From 5e7ef409f62aa75bb15f63691694c53318d9af9d Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Fri, 16 Nov 2012 14:53:52 +0000
Subject: [PATCH 1/6] ENH: motorBike: demonstrate secondary time controls

---
 .../incompressible/simpleFoam/motorBike/system/controlDict | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/tutorials/incompressible/simpleFoam/motorBike/system/controlDict b/tutorials/incompressible/simpleFoam/motorBike/system/controlDict
index e7c16adc8d..f075505d68 100644
--- a/tutorials/incompressible/simpleFoam/motorBike/system/controlDict
+++ b/tutorials/incompressible/simpleFoam/motorBike/system/controlDict
@@ -39,6 +39,13 @@ writeInterval   100;
 
 purgeWrite      0;
 
+
+//- Have regular restart files
+secondaryWriteControl    cpuTime;
+secondaryWriteInterval   120;
+secondaryPurgeWrite      1;
+
+
 writeFormat     ascii;
 
 writePrecision  6;

From 3e06dc98782c9ab01b3f30ee6b3e6bc39486c5bf Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Tue, 20 Nov 2012 16:02:14 +0000
Subject: [PATCH 2/6] ENH: renumberMesh: renumber cellZones and faceZones
 (pointZones were already handled)

---
 .../manipulation/renumberMesh/renumberMesh.C  | 41 +++++++++++++++++++
 1 file changed, 41 insertions(+)

diff --git a/applications/utilities/mesh/manipulation/renumberMesh/renumberMesh.C b/applications/utilities/mesh/manipulation/renumberMesh/renumberMesh.C
index e64f6cb78f..7eede94626 100644
--- a/applications/utilities/mesh/manipulation/renumberMesh/renumberMesh.C
+++ b/applications/utilities/mesh/manipulation/renumberMesh/renumberMesh.C
@@ -471,6 +471,47 @@ autoPtr<mapPolyMesh> reorderMesh
         true
     );
 
+
+    // Re-do the faceZones
+    {
+        faceZoneMesh& faceZones = mesh.faceZones();
+        faceZones.clearAddressing();
+        forAll(faceZones, zoneI)
+        {
+            faceZone& fZone = faceZones[zoneI];
+            labelList newAddressing(fZone.size());
+            boolList newFlipMap(fZone.size());
+            forAll(fZone, i)
+            {
+                label oldFaceI = fZone[i];
+                newAddressing[i] = reverseFaceOrder[oldFaceI];
+                if (flipFaceFlux.found(newAddressing[i]))
+                {
+                    newFlipMap[i] = !fZone.flipMap()[i];
+                }
+                else
+                {
+                    newFlipMap[i] = fZone.flipMap()[i];
+                }
+            }
+            fZone.resetAddressing(newAddressing, newFlipMap);
+        }
+    }
+    // Re-do the cellZones
+    {
+        cellZoneMesh& cellZones = mesh.cellZones();
+        cellZones.clearAddressing();
+        forAll(cellZones, zoneI)
+        {
+            cellZones[zoneI] = UIndirectList<label>
+            (
+                reverseCellOrder,
+                cellZones[zoneI]
+            )();
+        }
+    }
+
+
     return autoPtr<mapPolyMesh>
     (
         new mapPolyMesh

From 63b553bdf93bdb96811d17f25fe31aa4926f89e8 Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Wed, 21 Nov 2012 10:13:39 +0000
Subject: [PATCH 3/6] ENH: findInstance: better error message for if in
 directory-finding mode

---
 src/OpenFOAM/db/Time/findInstance.C | 35 ++++++++++++++++++++---------
 1 file changed, 25 insertions(+), 10 deletions(-)

diff --git a/src/OpenFOAM/db/Time/findInstance.C b/src/OpenFOAM/db/Time/findInstance.C
index 54d64fcf4c..556de4c98b 100644
--- a/src/OpenFOAM/db/Time/findInstance.C
+++ b/src/OpenFOAM/db/Time/findInstance.C
@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2011 OpenFOAM Foundation
+    \\  /    A nd           | Copyright (C) 2011-2012 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -132,15 +132,30 @@ Foam::word Foam::Time::findInstance
              || rOpt == IOobject::MUST_READ_IF_MODIFIED
             )
             {
-                FatalErrorIn
-                (
-                    "Time::findInstance"
-                    "(const fileName&, const word&"
-                    ", const IOobject::readOption, const word&)"
-                )   << "Cannot find file \"" << name << "\" in directory "
-                    << dir << " in times " << timeName()
-                    << " down to " << stopInstance
-                    << exit(FatalError);
+                if (name.empty())
+                {
+                    FatalErrorIn
+                    (
+                        "Time::findInstance"
+                        "(const fileName&, const word&"
+                        ", const IOobject::readOption, const word&)"
+                    )   << "Cannot find directory "
+                        << dir << " in times " << timeName()
+                        << " down to " << stopInstance
+                        << exit(FatalError);
+                }
+                else
+                {
+                    FatalErrorIn
+                    (
+                        "Time::findInstance"
+                        "(const fileName&, const word&"
+                        ", const IOobject::readOption, const word&)"
+                    )   << "Cannot find file \"" << name << "\" in directory "
+                        << dir << " in times " << timeName()
+                        << " down to " << stopInstance
+                        << exit(FatalError);
+                }
             }
 
             return ts[instanceI].name();

From 625534b40b9167cc4cb00cb6ea9daab04df2d23d Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Thu, 22 Nov 2012 09:06:13 +0000
Subject: [PATCH 4/6] ENH: synctools: get remote cell data

---
 .../meshes/polyMesh/syncTools/syncTools.H     | 11 ++++-
 .../polyMesh/syncTools/syncToolsTemplates.C   | 41 ++++++++++++++++++-
 2 files changed, 50 insertions(+), 2 deletions(-)

diff --git a/src/OpenFOAM/meshes/polyMesh/syncTools/syncTools.H b/src/OpenFOAM/meshes/polyMesh/syncTools/syncTools.H
index ebc4ba60c3..3eb6e71388 100644
--- a/src/OpenFOAM/meshes/polyMesh/syncTools/syncTools.H
+++ b/src/OpenFOAM/meshes/polyMesh/syncTools/syncTools.H
@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2011 OpenFOAM Foundation
+    \\  /    A nd           | Copyright (C) 2011-2012 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -481,6 +481,15 @@ public:
                 );
             }
 
+            //- Swap to obtain neighbour cell values for all boundary faces
+            template <class T>
+            static void swapBoundaryCellList
+            (
+                const polyMesh& mesh,
+                const UList<T>& cellData,
+                List<T>& neighbourCellData
+            );
+
         // Sparse versions
 
             //- Synchronize values on selected points.
diff --git a/src/OpenFOAM/meshes/polyMesh/syncTools/syncToolsTemplates.C b/src/OpenFOAM/meshes/polyMesh/syncTools/syncToolsTemplates.C
index 7db1a14178..4be6afcf2d 100644
--- a/src/OpenFOAM/meshes/polyMesh/syncTools/syncToolsTemplates.C
+++ b/src/OpenFOAM/meshes/polyMesh/syncTools/syncToolsTemplates.C
@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2011 OpenFOAM Foundation
+    \\  /    A nd           | Copyright (C) 2011-2012 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -1553,6 +1553,45 @@ void Foam::syncTools::syncFaceList
 }
 
 
+template <class T>
+void Foam::syncTools::swapBoundaryCellList
+(
+    const polyMesh& mesh,
+    const UList<T>& cellData,
+    List<T>& neighbourCellData
+)
+{
+    if (cellData.size() != mesh.nCells())
+    {
+        FatalErrorIn
+        (
+            "syncTools<class T>::swapBoundaryCellList"
+            "(const polyMesh&, const UList<T>&, List<T>&)"
+        )   << "Number of cell values " << cellData.size()
+            << " is not equal to the number of cells in the mesh "
+            << mesh.nCells() << abort(FatalError);
+    }
+
+    const polyBoundaryMesh& patches = mesh.boundaryMesh();
+
+    label nBnd = mesh.nFaces()-mesh.nInternalFaces();
+
+    neighbourCellData.setSize(nBnd);
+
+    forAll(patches, patchI)
+    {
+        const polyPatch& pp = patches[patchI];
+        const labelUList& faceCells = pp.faceCells();
+        forAll(faceCells, i)
+        {
+            label bFaceI = pp.start()+i-mesh.nInternalFaces();
+            neighbourCellData[bFaceI] = cellData[faceCells[i]];
+        }
+    }
+    syncTools::swapBoundaryFaceList(mesh, neighbourCellData);
+}
+
+
 template <unsigned nBits>
 void Foam::syncTools::swapFaceList
 (

From 449b7d77315f4539ec6ab3b1962dacdaa3bce88b Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Thu, 22 Nov 2012 09:11:39 +0000
Subject: [PATCH 5/6] ENH: polyMeshGeometry: added flatness check

---
 .../motionSmoother/motionSmootherCheck.C      |  51 ++++++-
 .../polyMeshGeometry/polyMeshGeometry.C       | 137 +++++++++++++++++-
 .../polyMeshGeometry/polyMeshGeometry.H       |  25 +++-
 3 files changed, 206 insertions(+), 7 deletions(-)

diff --git a/src/dynamicMesh/motionSmoother/motionSmootherCheck.C b/src/dynamicMesh/motionSmoother/motionSmootherCheck.C
index da20ea741e..77ce89ca71 100644
--- a/src/dynamicMesh/motionSmoother/motionSmootherCheck.C
+++ b/src/dynamicMesh/motionSmoother/motionSmootherCheck.C
@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2011 OpenFOAM Foundation
+    \\  /    A nd           | Copyright (C) 2011-2012 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -104,6 +104,8 @@ bool Foam::motionSmoother::checkMesh
     (
         readScalar(dict.lookup("minTriangleTwist", true))
     );
+    scalar minFaceFlatness = -1.0;
+    dict.readIfPresent("minFaceFlatness", minFaceFlatness, true);
     const scalar minDet
     (
         readScalar(dict.lookup("minDeterminant", true))
@@ -356,6 +358,30 @@ bool Foam::motionSmoother::checkMesh
         nWrongFaces = nNewWrongFaces;
     }
 
+    if (minFaceFlatness > -SMALL)
+    {
+        polyMeshGeometry::checkFaceFlatness
+        (
+            report,
+            minFaceFlatness,
+            mesh,
+            mesh.faceAreas(),
+            mesh.faceCentres(),
+            mesh.points(),
+            checkFaces,
+            &wrongFaces
+        );
+
+        label nNewWrongFaces = returnReduce(wrongFaces.size(), sumOp<label>());
+
+        Info<< "    faces with flatness < "
+            << setw(5) << minFaceFlatness
+            << "                      : "
+            << nNewWrongFaces-nWrongFaces << endl;
+
+        nWrongFaces = nNewWrongFaces;
+    }
+
     if (minDet > -1)
     {
         polyMeshGeometry::checkCellDeterminant
@@ -479,6 +505,8 @@ bool Foam::motionSmoother::checkMesh
     (
         readScalar(dict.lookup("minTriangleTwist", true))
     );
+    scalar minFaceFlatness = -1.0;
+    dict.readIfPresent("minFaceFlatness", minFaceFlatness, true);
     const scalar minDet
     (
         readScalar(dict.lookup("minDeterminant", true))
@@ -697,6 +725,27 @@ bool Foam::motionSmoother::checkMesh
         nWrongFaces = nNewWrongFaces;
     }
 
+    if (minFaceFlatness > -1)
+    {
+        meshGeom.checkFaceFlatness
+        (
+            report,
+            minFaceFlatness,
+            meshGeom.mesh().points(),
+            checkFaces,
+            &wrongFaces
+        );
+
+        label nNewWrongFaces = returnReduce(wrongFaces.size(), sumOp<label>());
+
+        Info<< "    faces with flatness < "
+            << setw(5) << minFaceFlatness
+            << "                      : "
+            << nNewWrongFaces-nWrongFaces << endl;
+
+        nWrongFaces = nNewWrongFaces;
+    }
+
     if (minDet > -1)
     {
         meshGeom.checkCellDeterminant
diff --git a/src/dynamicMesh/motionSmoother/polyMeshGeometry/polyMeshGeometry.C b/src/dynamicMesh/motionSmoother/polyMeshGeometry/polyMeshGeometry.C
index 1670de1c92..13786a1c1c 100644
--- a/src/dynamicMesh/motionSmoother/polyMeshGeometry/polyMeshGeometry.C
+++ b/src/dynamicMesh/motionSmoother/polyMeshGeometry/polyMeshGeometry.C
@@ -341,8 +341,8 @@ bool Foam::polyMeshGeometry::checkFaceTet
             {
                 Pout<< "bool polyMeshGeometry::checkFaceTets("
                     << "const bool, const scalar, const pointField&"
-                    << ", const pointField&, const labelList&,"
-                    << " labelHashSet*): "
+                    << ", const pointField&"
+                    << ", const labelList&, labelHashSet*) : "
                     << "face " << faceI
                     << " has a triangle that points the wrong way."
                      << endl
@@ -373,9 +373,6 @@ Foam::polyMeshGeometry::polyMeshGeometry(const polyMesh& mesh)
 }
 
 
-// * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
-
-
 // * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
 
 //- Take over properties from mesh
@@ -2014,6 +2011,113 @@ bool Foam::polyMeshGeometry::checkTriangleTwist
 }
 
 
+bool Foam::polyMeshGeometry::checkFaceFlatness
+(
+    const bool report,
+    const scalar minFlatness,
+    const polyMesh& mesh,
+    const vectorField& faceAreas,
+    const vectorField& faceCentres,
+    const pointField& p,
+    const labelList& checkFaces,
+    labelHashSet* setPtr
+)
+{
+    if (minFlatness < -SMALL || minFlatness > 1+SMALL)
+    {
+        FatalErrorIn
+        (
+            "polyMeshGeometry::checkFaceFlatness"
+            "(const bool, const scalar, const polyMesh&, const pointField&"
+            ", const pointField&, const labelList&, labelHashSet*)"
+        )   << "minFlatness should be [0..1] but is now " << minFlatness
+            << abort(FatalError);
+    }
+
+    const faceList& fcs = mesh.faces();
+
+    label nWarped = 0;
+
+    forAll(checkFaces, i)
+    {
+        label faceI = checkFaces[i];
+
+        const face& f = fcs[faceI];
+
+        if (f.size() > 3)
+        {
+            const point& fc = faceCentres[faceI];
+
+            // Sum triangle areas
+            scalar sumArea = 0.0;
+
+            forAll(f, fp)
+            {
+                sumArea += triPointRef
+                (
+                    p[f[fp]],
+                    p[f.nextLabel(fp)],
+                    fc
+                ).mag();
+            }
+
+            if (sumArea/mag(faceAreas[faceI]) < minFlatness)
+            {
+                nWarped++;
+
+                if (setPtr)
+                {
+                    setPtr->insert(faceI);
+                }
+            }
+        }
+    }
+
+    reduce(nWarped, sumOp<label>());
+
+    if (report)
+    {
+        if (nWarped> 0)
+        {
+            Info<< "There are " << nWarped
+                << " faces with area of invidual triangles"
+                << " compared to overall area less than "
+                << minFlatness << nl << endl;
+        }
+        else
+        {
+            Info<< "All faces are flat in that the area of invidual triangles"
+                << " compared to overall area is less than "
+                << minFlatness << nl << endl;
+        }
+    }
+
+    if (nWarped > 0)
+    {
+        if (report)
+        {
+            WarningIn
+            (
+                "polyMeshGeometry::checkFaceFlatness"
+                "(const bool, const scalar, const polyMesh&"
+                ", const pointField&, const pointField&, const labelList&"
+                ", labelHashSet*)"
+            )   << nWarped  << " non-flat faces "
+                << "(area of invidual triangles"
+                << " compared to overall area"
+                << " < " << minFlatness << ") found.\n"
+                << endl;
+        }
+
+        return true;
+    }
+    else
+    {
+        return false;
+    }
+}
+
+
 bool Foam::polyMeshGeometry::checkFaceArea
 (
     const bool report,
@@ -2398,6 +2502,29 @@ bool Foam::polyMeshGeometry::checkTriangleTwist
 }
 
 
+bool Foam::polyMeshGeometry::checkFaceFlatness
+(
+    const bool report,
+    const scalar minFlatness,
+    const pointField& p,
+    const labelList& checkFaces,
+    labelHashSet* setPtr
+) const
+{
+    return checkFaceFlatness
+    (
+        report,
+        minFlatness,
+        mesh_,
+        faceAreas_,
+        faceCentres_,
+        p,
+        checkFaces,
+        setPtr
+    );
+}
+
+
 bool Foam::polyMeshGeometry::checkFaceArea
 (
     const bool report,
diff --git a/src/dynamicMesh/motionSmoother/polyMeshGeometry/polyMeshGeometry.H b/src/dynamicMesh/motionSmoother/polyMeshGeometry/polyMeshGeometry.H
index 149fca822a..2ef8604cac 100644
--- a/src/dynamicMesh/motionSmoother/polyMeshGeometry/polyMeshGeometry.H
+++ b/src/dynamicMesh/motionSmoother/polyMeshGeometry/polyMeshGeometry.H
@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2011 OpenFOAM Foundation
+    \\  /    A nd           | Copyright (C) 2011-2012 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -303,6 +303,19 @@ public:
                 labelHashSet* setPtr
             );
 
+            //- Area of faces v.s. sum of triangle areas
+            static bool checkFaceFlatness
+            (
+                const bool report,
+                const scalar minFlatness,
+                const polyMesh&,
+                const vectorField& faceAreas,
+                const vectorField& faceCentres,
+                const pointField& p,
+                const labelList& checkFaces,
+                labelHashSet* setPtr
+            );
+
             //- Small faces
             static bool checkFaceArea
             (
@@ -314,6 +327,7 @@ public:
                 labelHashSet* setPtr
             );
 
+            //- Area of internal faces v.s. boundary faces
             static bool checkCellDeterminant
             (
                 const bool report,
@@ -413,6 +427,15 @@ public:
                 labelHashSet* setPtr
             ) const;
 
+            bool checkFaceFlatness
+            (
+                const bool report,
+                const scalar minFlatness,
+                const pointField& p,
+                const labelList& checkFaces,
+                labelHashSet* setPtr
+            ) const;
+
             bool checkFaceArea
             (
                 const bool report,

From 6ab24c9f65431c4908df255fa22ff57878f1dcdd Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Thu, 22 Nov 2012 09:14:46 +0000
Subject: [PATCH 6/6] STYLE: snappyHexMesh: improved comment

---
 .../autoHexMesh/refinementSurfaces/refinementSurfaces.H        | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/mesh/autoMesh/autoHexMesh/refinementSurfaces/refinementSurfaces.H b/src/mesh/autoMesh/autoHexMesh/refinementSurfaces/refinementSurfaces.H
index 2f685ed4ff..aed21821b5 100644
--- a/src/mesh/autoMesh/autoHexMesh/refinementSurfaces/refinementSurfaces.H
+++ b/src/mesh/autoMesh/autoHexMesh/refinementSurfaces/refinementSurfaces.H
@@ -168,7 +168,8 @@ public:
                 return names_;
             }
 
-            //- Per 'interface' surface : name of faceZone to put faces into
+            //- Per 'interface' surface : empty or name of faceZone to put
+            //  faces into
             const wordList& faceZoneNames() const
             {
                 return faceZoneNames_;