            const scalar tol
         ) const;
 
         //- Find the lambda value for a moving tri face
@@ -191,7 +193,8 @@ protected:
             const label tetPlaneBasePtI,
             const label cellI,
             const label tetFaceI,
-            const label tetPtI
+            const label tetPtI,
+            const scalar tol
         ) const;
 
         //- Modify the tet owner data by crossing triI
@@ -291,6 +294,10 @@ public:
         // 'rescue' it from a tracking problem
         static const scalar trackingCorrectionTol;
 
+        //- Fraction of the cell volume to use in determining tolerance values
+        //  for the denominator and numerator of lambda
+        static const scalar lambdaDistanceToleranceCoeff;
+
 
     // Constructors
 

src/lagrangian/basic/particle/particleI.H

@@ -34,7 +34,8 @@ inline void Foam::particle::findTris
     DynamicList<label>& faceList,
     const tetPointRef& tet,
     const FixedList<vector, 4>& tetAreas,
-    const FixedList<label, 4>& tetPlaneBasePtIs
+    const FixedList<label, 4>& tetPlaneBasePtIs,
+    const scalar tol
 ) const
 {
     faceList.clear();
@@ -52,7 +53,8 @@ inline void Foam::particle::findTris
             tetPlaneBasePtIs[i],
             cellI_,
             tetFaceI_,
-            tetPtI_
+            tetPtI_,
+            tol
         );
 
         if ((lambda > 0.0) && (lambda < 1.0))
@@ -72,7 +74,8 @@ inline Foam::scalar Foam::particle::tetLambda
     const label tetPlaneBasePtI,
     const label cellI,
     const label tetFaceI,
-    const label tetPtI
+    const label tetPtI,
+    const scalar tol
 ) const
 {
     const pointField& pPts = mesh_.points();
@@ -88,7 +91,8 @@ inline Foam::scalar Foam::particle::tetLambda
             tetPlaneBasePtI,
             cellI,
             tetFaceI,
-            tetPtI
+            tetPtI,
+            tol
         );
     }
 
@@ -97,12 +101,17 @@ inline Foam::scalar Foam::particle::tetLambda
     scalar lambdaNumerator = (base - from) & n;
     scalar lambdaDenominator = (to - from) & n;
 
-    if (mag(lambdaDenominator) < SMALL)
+    // n carries the area of the tet faces, so the dot product with a
+    // delta-length has the units of volume.  Comparing the component of each
+    // delta-length in the direction of n times the face area to a fraction of
+    // the cell volume.
+
+    if (mag(lambdaDenominator) < tol)
     {
-        if (mag(lambdaNumerator) < SMALL)
+        if (mag(lambdaNumerator) < tol)
         {
             // Track starts on the face, and is potentially
-            // parallel to it.  +-SMALL/+-SMALL is not a good
+            // parallel to it.  +-tol/+-tol is not a good
             // comparison, return 0.0, in anticipation of tet
             // centre correction.
 
@@ -110,10 +119,11 @@ inline Foam::scalar Foam::particle::tetLambda
         }
         else
         {
-            if (mag((to - from)) < SMALL)
+            if (mag((to - from)) < tol/mag(n))
             {
-                // Zero length track, not along the face, face
+                // 'Zero' length track (compared to the tolerance, which is
-                // cannot be crossed.
+                // based on the cell volume, divided by the tet face area), not
+                // along the face, face cannot be crossed.
 
                 return GREAT;
             }
@@ -139,7 +149,8 @@ inline Foam::scalar Foam::particle::movingTetLambda
     const label tetPlaneBasePtI,
     const label cellI,
     const label tetFaceI,
-    const label tetPtI
+    const label tetPtI,
+    const scalar tol
 ) const
 {
     const pointField& pPts = mesh_.points();
@@ -291,12 +302,12 @@ inline Foam::scalar Foam::particle::movingTetLambda
 
     }
 
-    if (mag(lambdaDenominator) < SMALL)
+    if (mag(lambdaDenominator) < tol)
     {
-        if (mag(lambdaNumerator) < SMALL)
+        if (mag(lambdaNumerator) < tol)
         {
             // Track starts on the face, and is potentially
-            // parallel to it.  +-SMALL)/+-SMALL is not a good
+            // parallel to it.  +-tol)/+-tol is not a good
             // comparison, return 0.0, in anticipation of tet
             // centre correction.
 
@@ -304,7 +315,7 @@ inline Foam::scalar Foam::particle::movingTetLambda
         }
         else
         {
-            if (mag((to - from)) < SMALL)
+            if (mag((to - from)) < tol/mag(n))
             {
                 // Zero length track, not along the face, face
                 // cannot be crossed.

src/lagrangian/basic/particle/particleTemplates.C

@@ -30,6 +30,7 @@ License
 #include "symmetryPolyPatch.H"
 #include "wallPolyPatch.H"
 #include "wedgePolyPatch.H"
+#include "meshTools.H"
 
 // * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //
 
@@ -285,6 +286,11 @@ Foam::scalar Foam::particle::trackToFace
     // be a different tet to the one that the particle occupies.
     tetIndices faceHitTetIs;
 
+    // What tolerance is appropriate the minimum lambda numerator and
+    // denominator for tracking in this cell.
+    scalar lambdaDistanceTolerance =
+        lambdaDistanceToleranceCoeff*mesh_.cellVolumes()[cellI_];
+
     do
     {
         if (triI != -1)
@@ -370,7 +376,15 @@ Foam::scalar Foam::particle::trackToFace
         tetPlaneBasePtIs[2] = basePtI;
         tetPlaneBasePtIs[3] = basePtI;
 
-        findTris(endPosition, tris, tet, tetAreas, tetPlaneBasePtIs);
+        findTris
+        (
+            endPosition,
+            tris,
+            tet,
+            tetAreas,
+            tetPlaneBasePtIs,
+            lambdaDistanceTolerance
+        );
 
         // Reset variables for new track
         triI = -1;
@@ -414,7 +428,8 @@ Foam::scalar Foam::particle::trackToFace
                     tetPlaneBasePtIs[tI],
                     cellI_,
                     tetFaceI_,
-                    tetPtI_
+                    tetPtI_,
+                    lambdaDistanceTolerance
                 );
 
                 if (lam < lambdaMin)
@@ -463,7 +478,7 @@ Foam::scalar Foam::particle::trackToFace
         //     << origId_ << " " << origProc_<< nl
         //     << "# face: " << tetFaceI_ << nl
         //     << "# tetPtI: " << tetPtI_ << nl
-        //     << "# tetBasePtI: " << mesh.tetBasePtIs()[tetFaceI_] << nl
+        //     << "# tetBasePtI: " << mesh_.tetBasePtIs()[tetFaceI_] << nl
         //     << "# tet.mag(): " << tet.mag() << nl
         //     << "# tet.quality(): " << tet.quality()
         //     << endl;
@@ -703,6 +718,9 @@ void Foam::particle::hitWallFaces
 
     const Foam::cell& thisCell = mesh_.cells()[cellI_];
 
+    scalar lambdaDistanceTolerance =
+        lambdaDistanceToleranceCoeff*mesh_.cellVolumes()[cellI_];
+
     const polyBoundaryMesh& patches = mesh_.boundaryMesh();
 
     forAll(thisCell, cFI)
@@ -754,7 +772,8 @@ void Foam::particle::hitWallFaces
                     f[tetIs.faceBasePt()],
                     cellI_,
                     fI,
-                    tetIs.tetPt()
+                    tetIs.tetPt(),
+                    lambdaDistanceTolerance
                 );
 
                 if ((tetClambda <= 0.0) || (tetClambda >= 1.0))
@@ -780,7 +799,8 @@ void Foam::particle::hitWallFaces
                     f[tetIs.faceBasePt()],
                     cellI_,
                     fI,
-                    tetIs.tetPt()
+                    tetIs.tetPt(),
+                    lambdaDistanceTolerance
                 );
 
                 pointHit hitInfo(vector::zero);

src/lagrangian/dieselSpray/parcel/parcel.C

@@ -440,7 +440,6 @@ void Foam::parcel::updateParcelProperties
     scalar oldhv = fuels.hl(pg, T(), X());
     scalar Np = N(oldDensity);
 
-    scalar newDensity = oldDensity;
     scalar newMass    = oldMass;
     scalar newhg      = oldhg;
     scalar newhv      = oldhv;
@@ -460,7 +459,6 @@ void Foam::parcel::updateParcelProperties
         // first time
         if (n > 1)
         {
-            newDensity = fuels.rho(pg, Tnew, X());
             newMass = m();
             newhg = 0.0;
             scalarField Ynew(fuels.Y(X()));

src/lagrangian/dieselSpray/spraySubModels/atomizationModel/LISA/LISA.C

@@ -112,11 +112,10 @@ void Foam::LISA::atomizeParcel
     vector uDir = p.U()/mag(p.U());
 
     scalar uGas = mag(vel & uDir);
-    vector Ug = uGas*uDir;
 
     // Might be the relative velocity between Liquid and Gas, but using the
     // absolute velocity of the parcel as suggested by the authors
-//    scalar U = mag(p.Urel(vel));
+    // scalar U = mag(p.Urel(vel));
     scalar U = mag(p.U());
 
     p.ct() += deltaT;

src/lagrangian/dieselSpray/spraySubModels/breakupModel/SHF/SHF.C

@@ -118,9 +118,6 @@ void Foam::SHF::breakupParcel
     scalar reLiquid   = p.Re(rhoLiquid, vel, muLiquid);
     scalar ohnesorge  = sqrt(weLiquid)/(reLiquid + VSMALL);
 
-    vector acceleration = p.Urel(vel)/p.tMom();
-    vector trajectory = p.U()/mag(p.U());
-
     vector vRel = p.Urel(vel);
 
     scalar weGasCorr = weGas/(1.0 + weCorrCoeff_*ohnesorge);

src/lagrangian/dieselSpray/spraySubModels/injectorModel/blobsSwirl/blobsSwirlInjector.C

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2004-2010 OpenCFD Ltd.
+    \\  /    A nd           | Copyright (C) 2004-2011 OpenCFD Ltd.
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -246,9 +246,6 @@ void Foam::blobsSwirlInjector::calculateHX
             )
         );
 
-    scalar hOLD = -100.0;
-    scalar xOLD = -100.0;
-
     label i;
 
     for (i=0; i<20; i++)
@@ -267,10 +264,6 @@ void Foam::blobsSwirlInjector::calculateHX
             );
 
         x_ = sqr(1.0 - 2.0*h_/injectorDiameter);
-
-        hOLD = h_;
-        xOLD = x_;
-
     }
 
     x_ = sqr(1.0 - 2.0*h_/injectorDiameter);

src/lagrangian/intermediate/submodels/Kinematic/InjectionModel/InjectionModel/InjectionModel.C

@@ -607,12 +607,17 @@ void Foam::InjectionModel<CloudType>::inject(TrackData& td)
                         pPtr->rho()
                     );
 
-                // Add the new parcel
+                if (pPtr->move(td, dt))
+                {
                     td.cloud().addParticle(pPtr);
-
                     massAdded += pPtr->nParticle()*pPtr->mass();
                     parcelsAdded++;
                 }
+                else
+                {
+                    delete pPtr;
+                }
+            }
         }
     }
 

src/lagrangian/intermediate/submodels/Kinematic/ParticleForces/NonInertialFrame/NonInertialFrameForce.C

@@ -163,13 +163,14 @@ void Foam::NonInertialFrameForce<CloudType>::cacheFields(const bool store)
             )
         )
         {
-            uniformDimensionedVectorField omegaDot = this->mesh().template
+            uniformDimensionedVectorField centreOfRotation =
+                this->mesh().template
                 lookupObject<uniformDimensionedVectorField>
                 (
                     centreOfRotationName_
                 );
 
-            centreOfRotation_ = omegaDot.value();
+            centreOfRotation_ = centreOfRotation.value();
         }
     }
 }
@@ -187,7 +188,7 @@ Foam::forceSuSp Foam::NonInertialFrameForce<CloudType>::calcNonCoupled
 {
     forceSuSp value(vector::zero, 0.0);
 
-    const vector& r = p.position() - centreOfRotation_;
+    const vector r = p.position() - centreOfRotation_;
 
     value.Su() =
         mass

src/mesh/autoMesh/Make/files

@@ -4,6 +4,7 @@ autoHexMeshDriver       = $(autoHexMesh)/autoHexMeshDriver
 $(autoHexMeshDriver)/autoLayerDriver.C
 $(autoHexMeshDriver)/autoLayerDriverShrink.C
 $(autoHexMeshDriver)/autoSnapDriver.C
+$(autoHexMeshDriver)/autoSnapDriverFeature.C
 $(autoHexMeshDriver)/autoRefineDriver.C
 
 $(autoHexMeshDriver)/layerParameters/layerParameters.C
@@ -16,6 +17,7 @@ $(autoHexMesh)/meshRefinement/meshRefinement.C
 $(autoHexMesh)/meshRefinement/meshRefinementMerge.C
 $(autoHexMesh)/meshRefinement/meshRefinementProblemCells.C
 $(autoHexMesh)/meshRefinement/meshRefinementRefine.C
+$(autoHexMesh)/refinementFeatures/refinementFeatures.C
 $(autoHexMesh)/refinementSurfaces/refinementSurfaces.C
 $(autoHexMesh)/shellSurfaces/shellSurfaces.C
 $(autoHexMesh)/trackedParticle/trackedParticle.C

src/mesh/autoMesh/autoHexMesh/autoHexMeshDriver/autoLayerDriver.C

@@ -59,622 +59,6 @@ defineTypeNameAndDebug(autoLayerDriver, 0);
 
 // * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //
 
-Foam::label Foam::autoLayerDriver::mergePatchFacesUndo
-(
-    const scalar minCos,
-    const scalar concaveCos,
-    const dictionary& motionDict
-)
-{
-    fvMesh& mesh = meshRefiner_.mesh();
-
-    // Patch face merging engine
-    combineFaces faceCombiner(mesh, true);
-
-    // Pick up all candidate cells on boundary
-    labelHashSet boundaryCells(mesh.nFaces()-mesh.nInternalFaces());
-
-    {
-        labelList patchIDs(meshRefiner_.meshedPatches());
-
-        const polyBoundaryMesh& patches = mesh.boundaryMesh();
-
-        forAll(patchIDs, i)
-        {
-            label patchI = patchIDs[i];
-
-            const polyPatch& patch = patches[patchI];
-
-            if (!patch.coupled())
-            {
-                forAll(patch, i)
-                {
-                    boundaryCells.insert(mesh.faceOwner()[patch.start()+i]);
-                }
-            }
-        }
-    }
-
-    // Get all sets of faces that can be merged
-    labelListList allFaceSets
-    (
-        faceCombiner.getMergeSets
-        (
-            minCos,
-            concaveCos,
-            boundaryCells
-        )
-    );
-
-    label nFaceSets = returnReduce(allFaceSets.size(), sumOp<label>());
-
-    Info<< "Merging " << nFaceSets << " sets of faces." << nl << endl;
-
-    if (nFaceSets > 0)
-    {
-        if (debug)
-        {
-            faceSet allSets(mesh, "allFaceSets", allFaceSets.size());
-            forAll(allFaceSets, setI)
-            {
-                forAll(allFaceSets[setI], i)
-                {
-                    allSets.insert(allFaceSets[setI][i]);
-                }
-            }
-            Pout<< "Writing all faces to be merged to set "
-                << allSets.objectPath() << endl;
-            allSets.instance() = mesh.time().timeName();
-            allSets.write();
-        }
-
-
-        // Topology changes container
-        polyTopoChange meshMod(mesh);
-
-        // Merge all faces of a set into the first face of the set.
-        faceCombiner.setRefinement(allFaceSets, meshMod);
-
-        // Experimental: store data for all the points that have been deleted
-        meshRefiner_.storeData
-        (
-            faceCombiner.savedPointLabels(),    // points to store
-            labelList(0),                       // faces to store
-            labelList(0)                        // cells to store
-        );
-
-        // Change the mesh (no inflation)
-        autoPtr<mapPolyMesh> map = meshMod.changeMesh(mesh, false, true);
-
-        // Update fields
-        mesh.updateMesh(map);
-
-        // Move mesh (since morphing does not do this)
-        if (map().hasMotionPoints())
-        {
-            mesh.movePoints(map().preMotionPoints());
-        }
-        else
-        {
-            // Delete mesh volumes.
-            mesh.clearOut();
-        }
-
-        faceCombiner.updateMesh(map);
-
-        meshRefiner_.updateMesh(map, labelList(0));
-
-
-        for (label iteration = 0; iteration < 100; iteration++)
-        {
-            Info<< nl
-                << "Undo iteration " << iteration << nl
-                << "----------------" << endl;
-
-
-            // Check mesh for errors
-            // ~~~~~~~~~~~~~~~~~~~~~
-
-            faceSet errorFaces
-            (
-                mesh,
-                "errorFaces",
-                mesh.nFaces()-mesh.nInternalFaces()
-            );
-            bool hasErrors = motionSmoother::checkMesh
-            (
-                false,  // report
-                mesh,
-                motionDict,
-                errorFaces
-            );
-
-            //if (checkEdgeConnectivity)
-            //{
-            //    Info<< "Checking edge-face connectivity (duplicate faces"
-            //        << " or non-consecutive shared vertices)" << endl;
-            //
-            //    label nOldSize = errorFaces.size();
-            //
-            //    hasErrors =
-            //        mesh.checkFaceFaces
-            //        (
-            //            false,
-            //            &errorFaces
-            //        )
-            //     || hasErrors;
-            //
-            //    Info<< "Detected additional "
-            //        <<  returnReduce
-            //            (
-            //                errorFaces.size() - nOldSize,
-            //                sumOp<label>()
-            //            )
-            //        << " faces with illegal face-face connectivity"
-            //        << endl;
-            //}
-
-            if (!hasErrors)
-            {
-                break;
-            }
-
-
-            if (debug)
-            {
-                errorFaces.instance() = mesh.time().timeName();
-                Pout<< "Writing all faces in error to faceSet "
-                    << errorFaces.objectPath() << nl << endl;
-                errorFaces.write();
-            }
-
-
-            // Check any master cells for using any of the error faces
-            // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-            DynamicList<label> mastersToRestore(allFaceSets.size());
-
-            forAll(allFaceSets, setI)
-            {
-                label masterFaceI = faceCombiner.masterFace()[setI];
-
-                if (masterFaceI != -1)
-                {
-                    label masterCellII = mesh.faceOwner()[masterFaceI];
-
-                    const cell& cFaces = mesh.cells()[masterCellII];
-
-                    forAll(cFaces, i)
-                    {
-                        if (errorFaces.found(cFaces[i]))
-                        {
-                            mastersToRestore.append(masterFaceI);
-                            break;
-                        }
-                    }
-                }
-            }
-            mastersToRestore.shrink();
-
-            label nRestore = returnReduce
-            (
-                mastersToRestore.size(),
-                sumOp<label>()
-            );
-
-            Info<< "Masters that need to be restored:"
-                << nRestore << endl;
-
-            if (debug)
-            {
-                faceSet restoreSet(mesh, "mastersToRestore", mastersToRestore);
-                restoreSet.instance() = mesh.time().timeName();
-                Pout<< "Writing all " << mastersToRestore.size()
-                    << " masterfaces to be restored to set "
-                    << restoreSet.objectPath() << endl;
-                restoreSet.write();
-            }
-
-
-            if (nRestore == 0)
-            {
-                break;
-            }
-
-
-            // Undo
-            // ~~~~
-
-            // Topology changes container
-            polyTopoChange meshMod(mesh);
-
-            // Merge all faces of a set into the first face of the set.
-            // Experimental:mark all points/faces/cells that have been restored.
-            Map<label> restoredPoints(0);
-            Map<label> restoredFaces(0);
-            Map<label> restoredCells(0);
-
-            faceCombiner.setUnrefinement
-            (
-                mastersToRestore,
-                meshMod,
-                restoredPoints,
-                restoredFaces,
-                restoredCells
-            );
-
-            // Change the mesh (no inflation)
-            autoPtr<mapPolyMesh> map = meshMod.changeMesh(mesh, false, true);
-
-            // Update fields
-            mesh.updateMesh(map);
-
-            // Move mesh (since morphing does not do this)
-            if (map().hasMotionPoints())
-            {
-                mesh.movePoints(map().preMotionPoints());
-            }
-            else
-            {
-                // Delete mesh volumes.
-                mesh.clearOut();
-            }
-
-            faceCombiner.updateMesh(map);
-
-            // Renumber restore maps
-            inplaceMapKey(map().reversePointMap(), restoredPoints);
-            inplaceMapKey(map().reverseFaceMap(), restoredFaces);
-            inplaceMapKey(map().reverseCellMap(), restoredCells);
-
-            // Experimental:restore all points/face/cells in maps
-            meshRefiner_.updateMesh
-            (
-                map,
-                labelList(0),       // changedFaces
-                restoredPoints,
-                restoredFaces,
-                restoredCells
-            );
-
-            Info<< endl;
-        }
-
-        if (debug)
-        {
-            Pout<< "Writing merged-faces mesh to time "
-                << meshRefiner_.timeName() << nl << endl;
-            mesh.write();
-        }
-    }
-    else
-    {
-        Info<< "No faces merged ..." << endl;
-    }
-
-    return nFaceSets;
-}
-
-
-// Remove points. pointCanBeDeleted is parallel synchronised.
-Foam::autoPtr<Foam::mapPolyMesh> Foam::autoLayerDriver::doRemovePoints
-(
-    removePoints& pointRemover,
-    const boolList& pointCanBeDeleted
-)
-{
-    fvMesh& mesh = meshRefiner_.mesh();
-
-    // Topology changes container
-    polyTopoChange meshMod(mesh);
-
-    pointRemover.setRefinement(pointCanBeDeleted, meshMod);
-
-    // Change the mesh (no inflation)
-    autoPtr<mapPolyMesh> map = meshMod.changeMesh(mesh, false, true);
-
-    // Update fields
-    mesh.updateMesh(map);
-
-    // Move mesh (since morphing does not do this)
-    if (map().hasMotionPoints())
-    {
-        mesh.movePoints(map().preMotionPoints());
-    }
-    else
-    {
-        // Delete mesh volumes.
-        mesh.clearOut();
-    }
-
-    pointRemover.updateMesh(map);
-    meshRefiner_.updateMesh(map, labelList(0));
-
-    return map;
-}
-
-
-// Restore faces (which contain removed points)
-Foam::autoPtr<Foam::mapPolyMesh> Foam::autoLayerDriver::doRestorePoints
-(
-    removePoints& pointRemover,
-    const labelList& facesToRestore
-)
-{
-    fvMesh& mesh = meshRefiner_.mesh();
-
-    // Topology changes container
-    polyTopoChange meshMod(mesh);
-
-    // Determine sets of points and faces to restore
-    labelList localFaces, localPoints;
-    pointRemover.getUnrefimentSet
-    (
-        facesToRestore,
-        localFaces,
-        localPoints
-    );
-
-    // Undo the changes on the faces that are in error.
-    pointRemover.setUnrefinement
-    (
-        localFaces,
-        localPoints,
-        meshMod
-    );
-
-    // Change the mesh (no inflation)
-    autoPtr<mapPolyMesh> map = meshMod.changeMesh(mesh, false, true);
-
-    // Update fields
-    mesh.updateMesh(map);
-
-    // Move mesh (since morphing does not do this)
-    if (map().hasMotionPoints())
-    {
-        mesh.movePoints(map().preMotionPoints());
-    }
-    else
-    {
-        // Delete mesh volumes.
-        mesh.clearOut();
-    }
-
-    pointRemover.updateMesh(map);
-    meshRefiner_.updateMesh(map, labelList(0));
-
-    return map;
-}
-
-
-// Collect all faces that are both in candidateFaces and in the set.
-// If coupled face also collects the coupled face.
-Foam::labelList Foam::autoLayerDriver::collectFaces
-(
-    const labelList& candidateFaces,
-    const labelHashSet& set
-) const
-{
-    const fvMesh& mesh = meshRefiner_.mesh();
-
-    // Has face been selected?
-    boolList selected(mesh.nFaces(), false);
-
-    forAll(candidateFaces, i)
-    {
-        label faceI = candidateFaces[i];
-
-        if (set.found(faceI))
-        {
-            selected[faceI] = true;
-        }
-    }
-    syncTools::syncFaceList
-    (
-        mesh,
-        selected,
-        orEqOp<bool>()      // combine operator
-    );
-
-    labelList selectedFaces(findIndices(selected, true));
-
-    return selectedFaces;
-}
-
-
-// Pick up faces of cells of faces in set.
-Foam::labelList Foam::autoLayerDriver::growFaceCellFace
-(
-    const labelHashSet& set
-) const
-{
-    const fvMesh& mesh = meshRefiner_.mesh();
-
-    boolList selected(mesh.nFaces(), false);
-
-    forAllConstIter(faceSet, set, iter)
-    {
-        label faceI = iter.key();
-
-        label own = mesh.faceOwner()[faceI];
-
-        const cell& ownFaces = mesh.cells()[own];
-        forAll(ownFaces, ownFaceI)
-        {
-            selected[ownFaces[ownFaceI]] = true;
-        }
-
-        if (mesh.isInternalFace(faceI))
-        {
-            label nbr = mesh.faceNeighbour()[faceI];
-
-            const cell& nbrFaces = mesh.cells()[nbr];
-            forAll(nbrFaces, nbrFaceI)
-            {
-                selected[nbrFaces[nbrFaceI]] = true;
-            }
-        }
-    }
-    syncTools::syncFaceList
-    (
-        mesh,
-        selected,
-        orEqOp<bool>()      // combine operator
-    );
-    return findIndices(selected, true);
-}
-
-
-// Remove points not used by any face or points used by only two faces where
-// the edges are in line
-Foam::label Foam::autoLayerDriver::mergeEdgesUndo
-(
-    const scalar minCos,
-    const dictionary& motionDict
-)
-{
-    fvMesh& mesh = meshRefiner_.mesh();
-
-    Info<< nl
-        << "Merging all points on surface that" << nl
-        << "- are used by only two boundary faces and" << nl
-        << "- make an angle with a cosine of more than " << minCos
-        << "." << nl << endl;
-
-    // Point removal analysis engine with undo
-    removePoints pointRemover(mesh, true);
-
-    // Count usage of points
-    boolList pointCanBeDeleted;
-    label nRemove = pointRemover.countPointUsage(minCos, pointCanBeDeleted);
-
-    if (nRemove > 0)
-    {
-        Info<< "Removing " << nRemove
-            << " straight edge points ..." << nl << endl;
-
-        // Remove points
-        // ~~~~~~~~~~~~~
-
-        doRemovePoints(pointRemover, pointCanBeDeleted);
-
-
-        for (label iteration = 0; iteration < 100; iteration++)
-        {
-            Info<< nl
-                << "Undo iteration " << iteration << nl
-                << "----------------" << endl;
-
-
-            // Check mesh for errors
-            // ~~~~~~~~~~~~~~~~~~~~~
-
-            faceSet errorFaces
-            (
-                mesh,
-                "errorFaces",
-                mesh.nFaces()-mesh.nInternalFaces()
-            );
-            bool hasErrors = motionSmoother::checkMesh
-            (
-                false,  // report
-                mesh,
-                motionDict,
-                errorFaces
-            );
-            //if (checkEdgeConnectivity)
-            //{
-            //    Info<< "Checking edge-face connectivity (duplicate faces"
-            //        << " or non-consecutive shared vertices)" << endl;
-            //
-            //    label nOldSize = errorFaces.size();
-            //
-            //    hasErrors =
-            //        mesh.checkFaceFaces
-            //        (
-            //            false,
-            //            &errorFaces
-            //        )
-            //     || hasErrors;
-            //
-            //    Info<< "Detected additional "
-            //        << returnReduce(errorFaces.size()-nOldSize,sumOp<label>())
-            //        << " faces with illegal face-face connectivity"
-            //        << endl;
-            //}
-
-            if (!hasErrors)
-            {
-                break;
-            }
-
-            if (debug)
-            {
-                errorFaces.instance() = mesh.time().timeName();
-                Pout<< "**Writing all faces in error to faceSet "
-                    << errorFaces.objectPath() << nl << endl;
-                errorFaces.write();
-            }
-
-            labelList masterErrorFaces
-            (
-                collectFaces
-                (
-                    pointRemover.savedFaceLabels(),
-                    errorFaces
-                )
-            );
-
-            label n = returnReduce(masterErrorFaces.size(), sumOp<label>());
-
-            Info<< "Detected " << n
-                << " error faces on boundaries that have been merged."
-                << " These will be restored to their original faces." << nl
-                << endl;
-
-            if (n == 0)
-            {
-                if (hasErrors)
-                {
-                    Info<< "Detected "
-                        << returnReduce(errorFaces.size(), sumOp<label>())
-                        << " error faces in mesh."
-                        << " Restoring neighbours of faces in error." << nl
-                        << endl;
-
-                    labelList expandedErrorFaces
-                    (
-                        growFaceCellFace
-                        (
-                            errorFaces
-                        )
-                    );
-
-                    doRestorePoints(pointRemover, expandedErrorFaces);
-                }
-
-                break;
-            }
-
-            doRestorePoints(pointRemover, masterErrorFaces);
-        }
-
-        if (debug)
-        {
-            Pout<< "Writing merged-edges mesh to time "
-                << meshRefiner_.timeName() << nl << endl;
-            mesh.write();
-        }
-    }
-    else
-    {
-        Info<< "No straight edges simplified and no points removed ..." << endl;
-    }
-
-    return nRemove;
-}
-
-
 // For debugging: Dump displacement to .obj files
 void Foam::autoLayerDriver::dumpDisplacement
 (
@@ -793,7 +177,7 @@ void Foam::autoLayerDriver::checkMeshManifold() const
             << " points where this happens to pointSet "
             << nonManifoldPoints.name() << endl;
 
-        nonManifoldPoints.instance() = mesh.time().timeName();
+        nonManifoldPoints.instance() = meshRefiner_.timeName();
         nonManifoldPoints.write();
     }
     Info<< endl;
@@ -1080,7 +464,6 @@ void Foam::autoLayerDriver::handleWarpedFaces
 }
 
 
-
 //// No extrusion on cells with multiple patch faces. There ususally is a reason
 //// why combinePatchFaces hasn't succeeded.
 //void Foam::autoLayerDriver::handleMultiplePatchFaces
@@ -1133,7 +516,7 @@ void Foam::autoLayerDriver::handleWarpedFaces
 //
 //    if (nMultiPatchCells > 0)
 //    {
-//        multiPatchCells.instance() = mesh.time().timeName();
+//        multiPatchCells.instance() = meshRefiner_.timeName();
 //        Info<< "Writing " << nMultiPatchCells
 //            << " cells with multiple (connected) patch faces to cellSet "
 //            << multiPatchCells.objectPath() << endl;
@@ -2547,9 +1930,15 @@ void Foam::autoLayerDriver::mergePatchFacesUndo
         << "      (0=straight, 180=fully concave)" << nl
         << endl;
 
-    label nChanged = mergePatchFacesUndo(minCos, concaveCos, motionDict);
+    label nChanged = meshRefiner_.mergePatchFacesUndo
+    (
+        minCos,
+        concaveCos,
+        meshRefiner_.meshedPatches(),
+        motionDict
+    );
 
-    nChanged += mergeEdgesUndo(minCos, motionDict);
+    nChanged += meshRefiner_.mergeEdgesUndo(minCos, motionDict);
 }
 
 
@@ -3191,6 +2580,7 @@ void Foam::autoLayerDriver::addLayers
                 "addedCells",
                 findIndices(flaggedCells, true)
             );
+            addedCellSet.instance() = meshRefiner_.timeName();
             Info<< "Writing "
                 << returnReduce(addedCellSet.size(), sumOp<label>())
                 << " added cells to cellSet "
@@ -3203,6 +2593,7 @@ void Foam::autoLayerDriver::addLayers
                 "layerFaces",
                 findIndices(flaggedCells, true)
             );
+            layerFacesSet.instance() = meshRefiner_.timeName();
             Info<< "Writing "
                 << returnReduce(layerFacesSet.size(), sumOp<label>())
                 << " faces inside added layer to faceSet "
@@ -3279,6 +2670,9 @@ void Foam::autoLayerDriver::addLayers
         mesh.clearOut();
     }
 
+    // Reset the instance for if in overwrite mode
+    mesh.setInstance(meshRefiner_.timeName());
+
     meshRefiner_.updateMesh(map, labelList(0));
 
 
@@ -3345,6 +2739,7 @@ void Foam::autoLayerDriver::addLayers
     // ~~~~~~~~~~
 
     cellSet addedCellSet(mesh, "addedCells", findIndices(flaggedCells, true));
+    addedCellSet.instance() = meshRefiner_.timeName();
     Info<< "Writing "
         << returnReduce(addedCellSet.size(), sumOp<label>())
         << " added cells to cellSet "
@@ -3352,6 +2747,7 @@ void Foam::autoLayerDriver::addLayers
     addedCellSet.write();
 
     faceSet layerFacesSet(mesh, "layerFaces", findIndices(flaggedFaces, true));
+    layerFacesSet.instance() = meshRefiner_.timeName();
     Info<< "Writing "
         << returnReduce(layerFacesSet.size(), sumOp<label>())
         << " faces inside added layer to faceSet "

src/mesh/autoMesh/autoHexMesh/autoHexMeshDriver/autoLayerDriver.H

@@ -105,46 +105,6 @@ class autoLayerDriver
 
     // Private Member Functions
 
-
-        // Face merging
-
-            //- Merge patch faces. Undo until no checkMesh errors.
-            label mergePatchFacesUndo
-            (
-                const scalar minCos,
-                const scalar concaveCos,
-                const dictionary&
-            );
-
-            //- Remove points.
-            autoPtr<mapPolyMesh> doRemovePoints
-            (
-                removePoints& pointRemover,
-                const boolList& pointCanBeDeleted
-            );
-
-            //- Restore faces (which contain removed points)
-            autoPtr<mapPolyMesh> doRestorePoints
-            (
-                removePoints& pointRemover,
-                const labelList& facesToRestore
-            );
-
-            //- Return candidateFaces that are also in set.
-            labelList collectFaces
-            (
-                const labelList& candidateFaces,
-                const labelHashSet& set
-            ) const;
-
-            //- Pick up faces of cells of faces in set.
-            labelList growFaceCellFace(const labelHashSet&) const;
-
-            //- Remove points not used by any face or points used by only
-            //  two faces where the edges are in line
-            label mergeEdgesUndo(const scalar minCos, const dictionary&);
-
-
         // Layers
 
             //- For debugging: Dump displacement to .obj files