From e2336fefd3be87c61b9f77eaaddaf9484de2b6e2 Mon Sep 17 00:00:00 2001
From: Henry Weller <http://cfd.direct>
Date: Sun, 12 Jun 2016 20:51:07 +0100
Subject: [PATCH] checkMesh: Added writing of faceSets and cellSets containing
 errors

In parallel the sets are reconstructed. e.g.

mpirun -np 6 checkMesh -parallel -allGeometry -allTopology -writeSets vtk

will create a postProcessing/ folder with the vtk files of the
(reconstructed) faceSets and cellSets.

Also improved analysis of disconnected regions now also checks for point
connectivity with is useful for detecting if AMI regions have duplicate
points.

Patch contributed by Mattijs Janssens
---
 .../mesh/manipulation/checkMesh/Make/files    |   2 +-
 .../mesh/manipulation/checkMesh/Make/options  |   4 +
 .../manipulation/checkMesh/checkGeometry.C    |  69 +++-
 .../manipulation/checkMesh/checkGeometry.H    |   8 +-
 .../mesh/manipulation/checkMesh/checkMesh.C   |  46 ++-
 .../manipulation/checkMesh/checkMeshQuality.C |  10 +-
 .../manipulation/checkMesh/checkMeshQuality.H |   9 +-
 .../mesh/manipulation/checkMesh/checkTools.C  | 374 ++++++++++++++++++
 .../mesh/manipulation/checkMesh/checkTools.H  |  33 ++
 .../manipulation/checkMesh/checkTopology.C    |  96 ++++-
 .../manipulation/checkMesh/checkTopology.H    |  11 +-
 .../primitiveMesh/PatchTools/PatchTools.H     |  29 ++
 .../PatchTools/PatchToolsGatherAndMerge.C     | 105 ++++-
 13 files changed, 775 insertions(+), 21 deletions(-)
 create mode 100644 applications/utilities/mesh/manipulation/checkMesh/checkTools.C
 create mode 100644 applications/utilities/mesh/manipulation/checkMesh/checkTools.H

diff --git a/applications/utilities/mesh/manipulation/checkMesh/Make/files b/applications/utilities/mesh/manipulation/checkMesh/Make/files
index 1a3130a23c..21febe2789 100644
--- a/applications/utilities/mesh/manipulation/checkMesh/Make/files
+++ b/applications/utilities/mesh/manipulation/checkMesh/Make/files
@@ -1,4 +1,4 @@
-printMeshStats.C
+checkTools.C
 checkTopology.C
 checkGeometry.C
 checkMeshQuality.C
diff --git a/applications/utilities/mesh/manipulation/checkMesh/Make/options b/applications/utilities/mesh/manipulation/checkMesh/Make/options
index 2ff5dbabfe..4700e225a5 100644
--- a/applications/utilities/mesh/manipulation/checkMesh/Make/options
+++ b/applications/utilities/mesh/manipulation/checkMesh/Make/options
@@ -1,8 +1,12 @@
 EXE_INC = \
     -I$(LIB_SRC)/meshTools/lnInclude \
     -I$(LIB_SRC)/finiteVolume/lnInclude \
+    -I$(LIB_SRC)/sampling/lnInclude \
+    -I$(LIB_SRC)/surfMesh/lnInclude \
     -I$(LIB_SRC)/dynamicMesh/lnInclude
 
 EXE_LIBS = \
     -lmeshTools \
+    -lsampling \
+    -lsurfMesh \
     -ldynamicMesh
diff --git a/applications/utilities/mesh/manipulation/checkMesh/checkGeometry.C b/applications/utilities/mesh/manipulation/checkMesh/checkGeometry.C
index 655b43a1b2..6646456d54 100644
--- a/applications/utilities/mesh/manipulation/checkMesh/checkGeometry.C
+++ b/applications/utilities/mesh/manipulation/checkMesh/checkGeometry.C
@@ -7,6 +7,8 @@
 #include "wedgePolyPatch.H"
 #include "unitConversion.H"
 #include "polyMeshTetDecomposition.H"
+#include "surfaceWriter.H"
+#include "checkTools.H"
 
 
 // Find wedge with opposite orientation. Note: does not actually check that
@@ -472,7 +474,12 @@ bool Foam::checkCoupledPoints
 }
 
 
-Foam::label Foam::checkGeometry(const polyMesh& mesh, const bool allGeometry)
+Foam::label Foam::checkGeometry
+(
+    const polyMesh& mesh,
+    const bool allGeometry,
+    const autoPtr<surfaceWriter>& writer
+)
 {
     label noFailedChecks = 0;
 
@@ -558,6 +565,10 @@ Foam::label Foam::checkGeometry(const polyMesh& mesh, const bool allGeometry)
                     << " non closed cells to set " << cells.name() << endl;
                 cells.instance() = mesh.pointsInstance();
                 cells.write();
+                if (writer.valid())
+                {
+                    mergeAndWrite(writer(), cells);
+                }
             }
         }
 
@@ -570,6 +581,10 @@ Foam::label Foam::checkGeometry(const polyMesh& mesh, const bool allGeometry)
                 << aspectCells.name() << endl;
             aspectCells.instance() = mesh.pointsInstance();
             aspectCells.write();
+            if (writer.valid())
+            {
+                mergeAndWrite(writer(), aspectCells);
+            }
         }
     }
 
@@ -587,6 +602,10 @@ Foam::label Foam::checkGeometry(const polyMesh& mesh, const bool allGeometry)
                     << " zero area faces to set " << faces.name() << endl;
                 faces.instance() = mesh.pointsInstance();
                 faces.write();
+                if (writer.valid())
+                {
+                    mergeAndWrite(writer(), faces);
+                }
             }
         }
     }
@@ -605,6 +624,10 @@ Foam::label Foam::checkGeometry(const polyMesh& mesh, const bool allGeometry)
                     << " zero volume cells to set " << cells.name() << endl;
                 cells.instance() = mesh.pointsInstance();
                 cells.write();
+                if (writer.valid())
+                {
+                    mergeAndWrite(writer(), cells);
+                }
             }
         }
     }
@@ -624,6 +647,10 @@ Foam::label Foam::checkGeometry(const polyMesh& mesh, const bool allGeometry)
                 << " non-orthogonal faces to set " << faces.name() << endl;
             faces.instance() = mesh.pointsInstance();
             faces.write();
+            if (writer.valid())
+            {
+                mergeAndWrite(writer(), faces);
+            }
         }
     }
 
@@ -642,6 +669,10 @@ Foam::label Foam::checkGeometry(const polyMesh& mesh, const bool allGeometry)
                     << faces.name() << endl;
                 faces.instance() = mesh.pointsInstance();
                 faces.write();
+                if (writer.valid())
+                {
+                    mergeAndWrite(writer(), faces);
+                }
             }
         }
     }
@@ -660,6 +691,10 @@ Foam::label Foam::checkGeometry(const polyMesh& mesh, const bool allGeometry)
                     << " skew faces to set " << faces.name() << endl;
                 faces.instance() = mesh.pointsInstance();
                 faces.write();
+                if (writer.valid())
+                {
+                    mergeAndWrite(writer(), faces);
+                }
             }
         }
     }
@@ -680,6 +715,10 @@ Foam::label Foam::checkGeometry(const polyMesh& mesh, const bool allGeometry)
                     << faces.name() << endl;
                 faces.instance() = mesh.pointsInstance();
                 faces.write();
+                if (writer.valid())
+                {
+                    mergeAndWrite(writer(), faces);
+                }
             }
         }
     }
@@ -709,6 +748,10 @@ Foam::label Foam::checkGeometry(const polyMesh& mesh, const bool allGeometry)
                     << "decomposition tets to set " << faces.name() << endl;
                 faces.instance() = mesh.pointsInstance();
                 faces.write();
+                if (writer.valid())
+                {
+                    mergeAndWrite(writer(), faces);
+                }
             }
         }
     }
@@ -769,6 +812,10 @@ Foam::label Foam::checkGeometry(const polyMesh& mesh, const bool allGeometry)
                     << endl;
                 faces.instance() = mesh.pointsInstance();
                 faces.write();
+                if (writer.valid())
+                {
+                    mergeAndWrite(writer(), faces);
+                }
             }
         }
     }
@@ -788,6 +835,10 @@ Foam::label Foam::checkGeometry(const polyMesh& mesh, const bool allGeometry)
                     << " warped faces to set " << faces.name() << endl;
                 faces.instance() = mesh.pointsInstance();
                 faces.write();
+                if (writer.valid())
+                {
+                    mergeAndWrite(writer(), faces);
+                }
             }
         }
     }
@@ -805,6 +856,10 @@ Foam::label Foam::checkGeometry(const polyMesh& mesh, const bool allGeometry)
                 << " under-determined cells to set " << cells.name() << endl;
             cells.instance() = mesh.pointsInstance();
             cells.write();
+            if (writer.valid())
+            {
+                mergeAndWrite(writer(), cells);
+            }
         }
     }
 
@@ -821,6 +876,10 @@ Foam::label Foam::checkGeometry(const polyMesh& mesh, const bool allGeometry)
                 << " concave cells to set " << cells.name() << endl;
             cells.instance() = mesh.pointsInstance();
             cells.write();
+            if (writer.valid())
+            {
+                mergeAndWrite(writer(), cells);
+            }
         }
     }
 
@@ -838,6 +897,10 @@ Foam::label Foam::checkGeometry(const polyMesh& mesh, const bool allGeometry)
                 << faces.name() << endl;
             faces.instance() = mesh.pointsInstance();
             faces.write();
+            if (writer.valid())
+            {
+                mergeAndWrite(writer(), faces);
+            }
         }
     }
 
@@ -855,6 +918,10 @@ Foam::label Foam::checkGeometry(const polyMesh& mesh, const bool allGeometry)
                 << faces.name() << endl;
             faces.instance() = mesh.pointsInstance();
             faces.write();
+            if (writer.valid())
+            {
+                mergeAndWrite(writer(), faces);
+            }
         }
     }
 
diff --git a/applications/utilities/mesh/manipulation/checkMesh/checkGeometry.H b/applications/utilities/mesh/manipulation/checkMesh/checkGeometry.H
index edc1f44826..9658512eb1 100644
--- a/applications/utilities/mesh/manipulation/checkMesh/checkGeometry.H
+++ b/applications/utilities/mesh/manipulation/checkMesh/checkGeometry.H
@@ -6,6 +6,7 @@ namespace Foam
 {
     class polyMesh;
     class wedgePolyPatch;
+    class surfaceWriter;
 
     label findOppositeWedge(const polyMesh&, const wedgePolyPatch&);
 
@@ -21,5 +22,10 @@ namespace Foam
     //- Check 0th vertex on coupled faces
     bool checkCoupledPoints(const polyMesh&, const bool report, labelHashSet*);
 
-    label checkGeometry(const polyMesh& mesh, const bool allGeometry);
+    label checkGeometry
+    (
+        const polyMesh& mesh,
+        const bool allGeometry,
+        const autoPtr<surfaceWriter>&
+    );
 }
diff --git a/applications/utilities/mesh/manipulation/checkMesh/checkMesh.C b/applications/utilities/mesh/manipulation/checkMesh/checkMesh.C
index 93f4b27288..07b831e1fd 100644
--- a/applications/utilities/mesh/manipulation/checkMesh/checkMesh.C
+++ b/applications/utilities/mesh/manipulation/checkMesh/checkMesh.C
@@ -42,16 +42,20 @@ Usage
     \param -region \<name\> \n
     Specify an alternative mesh region.
 
+    \param -writeSets \<surfaceFormat\> \n
+    Reconstruct all cellSets and faceSets geometry and write to postProcessing/
+    directory according to surfaceFormat (e.g. vtk or ensight)
+
 \*---------------------------------------------------------------------------*/
 
 #include "argList.H"
 #include "timeSelector.H"
 #include "Time.H"
-
 #include "polyMesh.H"
 #include "globalMeshData.H"
+#include "vtkSurfaceWriter.H"
 
-#include "printMeshStats.H"
+#include "checkTools.H"
 #include "checkTopology.H"
 #include "checkGeometry.H"
 #include "checkMeshQuality.H"
@@ -84,6 +88,12 @@ int main(int argc, char *argv[])
         "meshQuality",
         "read user-defined mesh quality criterions from system/meshQualityDict"
     );
+    argList::addOption
+    (
+        "writeSets",
+        "<surfaceFormat>"
+        "reconstruct and write all faceSets and cellSets in selected format"
+    );
 
     #include "setRootCase.H"
     #include "createTime.H"
@@ -95,6 +105,9 @@ int main(int argc, char *argv[])
     const bool allTopology = args.optionFound("allTopology");
     const bool meshQuality = args.optionFound("meshQuality");
 
+    word surfaceFormat;
+    const bool writeSets = args.optionReadIfPresent("writeSets", surfaceFormat);
+
     if (noTopology)
     {
         Info<< "Disabling all topology checks." << nl << endl;
@@ -112,6 +125,12 @@ int main(int argc, char *argv[])
     {
         Info<< "Enabling user-defined geometry checks." << nl << endl;
     }
+    if (writeSets)
+    {
+        Info<< "Reconstructing and writing " << surfaceFormat
+            << " representation"
+            << " of all faceSets and cellSets." << nl << endl;
+    }
 
 
     autoPtr<IOdictionary> qualDict;
@@ -134,6 +153,13 @@ int main(int argc, char *argv[])
     }
 
 
+    autoPtr<surfaceWriter> writer;
+    if (writeSets)
+    {
+        writer = surfaceWriter::New(surfaceFormat);
+    }
+
+
     forAll(timeDirs, timeI)
     {
         runTime.setTime(timeDirs[timeI], timeI);
@@ -158,14 +184,20 @@ int main(int argc, char *argv[])
 
             if (!noTopology)
             {
-                nFailedChecks += checkTopology(mesh, allTopology, allGeometry);
+                nFailedChecks += checkTopology
+                (
+                    mesh,
+                    allTopology,
+                    allGeometry,
+                    writer
+                );
             }
 
-            nFailedChecks += checkGeometry(mesh, allGeometry);
+            nFailedChecks += checkGeometry(mesh, allGeometry, writer);
 
             if (meshQuality)
             {
-                nFailedChecks += checkMeshQuality(mesh, qualDict());
+                nFailedChecks += checkMeshQuality(mesh, qualDict(), writer);
             }
 
 
@@ -186,11 +218,11 @@ int main(int argc, char *argv[])
         {
             Info<< "Time = " << runTime.timeName() << nl << endl;
 
-            label nFailedChecks = checkGeometry(mesh, allGeometry);
+            label nFailedChecks = checkGeometry(mesh, allGeometry, writer);
 
             if (meshQuality)
             {
-                nFailedChecks += checkMeshQuality(mesh, qualDict());
+                nFailedChecks += checkMeshQuality(mesh, qualDict(), writer);
             }
 
 
diff --git a/applications/utilities/mesh/manipulation/checkMesh/checkMeshQuality.C b/applications/utilities/mesh/manipulation/checkMesh/checkMeshQuality.C
index b00f02f8ef..a6a01c7336 100644
--- a/applications/utilities/mesh/manipulation/checkMesh/checkMeshQuality.C
+++ b/applications/utilities/mesh/manipulation/checkMesh/checkMeshQuality.C
@@ -3,12 +3,14 @@
 #include "cellSet.H"
 #include "faceSet.H"
 #include "motionSmoother.H"
-
+#include "surfaceWriter.H"
+#include "checkTools.H"
 
 Foam::label Foam::checkMeshQuality
 (
     const polyMesh& mesh,
-    const dictionary& dict
+    const dictionary& dict,
+    const autoPtr<surfaceWriter>& writer
 )
 {
     label noFailedChecks = 0;
@@ -27,6 +29,10 @@ Foam::label Foam::checkMeshQuality
                 << " faces in error to set " << faces.name() << endl;
             faces.instance() = mesh.pointsInstance();
             faces.write();
+            if (writer.valid())
+            {
+                mergeAndWrite(writer(), faces);
+            }
         }
     }
 
diff --git a/applications/utilities/mesh/manipulation/checkMesh/checkMeshQuality.H b/applications/utilities/mesh/manipulation/checkMesh/checkMeshQuality.H
index 1e5b3489c9..52507986bf 100644
--- a/applications/utilities/mesh/manipulation/checkMesh/checkMeshQuality.H
+++ b/applications/utilities/mesh/manipulation/checkMesh/checkMeshQuality.H
@@ -2,5 +2,12 @@
 
 namespace Foam
 {
-    label checkMeshQuality(const polyMesh& mesh, const dictionary&);
+    class surfaceWriter;
+
+    label checkMeshQuality
+    (
+        const polyMesh&,
+        const dictionary&,
+        const autoPtr<surfaceWriter>&
+    );
 }
diff --git a/applications/utilities/mesh/manipulation/checkMesh/checkTools.C b/applications/utilities/mesh/manipulation/checkMesh/checkTools.C
new file mode 100644
index 0000000000..e68ff5d7eb
--- /dev/null
+++ b/applications/utilities/mesh/manipulation/checkMesh/checkTools.C
@@ -0,0 +1,374 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 2015-2016 OpenFOAM Foundation
+     \\/     M anipulation  |
+-------------------------------------------------------------------------------
+License
+    This file is part of OpenFOAM.
+
+    OpenFOAM is free software: you can redistribute it and/or modify it
+    under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
+    ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+    FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
+    for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
+
+\*---------------------------------------------------------------------------*/
+
+#include "checkTools.H"
+#include "polyMesh.H"
+#include "globalMeshData.H"
+#include "hexMatcher.H"
+#include "wedgeMatcher.H"
+#include "prismMatcher.H"
+#include "pyrMatcher.H"
+#include "tetWedgeMatcher.H"
+#include "tetMatcher.H"
+#include "IOmanip.H"
+#include "faceSet.H"
+#include "cellSet.H"
+#include "Time.H"
+#include "surfaceWriter.H"
+#include "syncTools.H"
+#include "globalIndex.H"
+#include "PatchTools.H"
+
+
+void Foam::printMeshStats(const polyMesh& mesh, const bool allTopology)
+{
+    Info<< "Mesh stats" << nl
+        << "    points:           "
+        << returnReduce(mesh.points().size(), sumOp<label>()) << nl;
+
+    label nInternalPoints = returnReduce
+    (
+        mesh.nInternalPoints(),
+        sumOp<label>()
+    );
+
+    if (nInternalPoints != -Pstream::nProcs())
+    {
+        Info<< "    internal points:  " << nInternalPoints << nl;
+
+        if (returnReduce(mesh.nInternalPoints(), minOp<label>()) == -1)
+        {
+            WarningInFunction
+                << "Some processors have their points sorted into internal"
+                << " and external and some do not." << endl
+                << "This can cause problems later on." << endl;
+        }
+    }
+
+    if (allTopology && nInternalPoints != -Pstream::nProcs())
+    {
+        label nEdges = returnReduce(mesh.nEdges(), sumOp<label>());
+        label nInternalEdges = returnReduce
+        (
+            mesh.nInternalEdges(),
+            sumOp<label>()
+        );
+        label nInternal1Edges = returnReduce
+        (
+            mesh.nInternal1Edges(),
+            sumOp<label>()
+        );
+        label nInternal0Edges = returnReduce
+        (
+            mesh.nInternal0Edges(),
+            sumOp<label>()
+        );
+
+        Info<< "    edges:            " << nEdges << nl
+            << "    internal edges:   " << nInternalEdges << nl
+            << "    internal edges using one boundary point:   "
+            << nInternal1Edges-nInternal0Edges << nl
+            << "    internal edges using two boundary points:  "
+            << nInternalEdges-nInternal1Edges << nl;
+    }
+
+    label nFaces = returnReduce(mesh.faces().size(), sumOp<label>());
+    label nIntFaces = returnReduce(mesh.faceNeighbour().size(), sumOp<label>());
+    label nCells = returnReduce(mesh.cells().size(), sumOp<label>());
+
+    Info<< "    faces:            " << nFaces << nl
+        << "    internal faces:   " << nIntFaces << nl
+        << "    cells:            " << nCells << nl
+        << "    faces per cell:   "
+        << scalar(nFaces + nIntFaces)/max(1, nCells) << nl
+        << "    boundary patches: " << mesh.boundaryMesh().size() << nl
+        << "    point zones:      " << mesh.pointZones().size() << nl
+        << "    face zones:       " << mesh.faceZones().size() << nl
+        << "    cell zones:       " << mesh.cellZones().size() << nl
+        << endl;
+
+    // Construct shape recognizers
+    hexMatcher hex;
+    prismMatcher prism;
+    wedgeMatcher wedge;
+    pyrMatcher pyr;
+    tetWedgeMatcher tetWedge;
+    tetMatcher tet;
+
+    // Counters for different cell types
+    label nHex = 0;
+    label nWedge = 0;
+    label nPrism = 0;
+    label nPyr = 0;
+    label nTet = 0;
+    label nTetWedge = 0;
+    label nUnknown = 0;
+
+    Map<label> polyhedralFaces;
+
+    for (label celli = 0; celli < mesh.nCells(); celli++)
+    {
+        if (hex.isA(mesh, celli))
+        {
+            nHex++;
+        }
+        else if (tet.isA(mesh, celli))
+        {
+            nTet++;
+        }
+        else if (pyr.isA(mesh, celli))
+        {
+            nPyr++;
+        }
+        else if (prism.isA(mesh, celli))
+        {
+            nPrism++;
+        }
+        else if (wedge.isA(mesh, celli))
+        {
+            nWedge++;
+        }
+        else if (tetWedge.isA(mesh, celli))
+        {
+            nTetWedge++;
+        }
+        else
+        {
+            nUnknown++;
+            polyhedralFaces(mesh.cells()[celli].size())++;
+        }
+    }
+
+    reduce(nHex,sumOp<label>());
+    reduce(nPrism,sumOp<label>());
+    reduce(nWedge,sumOp<label>());
+    reduce(nPyr,sumOp<label>());
+    reduce(nTetWedge,sumOp<label>());
+    reduce(nTet,sumOp<label>());
+    reduce(nUnknown,sumOp<label>());
+
+    Info<< "Overall number of cells of each type:" << nl
+        << "    hexahedra:     " << nHex << nl
+        << "    prisms:        " << nPrism << nl
+        << "    wedges:        " << nWedge << nl
+        << "    pyramids:      " << nPyr << nl
+        << "    tet wedges:    " << nTetWedge << nl
+        << "    tetrahedra:    " << nTet << nl
+        << "    polyhedra:     " << nUnknown
+        << endl;
+
+    if (nUnknown > 0)
+    {
+        Pstream::mapCombineGather(polyhedralFaces, plusEqOp<label>());
+
+        Info<< "    Breakdown of polyhedra by number of faces:" << nl
+            << "        faces" << "   number of cells" << endl;
+
+        const labelList sortedKeys = polyhedralFaces.sortedToc();
+
+        forAll(sortedKeys, keyI)
+        {
+            const label nFaces = sortedKeys[keyI];
+
+            Info<< setf(std::ios::right) << setw(13)
+                << nFaces << "   " << polyhedralFaces[nFaces] << nl;
+        }
+    }
+
+    Info<< endl;
+}
+
+
+void Foam::mergeAndWrite
+(
+    const polyMesh& mesh,
+    const surfaceWriter& writer,
+    const word& name,
+    const indirectPrimitivePatch setPatch,
+    const fileName& outputDir
+)
+{
+    if (Pstream::parRun())
+    {
+        labelList pointToGlobal;
+        labelList uniqueMeshPointLabels;
+        autoPtr<globalIndex> globalPoints;
+        autoPtr<globalIndex> globalFaces;
+        faceList mergedFaces;
+        pointField mergedPoints;
+        Foam::PatchTools::gatherAndMerge
+        (
+            mesh,
+            setPatch.localFaces(),
+            setPatch.meshPoints(),
+            setPatch.meshPointMap(),
+
+            pointToGlobal,
+            uniqueMeshPointLabels,
+            globalPoints,
+            globalFaces,
+
+            mergedFaces,
+            mergedPoints
+        );
+
+        // Write
+        if (Pstream::master())
+        {
+            writer.write(outputDir, name, mergedPoints, mergedFaces);
+        }
+    }
+    else
+    {
+        writer.write
+        (
+            outputDir,
+            name,
+            setPatch.localPoints(),
+            setPatch.localFaces()
+        );
+    }
+}
+
+
+void Foam::mergeAndWrite
+(
+    const surfaceWriter& writer,
+    const faceSet& set
+)
+{
+    const polyMesh& mesh = refCast<const polyMesh>(set.db());
+
+    const indirectPrimitivePatch setPatch
+    (
+        IndirectList<face>(mesh.faces(), set.sortedToc()),
+        mesh.points()
+    );
+
+    const fileName outputDir
+    (
+        set.time().path()
+      / (Pstream::parRun() ? ".." : "")
+      / "postProcessing"
+      / mesh.pointsInstance()
+      / set.name()
+    );
+
+    mergeAndWrite(mesh, writer, set.name(), setPatch, outputDir);
+}
+
+
+void Foam::mergeAndWrite
+(
+    const surfaceWriter& writer,
+    const cellSet& set
+)
+{
+    const polyMesh& mesh = refCast<const polyMesh>(set.db());
+    const polyBoundaryMesh& pbm = mesh.boundaryMesh();
+
+
+    // Determine faces on outside of cellSet
+    PackedBoolList isInSet(mesh.nCells());
+    forAllConstIter(cellSet, set, iter)
+    {
+        isInSet[iter.key()] = true;
+    }
+
+
+    boolList bndInSet(mesh.nFaces()-mesh.nInternalFaces());
+    forAll(pbm, patchi)
+    {
+        const polyPatch& pp = pbm[patchi];
+        const labelList& fc = pp.faceCells();
+        forAll(fc, i)
+        {
+            bndInSet[pp.start()+i-mesh.nInternalFaces()] = isInSet[fc[i]];
+        }
+    }
+    syncTools::swapBoundaryFaceList(mesh, bndInSet);
+
+
+    DynamicList<label> outsideFaces(3*set.size());
+    for (label facei = 0; facei < mesh.nInternalFaces(); facei++)
+    {
+        bool ownVal = isInSet[mesh.faceOwner()[facei]];
+        bool neiVal = isInSet[mesh.faceNeighbour()[facei]];
+
+        if (ownVal != neiVal)
+        {
+            outsideFaces.append(facei);
+        }
+    }
+
+
+    forAll(pbm, patchi)
+    {
+        const polyPatch& pp = pbm[patchi];
+        const labelList& fc = pp.faceCells();
+        if (pp.coupled())
+        {
+            forAll(fc, i)
+            {
+                label facei = pp.start()+i;
+
+                bool neiVal = bndInSet[facei-mesh.nInternalFaces()];
+                if (isInSet[fc[i]] && !neiVal)
+                {
+                    outsideFaces.append(facei);
+                }
+            }
+        }
+        else
+        {
+            forAll(fc, i)
+            {
+                if (isInSet[fc[i]])
+                {
+                    outsideFaces.append(pp.start()+i);
+                }
+            }
+        }
+    }
+
+
+    const indirectPrimitivePatch setPatch
+    (
+        IndirectList<face>(mesh.faces(), outsideFaces),
+        mesh.points()
+    );
+
+    const fileName outputDir
+    (
+        set.time().path()
+      / (Pstream::parRun() ? ".." : "")
+      / "postProcessing"
+      / mesh.pointsInstance()
+      / set.name()
+    );
+
+
+    mergeAndWrite(mesh, writer, set.name(), setPatch, outputDir);
+}
diff --git a/applications/utilities/mesh/manipulation/checkMesh/checkTools.H b/applications/utilities/mesh/manipulation/checkMesh/checkTools.H
new file mode 100644
index 0000000000..edde0acdf0
--- /dev/null
+++ b/applications/utilities/mesh/manipulation/checkMesh/checkTools.H
@@ -0,0 +1,33 @@
+#include "scalar.H"
+#include "indirectPrimitivePatch.H"
+
+namespace Foam
+{
+    class polyMesh;
+    class surfaceWriter;
+    class faceSet;
+    class cellSet;
+    class fileName;
+    class polyMesh;
+
+    void printMeshStats(const polyMesh& mesh, const bool allTopology);
+
+    //- Generate merged surface on master and write. Needs input patch
+    //  to be of mesh faces.
+    void mergeAndWrite
+    (
+        const polyMesh& mesh,
+        const surfaceWriter& writer,
+        const word& name,
+        const indirectPrimitivePatch setPatch,
+        const fileName& outputDir
+    );
+
+    //- Write vtk representation of (assembled) faceSet to vtk file in
+    //  postProcessing/ directory
+    void mergeAndWrite(const surfaceWriter&, const faceSet&);
+
+    //- Write vtk representation of (assembled) cellSet to vtk file in
+    //  postProcessing/ directory
+    void mergeAndWrite(const surfaceWriter&, const cellSet&);
+}
diff --git a/applications/utilities/mesh/manipulation/checkMesh/checkTopology.C b/applications/utilities/mesh/manipulation/checkMesh/checkTopology.C
index fa8dc854b2..f7dc98ac6e 100644
--- a/applications/utilities/mesh/manipulation/checkMesh/checkTopology.C
+++ b/applications/utilities/mesh/manipulation/checkMesh/checkTopology.C
@@ -33,6 +33,8 @@ License
 #include "IOmanip.H"
 #include "emptyPolyPatch.H"
 #include "processorPolyPatch.H"
+#include "surfaceWriter.H"
+#include "checkTools.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
@@ -40,7 +42,8 @@ Foam::label Foam::checkTopology
 (
     const polyMesh& mesh,
     const bool allTopology,
-    const bool allGeometry
+    const bool allGeometry,
+    const autoPtr<surfaceWriter>& writer
 )
 {
     label noFailedChecks = 0;
@@ -126,6 +129,11 @@ Foam::label Foam::checkTopology
                 << " illegal cells to set " << cells.name() << endl;
             cells.instance() = mesh.pointsInstance();
             cells.write();
+            if (writer.valid())
+            {
+                mergeAndWrite(writer(), cells);
+            }
+
         }
         else
         {
@@ -164,6 +172,10 @@ Foam::label Foam::checkTopology
                 << " unordered faces to set " << faces.name() << endl;
             faces.instance() = mesh.pointsInstance();
             faces.write();
+            if (writer.valid())
+            {
+                mergeAndWrite(writer(), faces);
+            }
         }
     }
 
@@ -180,6 +192,10 @@ Foam::label Foam::checkTopology
                 << faces.name() << endl;
             faces.instance() = mesh.pointsInstance();
             faces.write();
+            if (writer.valid())
+            {
+                mergeAndWrite(writer(), faces);
+            }
         }
     }
 
@@ -197,6 +213,11 @@ Foam::label Foam::checkTopology
                 << endl;
             cells.instance() = mesh.pointsInstance();
             cells.write();
+            if (writer.valid())
+            {
+                mergeAndWrite(writer(), cells);
+            }
+
         }
     }
 
@@ -216,6 +237,10 @@ Foam::label Foam::checkTopology
                 << faces.name() << endl;
             faces.instance() = mesh.pointsInstance();
             faces.write();
+            if (writer.valid())
+            {
+                mergeAndWrite(writer(), faces);
+            }
         }
     }
 
@@ -267,6 +292,10 @@ Foam::label Foam::checkTopology
                 << endl;
             oneCells.instance() = mesh.pointsInstance();
             oneCells.write();
+            if (writer.valid())
+            {
+                mergeAndWrite(writer(), oneCells);
+            }
         }
 
         label nTwoCells = returnReduce(twoCells.size(), sumOp<label>());
@@ -279,6 +308,10 @@ Foam::label Foam::checkTopology
                 << endl;
             twoCells.instance() = mesh.pointsInstance();
             twoCells.write();
+            if (writer.valid())
+            {
+                mergeAndWrite(writer(), twoCells);
+            }
         }
     }
 
@@ -316,6 +349,53 @@ Foam::label Foam::checkTopology
             ctr.write();
 
 
+
+            // Is region disconnected
+            boolList regionDisconnected(rs.nRegions(), true);
+            if (allTopology)
+            {
+                // -1   : not assigned
+                // -2   : multiple regions
+                // >= 0 : single region
+                labelList pointToRegion(mesh.nPoints(), -1);
+
+                for
+                (
+                    label faceI = mesh.nInternalFaces();
+                    faceI < mesh.nFaces();
+                    faceI++
+                )
+                {
+                    label regionI = rs[mesh.faceOwner()[faceI]];
+                    const face& f = mesh.faces()[faceI];
+                    forAll(f, fp)
+                    {
+                        label& pRegion = pointToRegion[f[fp]];
+                        if (pRegion == -1)
+                        {
+                            pRegion = regionI;
+                        }
+                        else if (pRegion == -2)
+                        {
+                            // Already marked
+                            regionDisconnected[regionI] = false;
+                        }
+                        else if (pRegion != regionI)
+                        {
+                            // Multiple regions
+                            regionDisconnected[regionI] = false;
+                            regionDisconnected[pRegion] = false;
+                            pRegion = -2;
+                        }
+                    }
+                }
+
+                Pstream::listCombineGather(regionDisconnected, andEqOp<bool>());
+                Pstream::listCombineScatter(regionDisconnected);
+            }
+
+
+
             // write cellSet for each region
             PtrList<cellSet> cellRegions(rs.nRegions());
             for (label i = 0; i < rs.nRegions(); i++)
@@ -339,7 +419,19 @@ Foam::label Foam::checkTopology
 
             for (label i = 0; i < rs.nRegions(); i++)
             {
-                Info<< "  <<Writing region " << i << " with "
+                Info<< "  <<Writing region " << i;
+                if (allTopology)
+                {
+                    if (regionDisconnected[i])
+                    {
+                        Info<< " (fully disconnected)";
+                    }
+                    else
+                    {
+                        Info<< " (point connected)";
+                    }
+                }
+                Info<< " with "
                     << returnReduce(cellRegions[i].size(), sumOp<scalar>())
                     << " cells to cellSet " << cellRegions[i].name() << endl;
 
diff --git a/applications/utilities/mesh/manipulation/checkMesh/checkTopology.H b/applications/utilities/mesh/manipulation/checkMesh/checkTopology.H
index 70443a86b6..8e39fd9288 100644
--- a/applications/utilities/mesh/manipulation/checkMesh/checkTopology.H
+++ b/applications/utilities/mesh/manipulation/checkMesh/checkTopology.H
@@ -1,9 +1,16 @@
 #include "label.H"
-#include "wordList.H"
+#include "autoPtr.H"
 
 namespace Foam
 {
     class polyMesh;
+    class surfaceWriter;
 
-    label checkTopology(const polyMesh&, const bool, const bool);
+    label checkTopology
+    (
+        const polyMesh&,
+        const bool,
+        const bool,
+        const autoPtr<surfaceWriter>&
+    );
 }
diff --git a/src/OpenFOAM/meshes/primitiveMesh/PatchTools/PatchTools.H b/src/OpenFOAM/meshes/primitiveMesh/PatchTools/PatchTools.H
index c68f897346..dee687334c 100644
--- a/src/OpenFOAM/meshes/primitiveMesh/PatchTools/PatchTools.H
+++ b/src/OpenFOAM/meshes/primitiveMesh/PatchTools/PatchTools.H
@@ -47,6 +47,8 @@ SourceFiles
 
 #include "PrimitivePatch.H"
 #include "HashSet.H"
+#include "globalIndex.H"
+#include "autoPtr.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
@@ -301,6 +303,33 @@ public:
         List<Face>& mergedFaces,
         labelList& pointMergeMap
     );
+
+    //- Gather (mesh!) points and faces onto master and merge collocated
+    //  points into a single patch. Uses coupled point mesh
+    //  structure so does not need tolerances.
+    //  On master and slave returns:
+    //  - pointToGlobal : for every local point index the global point index
+    //  - uniqueMeshPointLabels : my local mesh points
+    //  - globalPoints : global numbering for the global points
+    //  - globalFaces : global numbering for the faces
+    //  On master only:
+    //  - mergedFaces : the merged faces
+    //  - mergedPoints : the merged points
+    template<class FaceList>
+    static void gatherAndMerge
+    (
+        const polyMesh& mesh,
+        const FaceList& faces,
+        const labelList& meshPoints,
+        const Map<label>& meshPointMap,
+
+        labelList& pointToGlobal,
+        labelList& uniqueMeshPointLabels,
+        autoPtr<globalIndex>& globalPoints,
+        autoPtr<globalIndex>& globalFaces,
+        List<typename FaceList::value_type>& mergedFaces,
+        pointField& mergedPoints
+    );
 };
 
 
diff --git a/src/OpenFOAM/meshes/primitiveMesh/PatchTools/PatchToolsGatherAndMerge.C b/src/OpenFOAM/meshes/primitiveMesh/PatchTools/PatchToolsGatherAndMerge.C
index 5a77d50858..3fd7b66000 100644
--- a/src/OpenFOAM/meshes/primitiveMesh/PatchTools/PatchToolsGatherAndMerge.C
+++ b/src/OpenFOAM/meshes/primitiveMesh/PatchTools/PatchToolsGatherAndMerge.C
@@ -24,11 +24,9 @@ License
 \*---------------------------------------------------------------------------*/
 
 #include "PatchTools.H"
-#include "ListListOps.H"
+#include "polyMesh.H"
+#include "globalMeshData.H"
 #include "mergePoints.H"
-#include "face.H"
-#include "triFace.H"
-#include "ListListOps.H"
 
 // * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
 
@@ -128,4 +126,103 @@ void Foam::PatchTools::gatherAndMerge
 }
 
 
+template<class FaceList>
+void Foam::PatchTools::gatherAndMerge
+(
+    const polyMesh& mesh,
+    const FaceList& localFaces,
+    const labelList& meshPoints,
+    const Map<label>& meshPointMap,
+
+    labelList& pointToGlobal,
+    labelList& uniqueMeshPointLabels,
+    autoPtr<globalIndex>& globalPointsPtr,
+    autoPtr<globalIndex>& globalFacesPtr,
+    List<typename FaceList::value_type>& mergedFaces,
+    pointField& mergedPoints
+)
+{
+    typedef typename FaceList::value_type FaceType;
+
+    if (Pstream::parRun())
+    {
+        // Renumber the setPatch points/faces into unique points
+        globalPointsPtr = mesh.globalData().mergePoints
+        (
+            meshPoints,
+            meshPointMap,
+            pointToGlobal,
+            uniqueMeshPointLabels
+        );
+
+        globalFacesPtr.reset(new globalIndex(localFaces.size()));
+
+        if (Pstream::master())
+        {
+            // Get renumbered local data
+            pointField myPoints(mesh.points(), uniqueMeshPointLabels);
+            List<FaceType> myFaces(localFaces);
+            forAll(myFaces, i)
+            {
+                inplaceRenumber(pointToGlobal, myFaces[i]);
+            }
+
+
+            mergedFaces.setSize(globalFacesPtr().size());
+            mergedPoints.setSize(globalPointsPtr().size());
+
+            // Insert master data first
+            label pOffset = globalPointsPtr().offset(Pstream::masterNo());
+            SubList<point>(mergedPoints, myPoints.size(), pOffset) = myPoints;
+
+            label fOffset = globalFacesPtr().offset(Pstream::masterNo());
+            SubList<FaceType>(mergedFaces, myFaces.size(), fOffset) = myFaces;
+
+
+            // Receive slave ones
+            for (int slave=1; slave<Pstream::nProcs(); slave++)
+            {
+                IPstream fromSlave(Pstream::scheduled, slave);
+
+                pointField slavePoints(fromSlave);
+                List<FaceType> slaveFaces(fromSlave);
+
+                label pOffset = globalPointsPtr().offset(slave);
+                SubList<point>(mergedPoints, slavePoints.size(), pOffset) =
+                    slavePoints;
+
+                label fOffset = globalFacesPtr().offset(slave);
+                SubList<FaceType>(mergedFaces, slaveFaces.size(), fOffset) =
+                    slaveFaces;
+            }
+        }
+        else
+        {
+            // Get renumbered local data
+            pointField myPoints(mesh.points(), uniqueMeshPointLabels);
+            List<FaceType> myFaces(localFaces);
+            forAll(myFaces, i)
+            {
+                inplaceRenumber(pointToGlobal, myFaces[i]);
+            }
+
+            // Construct processor stream with estimate of size. Could
+            // be improved.
+            OPstream toMaster
+            (
+                Pstream::scheduled,
+                Pstream::masterNo(),
+                myPoints.byteSize() + 4*sizeof(label)*myFaces.size()
+            );
+            toMaster << myPoints << myFaces;
+        }
+    }
+    else
+    {
+        mergedFaces = localFaces;
+        mergedPoints = pointField(mesh.points(), meshPoints);
+    }
+}
+
+
 // ************************************************************************* //