From a922f819996665dc34d82705e80c808f051373da Mon Sep 17 00:00:00 2001
From: mattijs <mattijs@hunt.opencfd.co.uk>
Date: Fri, 23 Jan 2009 17:57:30 +0000
Subject: [PATCH 1/7] one-off warning for unsorted boundaries

---
 .../meshes/polyMesh/polyBoundaryMesh/polyBoundaryMesh.C     | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/OpenFOAM/meshes/polyMesh/polyBoundaryMesh/polyBoundaryMesh.C b/src/OpenFOAM/meshes/polyMesh/polyBoundaryMesh/polyBoundaryMesh.C
index 261a952b06..ca11a21ec9 100644
--- a/src/OpenFOAM/meshes/polyMesh/polyBoundaryMesh/polyBoundaryMesh.C
+++ b/src/OpenFOAM/meshes/polyMesh/polyBoundaryMesh/polyBoundaryMesh.C
@@ -538,7 +538,7 @@ bool Foam::polyBoundaryMesh::checkDefinition(const bool report) const
 
     forAll (bm, patchI)
     {
-        if (bm[patchI].start() != nextPatchStart)
+        if (bm[patchI].start() != nextPatchStart && !boundaryError)
         {
             boundaryError = true;
 
@@ -547,7 +547,9 @@ bool Foam::polyBoundaryMesh::checkDefinition(const bool report) const
                 << " of type " <<  bm[patchI].type()
                 << ". The patch should start on face no " << nextPatchStart
                 << " and the patch specifies " << bm[patchI].start()
-                << "." << endl;
+                << "." << endl
+                << "Possibly consecutive patches have this same problem."
+                << " Suppressing future warnings." << endl;
         }
 
         nextPatchStart += bm[patchI].size();

From 1d46bf6fb095a3c9c8978780f6b21b1329ba59eb Mon Sep 17 00:00:00 2001
From: henry <Henry Weller h.weller@opencfd.co.uk>
Date: Mon, 26 Jan 2009 13:26:07 +0000
Subject: [PATCH 2/7] Corrected the handling of no transformation.

---
 src/OpenFOAM/fields/Fields/transformField/transformField.C | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/OpenFOAM/fields/Fields/transformField/transformField.C b/src/OpenFOAM/fields/Fields/transformField/transformField.C
index 11fe39e225..eef930b954 100644
--- a/src/OpenFOAM/fields/Fields/transformField/transformField.C
+++ b/src/OpenFOAM/fields/Fields/transformField/transformField.C
@@ -94,7 +94,7 @@ void Foam::transform
         }
         else
         {
-            rtf = vector::zero;
+            rtf = tf;
         }
     }
 }

From 038c1990515fb17c13b8e9cd1c957d4dc804ce8c Mon Sep 17 00:00:00 2001
From: henry <Henry Weller h.weller@opencfd.co.uk>
Date: Mon, 26 Jan 2009 13:26:42 +0000
Subject: [PATCH 3/7] Corrected the implementation of the spectral function.

---
 .../incompressible/LES/spectEddyVisc/spectEddyVisc.C   | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/turbulenceModels/incompressible/LES/spectEddyVisc/spectEddyVisc.C b/src/turbulenceModels/incompressible/LES/spectEddyVisc/spectEddyVisc.C
index 1f56b36328..28a563b4c6 100644
--- a/src/turbulenceModels/incompressible/LES/spectEddyVisc/spectEddyVisc.C
+++ b/src/turbulenceModels/incompressible/LES/spectEddyVisc/spectEddyVisc.C
@@ -108,13 +108,13 @@ spectEddyVisc::spectEddyVisc
 
 tmp<volScalarField> spectEddyVisc::k() const
 {
-    volScalarField Eps = 2*nuEff()*magSqr(symm(fvc::grad(U())));
+    volScalarField eps = 2*nuEff()*magSqr(symm(fvc::grad(U())));
 
     return
-        cK1_*pow(delta(), 2.0/3.0)*pow(Eps, 2.0/3.0)
-        *exp(-cK2_*pow(delta(), -4.0/3.0)*nu()/pow(Eps, 1.0/3.0))
-      - cK3_*pow(Eps*nu(), 1.0/2.0)
-       *erfc(cK4_*pow(delta(), -2.0/3.0)*pow(Eps, -1.0/6.0));
+        cK1_*pow(delta()*eps, 2.0/3.0)
+       *exp(-cK2_*pow(delta(), -4.0/3.0)*nu()/pow(eps, 1.0/3.0))
+      - cK3_*sqrt(eps*nu())
+       *erfc(cK4_*pow(delta(), -2.0/3.0)*sqrt(nu())*pow(eps, -1.0/6.0));
 }
 
 

From 1a1a919c70b73299648dd89c444d570941b3d957 Mon Sep 17 00:00:00 2001
From: henry <Henry Weller h.weller@opencfd.co.uk>
Date: Mon, 26 Jan 2009 13:27:03 +0000
Subject: [PATCH 4/7] Minor format change.

---
 .../containers/LinkedLists/linkTypes/SLListBase/SLListBase.H    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/OpenFOAM/containers/LinkedLists/linkTypes/SLListBase/SLListBase.H b/src/OpenFOAM/containers/LinkedLists/linkTypes/SLListBase/SLListBase.H
index 4f660a1e4d..0c67d7a56e 100644
--- a/src/OpenFOAM/containers/LinkedLists/linkTypes/SLListBase/SLListBase.H
+++ b/src/OpenFOAM/containers/LinkedLists/linkTypes/SLListBase/SLListBase.H
@@ -247,6 +247,7 @@ public:
         inline const_iterator begin() const;
         inline const const_iterator& end() const;
 
+
 private:
 
         //- iterator returned by end()
@@ -254,7 +255,6 @@ private:
 
         //- const_iterator returned by end()
         static const_iterator endConstIter_;
-
 };
 
 

From 8abbcc08c1ade31322145f89806d1df4e9778d0e Mon Sep 17 00:00:00 2001
From: mattijs <mattijs@hunt.opencfd.co.uk>
Date: Tue, 27 Jan 2009 20:18:35 +0000
Subject: [PATCH 5/7] added option for sloppily matching cell zones to regions

---
 .../splitMeshRegions/splitMeshRegions.C       | 385 ++++++++++++++----
 1 file changed, 309 insertions(+), 76 deletions(-)

diff --git a/applications/utilities/mesh/manipulation/splitMeshRegions/splitMeshRegions.C b/applications/utilities/mesh/manipulation/splitMeshRegions/splitMeshRegions.C
index a4b33b97dd..02accb32a8 100644
--- a/applications/utilities/mesh/manipulation/splitMeshRegions/splitMeshRegions.C
+++ b/applications/utilities/mesh/manipulation/splitMeshRegions/splitMeshRegions.C
@@ -30,12 +30,17 @@ Description
     - any face inbetween differing cellZones (-cellZones)
 
     Output is:
-    - mesh with multiple regions
+    - mesh with multiple regions or
     - mesh with cells put into cellZones (-makeCellZones)
 
-    Should work in parallel but cellZone interfaces cannot align with
+    Note:
+    - Should work in parallel but cellZone interfaces cannot align with
     processor boundaries so use the correct option in decomposition to
     preserve those interfaces.
+    - If a cell zone gets split into more than one region it can detect
+    the largest matching region (-sloppyCellZones). This will accept any
+    region that covers more than 50% of the zone. It has to be a subset
+    so cannot have any cells in any other zone.
 
 \*---------------------------------------------------------------------------*/
 
@@ -1036,78 +1041,181 @@ EdgeMap<label> addRegionPatches
 }
 
 
-// Checks if regionI in cellRegion corresponds to existing zone.
-label findCorrespondingZone
+//// Checks if regionI in cellRegion is subset of existing cellZone. Returns -1
+//// if no zone found, zone otherwise
+//label findCorrespondingSubZone
+//(
+//    const cellZoneMesh& cellZones,
+//    const labelList& existingZoneID,
+//    const labelList& cellRegion,
+//    const label regionI
+//)
+//{
+//    // Zone corresponding to region. No corresponding zone.
+//    label zoneI = labelMax;
+//
+//    labelList regionCells = findIndices(cellRegion, regionI);
+//
+//    if (regionCells.empty())
+//    {
+//        // My local portion is empty. Maps to any empty cellZone. Mark with
+//        // special value which can get overwritten by other processors.
+//        zoneI = -1;
+//    }
+//    else
+//    {
+//        // Get zone for first element.
+//        zoneI = existingZoneID[regionCells[0]];
+//
+//        if (zoneI == -1)
+//        {
+//            zoneI = labelMax;
+//        }
+//        else
+//        {
+//            // 1. All regionCells in zoneI?
+//            forAll(regionCells, i)
+//            {
+//                if (existingZoneID[regionCells[i]] != zoneI)
+//                {
+//                    zoneI = labelMax;
+//                    break;
+//                }
+//            }
+//        }
+//    }
+//
+//    // Determine same zone over all processors.
+//    reduce(zoneI, maxOp<label>());
+//
+//    if (zoneI == labelMax)
+//    {
+//        // Cells in region that are not in zoneI
+//        zoneI = -1;
+//    }
+//
+//    return zoneI;
+//}
+
+
+//XXXXXXXXX
+// Find region that covers most of cell zone
+label findCorrespondingRegion
 (
-    const cellZoneMesh& cellZones,
-    const labelList& existingZoneID,
-    const labelList& cellRegion,
-    const label regionI
+    const labelList& existingZoneID,    // per cell the (unique) zoneID
+    const regionSplit& cellRegion,
+    const label zoneI,
+    const label minOverlapSize
 )
 {
-    // Zone corresponding to region. No corresponding zone.
-    label zoneI = labelMax;
+    // Per region the number of cells in zoneI
+    labelList cellsInZone(cellRegion.nRegions(), 0);
 
-    labelList regionCells = findIndices(cellRegion, regionI);
-
-    if (regionCells.empty())
+    forAll(cellRegion, cellI)
     {
-        // My local portion is empty. Maps to any empty cellZone. Mark with
-        // special value which can get overwritten by other processors.
-        zoneI = -1;
+        if (existingZoneID[cellI] == zoneI)
+        {
+            cellsInZone[cellRegion[cellI]]++;
+        }
+    }
+
+    Pstream::listCombineGather(cellsInZone, plusEqOp<label>());
+    Pstream::listCombineScatter(cellsInZone);
+
+    // Pick region with largest overlap of zoneI
+    label regionI = findMax(cellsInZone);
+
+
+    if (cellsInZone[regionI] < minOverlapSize)
+    {
+        // Region covers too little of zone. Not good enough.
+        regionI = -1;
     }
     else
     {
-        // Get zone for first element.
-        zoneI = existingZoneID[regionCells[0]];
-
-        if (zoneI == -1)
+        // Check that region contains no cells that aren't in cellZone.
+        forAll(cellRegion, cellI)
         {
-            zoneI = labelMax;
-        }
-        else
-        {
-            // 1. All regionCells in zoneI?
-            forAll(regionCells, i)
+            if (cellRegion[cellI] == regionI && existingZoneID[cellI] != zoneI)
             {
-                if (existingZoneID[regionCells[i]] != zoneI)
-                {
-                    zoneI = labelMax;
-                    break;
-                }
-            }
-        }
-    }
-
-    // Determine same zone over all processors.
-    reduce(zoneI, maxOp<label>());
-
-
-    // 2. All of cellZone present?
-
-    if (zoneI == labelMax)
-    {
-        zoneI = -1;
-    }
-    else if (zoneI != -1)
-    {
-        const cellZone& cz = cellZones[zoneI];
-
-        forAll(cz, i)
-        {
-            if (cellRegion[cz[i]] != regionI)
-            {
-                zoneI = -1;
+                // cellI in regionI but not in zoneI
+                regionI = -1;
                 break;
             }
         }
         // If one in error, all should be in error. Note that branch gets taken
         // on all procs.
-        reduce(zoneI, minOp<label>());
+        reduce(regionI, minOp<label>());
     }
 
-    return zoneI;
+    return regionI;
 }
+//XXXXXXXXX
+
+
+//// Checks if cellZone has corresponding cellRegion.
+//label findCorrespondingRegion
+//(
+//    const cellZoneMesh& cellZones,
+//    const labelList& existingZoneID,    // per cell the (unique) zoneID
+//    const regionSplit& cellRegion,
+//    const label zoneI
+//)
+//{
+//    // Region corresponding to zone. Start off with special value: no
+//    // corresponding region.
+//    label regionI = labelMax;
+//
+//    const cellZone& cz = cellZones[zoneI];
+//
+//    if (cz.empty())
+//    {
+//        // My local portion is empty. Maps to any empty cellZone. Mark with
+//        // special value which can get overwritten by other processors.
+//        regionI = -1;
+//    }
+//    else
+//    {
+//        regionI = cellRegion[cz[0]];
+//
+//        forAll(cz, i)
+//        {
+//            if (cellRegion[cz[i]] != regionI)
+//            {
+//                regionI = labelMax;
+//                break;
+//            }
+//        }
+//    }
+//
+//    // Determine same zone over all processors.
+//    reduce(regionI, maxOp<label>());
+//
+//
+//    // 2. All of region present?
+//
+//    if (regionI == labelMax)
+//    {
+//        regionI = -1;
+//    }
+//    else if (regionI != -1)
+//    {
+//        forAll(cellRegion, cellI)
+//        {
+//            if (cellRegion[cellI] == regionI && existingZoneID[cellI] != zoneI)
+//            {
+//                // cellI in regionI but not in zoneI
+//                regionI = -1;
+//                break;
+//            }
+//        }
+//        // If one in error, all should be in error. Note that branch gets taken
+//        // on all procs.
+//        reduce(regionI, minOp<label>());
+//    }
+//
+//    return regionI;
+//}
 
 
 // Main program:
@@ -1120,6 +1228,8 @@ int main(int argc, char *argv[])
     argList::validOptions.insert("largestOnly", "");
     argList::validOptions.insert("insidePoint", "point");
     argList::validOptions.insert("overwrite", "");
+    argList::validOptions.insert("detectOnly", "");
+    argList::validOptions.insert("sloppyCellZones", "");
 
 #   include "setRootCase.H"
 #   include "createTime.H"
@@ -1134,10 +1244,13 @@ int main(int argc, char *argv[])
             << blockedFacesName << nl << endl;
     }
 
+    bool makeCellZones = args.options().found("makeCellZones");
     bool largestOnly = args.options().found("largestOnly");
     bool insidePoint = args.options().found("insidePoint");
     bool useCellZones = args.options().found("cellZones");
     bool overwrite = args.options().found("overwrite");
+    bool detectOnly = args.options().found("detectOnly");
+    bool sloppyCellZones = args.options().found("sloppyCellZones");
 
     if (insidePoint && largestOnly)
     {
@@ -1281,6 +1394,31 @@ int main(int argc, char *argv[])
         Info<< "Writing region per cell file (for manual decomposition) to "
             << cellToRegion.objectPath() << nl << endl;
     }
+    // Write for postprocessing
+    {
+        volScalarField cellToRegion
+        (
+            IOobject
+            (
+                "cellToRegion",
+                mesh.facesInstance(),
+                mesh,
+                IOobject::NO_READ,
+                IOobject::NO_WRITE,
+                false
+            ),
+            mesh,
+            dimensionedScalar("zero", dimless, 0)
+        );
+        forAll(cellRegion, cellI)
+        {
+            cellToRegion[cellI] = cellRegion[cellI];
+        }
+        cellToRegion.write();
+
+        Info<< "Writing region per cell as volScalarField to "
+            << cellToRegion.objectPath() << nl << endl;
+    }
 
 
     // Sizes per region
@@ -1307,40 +1445,131 @@ int main(int argc, char *argv[])
     Info<< endl;
 
 
+    // Sizes per cellzone
+    // ~~~~~~~~~~~~~~~~~~
+
+    labelList zoneSizes(cellZones.size(), 0);
+    if (useCellZones || makeCellZones || sloppyCellZones)
+    {
+        List<wordList> zoneNames(Pstream::nProcs());
+        zoneNames[Pstream::myProcNo()] = cellZones.names();
+        Pstream::gatherList(zoneNames);
+        Pstream::scatterList(zoneNames);
+
+        forAll(zoneNames, procI)
+        {
+            if (zoneNames[procI] != zoneNames[0])
+            {
+                FatalErrorIn(args.executable())
+                    << "cellZones not synchronised across processors." << endl
+                    << "Master has cellZones " << zoneNames[0] << endl
+                    << "Processor " << procI
+                    << " has cellZones " << zoneNames[procI]
+                    << exit(FatalError);
+            }
+        }
+
+        forAll(cellZones, zoneI)
+        {
+            zoneSizes[zoneI] = returnReduce
+            (
+                cellZones[zoneI].size(),
+                sumOp<label>()
+            );
+        }
+    }
+
+
     // Whether region corresponds to a cellzone
     // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-    Info<< "Region\tZone\tName" << nl
-        << "------\t----\t----" << endl;
-
     // Region per zone
-    labelList regionToZone(cellRegion.nRegions());
+    labelList regionToZone(cellRegion.nRegions(), -1);
     // Name of region
     wordList regionNames(cellRegion.nRegions());
+    // Zone to region
+    labelList zoneToRegion(cellZones.size(), -1);
+
+    if (sloppyCellZones)
+    {
+        Info<< "Trying to match regions to existing cell zones;"
+            << " region can be subset of cell zone." << nl << endl;
+
+        forAll(cellZones, zoneI)
+        {
+            label regionI = findCorrespondingRegion
+            (
+                zoneID,
+                cellRegion,
+                zoneI,
+                label(0.5*zoneSizes[zoneI]) // minimum overlap
+            );
+
+            if (regionI != -1)
+            {
+                Info<< "Sloppily matched region " << regionI
+                    << " size " << regionSizes[regionI]
+                    << " to zone " << zoneI << " size " << zoneSizes[zoneI]
+                    << endl;
+                zoneToRegion[zoneI] = regionI;
+                regionToZone[regionI] = zoneI;
+                regionNames[regionI] = cellZones[zoneI].name();
+            }
+        }
+    }
+    else
+    {
+        Info<< "Trying to match regions to existing cell zones." << nl << endl;
+
+        forAll(cellZones, zoneI)
+        {
+            label regionI = findCorrespondingRegion
+            (
+                zoneID,
+                cellRegion,
+                zoneI,
+                1               // minimum overlap
+            );
+
+            if (regionI != -1)
+            {
+                zoneToRegion[zoneI] = regionI;
+                regionToZone[regionI] = zoneI;
+                regionNames[regionI] = cellZones[zoneI].name();
+            }
+        }
+    }
+    // Allocate region names for unmatched regions.
     forAll(regionToZone, regionI)
     {
-        regionToZone[regionI] = findCorrespondingZone
-        (
-            cellZones,
-            zoneID,
-            cellRegion,
-            regionI
-        );
-
-        if (regionToZone[regionI] != -1)
-        {
-            regionNames[regionI] = cellZones[regionToZone[regionI]].name();
-        }
-        else
+        if (regionToZone[regionI] == -1)
         {
             regionNames[regionI] = "domain" + Foam::name(regionI);
         }
+    }
 
+
+    // Print region to zone
+    Info<< "Region\tZone\tName" << nl
+        << "------\t----\t----" << endl;
+    forAll(regionToZone, regionI)
+    {
         Info<< regionI << '\t' << regionToZone[regionI] << '\t'
             << regionNames[regionI] << nl;
     }
     Info<< endl;
 
+    //// Print zone to region
+    //Info<< "Zone\tName\tRegion" << nl
+    //    << "----\t----\t------" << endl;
+    //forAll(zoneToRegion, zoneI)
+    //{
+    //    Info<< zoneI << '\t' << cellZones[zoneI].name() << '\t'
+    //        << zoneToRegion[zoneI] << nl;
+    //}
+    //Info<< endl;
+
+
 
     // Since we're going to mess with patches make sure all non-processor ones
     // are on all processors.
@@ -1361,7 +1590,8 @@ int main(int argc, char *argv[])
         interfaceSizes
     );
 
-    Info<< "Region\tRegion\tFaces" << nl
+    Info<< "Sizes inbetween regions:" << nl << nl
+        << "Region\tRegion\tFaces" << nl
         << "------\t------\t-----" << endl;
 
     forAll(interfaces, interI)
@@ -1373,7 +1603,10 @@ int main(int argc, char *argv[])
     Info<< endl;
 
 
-
+    if (detectOnly)
+    {
+        return 0;
+    }
 
 
     // Read objects in time directory
@@ -1423,7 +1656,7 @@ int main(int argc, char *argv[])
     {
         Info<< "Only one region. Doing nothing." << endl;
     }
-    else if (args.options().found("makeCellZones"))
+    else if (makeCellZones)
     {
         Info<< "Putting cells into cellZones instead of splitting mesh."
             << endl;

From 326a2e501d0f075983fbe68868f80c61f10e86eb Mon Sep 17 00:00:00 2001
From: mattijs <mattijs@hunt.opencfd.co.uk>
Date: Tue, 27 Jan 2009 20:19:07 +0000
Subject: [PATCH 6/7] face surface data consistent with cell

---
 .../meshRefinement/meshRefinement.H           |  16 +
 .../meshRefinement/meshRefinementBaffles.C    | 297 +++++++++++++-----
 2 files changed, 234 insertions(+), 79 deletions(-)

diff --git a/src/autoMesh/autoHexMesh/meshRefinement/meshRefinement.H b/src/autoMesh/autoHexMesh/meshRefinement/meshRefinement.H
index c684fbaad4..7720386219 100644
--- a/src/autoMesh/autoHexMesh/meshRefinement/meshRefinement.H
+++ b/src/autoMesh/autoHexMesh/meshRefinement/meshRefinement.H
@@ -413,6 +413,16 @@ private:
                 labelList& cellToZone
             ) const;
 
+            //- Determines cell zone from cell region information.
+            bool calcRegionToZone
+            (
+                const label surfZoneI,
+                const label ownRegion,
+                const label neiRegion,
+
+                labelList& regionToCellZone
+            ) const;
+
             //- Finds zone per cell. Uses topological walk with all faces
             //  marked in namedSurfaceIndex regarded as blocked.
             void findCellZoneTopo
@@ -423,6 +433,12 @@ private:
                 labelList& cellToZone
             ) const;
 
+            void makeConsistentFaceIndex
+            (
+                const labelList& cellToZone,
+                labelList& namedSurfaceIndex
+            ) const;
+
 
         //- Disallow default bitwise copy construct
         meshRefinement(const meshRefinement&);
diff --git a/src/autoMesh/autoHexMesh/meshRefinement/meshRefinementBaffles.C b/src/autoMesh/autoHexMesh/meshRefinement/meshRefinementBaffles.C
index 2d7ca7314b..c27c74abb2 100644
--- a/src/autoMesh/autoHexMesh/meshRefinement/meshRefinementBaffles.C
+++ b/src/autoMesh/autoHexMesh/meshRefinement/meshRefinementBaffles.C
@@ -1011,15 +1011,21 @@ void Foam::meshRefinement::findCellZoneGeometric
     }
 
     labelList neiCellZone(mesh_.nFaces()-mesh_.nInternalFaces());
-    for
-    (
-        label faceI = mesh_.nInternalFaces();
-        faceI < mesh_.nFaces();
-        faceI++
-    )
+    const polyBoundaryMesh& patches = mesh_.boundaryMesh();
+
+    forAll(patches, patchI)
     {
-        label own = mesh_.faceOwner()[faceI];
-        neiCellZone[faceI-mesh_.nInternalFaces()] = cellToZone[own];
+        const polyPatch& pp = patches[patchI];
+
+        if (pp.coupled())
+        {
+            forAll(pp, i)
+            {
+                label faceI = pp.start()+i;
+                label ownZone = cellToZone[mesh_.faceOwner()[faceI]];
+                neiCellZone[faceI-mesh_.nInternalFaces()] = ownZone;
+            }
+        }
     }
     syncTools::swapBoundaryFaceList(mesh_, neiCellZone, false);
 
@@ -1061,6 +1067,64 @@ void Foam::meshRefinement::findCellZoneGeometric
 }
 
 
+bool Foam::meshRefinement::calcRegionToZone
+(
+    const label surfZoneI,
+    const label ownRegion,
+    const label neiRegion,
+
+    labelList& regionToCellZone
+) const
+{
+    bool changed = false;
+
+    // Check whether inbetween different regions
+    if (ownRegion != neiRegion)
+    {
+        // Jump. Change one of the sides to my type.
+
+        // 1. Interface between my type and unset region.
+        // Set region to keepRegion
+
+        if (regionToCellZone[ownRegion] == -2)
+        {
+            if (regionToCellZone[neiRegion] == surfZoneI)
+            {
+                // Face between unset and my region. Put unset
+                // region into keepRegion
+                regionToCellZone[ownRegion] = -1;
+                changed = true;
+            }
+            else if (regionToCellZone[neiRegion] != -2)
+            {
+                // Face between unset and other region.
+                // Put unset region into my region
+                regionToCellZone[ownRegion] = surfZoneI;
+                changed = true;
+            }
+        }
+        else if (regionToCellZone[neiRegion] == -2)
+        {
+            if (regionToCellZone[ownRegion] == surfZoneI)
+            {
+                // Face between unset and my region. Put unset
+                // region into keepRegion
+                regionToCellZone[neiRegion] = -1;
+                changed = true;
+            }
+            else if (regionToCellZone[ownRegion] != -2)
+            {
+                // Face between unset and other region.
+                // Put unset region into my region
+                regionToCellZone[neiRegion] = surfZoneI;
+                changed = true;
+            }
+        }
+    }
+    return changed;
+}
+
+
 // Finds region per cell. Assumes:
 // - region containing keepPoint does not go into a cellZone
 // - all other regions can be found by crossing faces marked in
@@ -1152,59 +1216,75 @@ void Foam::meshRefinement::findCellZoneTopo
     {
         bool changed = false;
 
+        // Internal faces
+
         for (label faceI = 0; faceI < mesh_.nInternalFaces(); faceI++)
         {
             label surfI = namedSurfaceIndex[faceI];
 
             if (surfI != -1)
             {
-                // Get cell zone that surface cells are in
-                label surfZoneI = surfaceToCellZone[surfI];
+                // Calculate region to zone from cellRegions on either side
+                // of internal face.
+                bool changedCell = calcRegionToZone
+                (
+                    surfaceToCellZone[surfI],
+                    cellRegion[mesh_.faceOwner()[faceI]],
+                    cellRegion[mesh_.faceNeighbour()[faceI]],
+                    regionToCellZone
+                );
 
-                // Check whether inbetween different regions
-                label ownRegion = cellRegion[mesh_.faceOwner()[faceI]];
-                label neiRegion = cellRegion[mesh_.faceNeighbour()[faceI]];
+                changed = changed | changedCell;
+            }
+        }
 
-                if (ownRegion != neiRegion)
+        // Boundary faces
+
+        const polyBoundaryMesh& patches = mesh_.boundaryMesh();
+
+        // Get coupled neighbour cellRegion
+        labelList neiCellRegion(mesh_.nFaces()-mesh_.nInternalFaces());
+        forAll(patches, patchI)
+        {
+            const polyPatch& pp = patches[patchI];
+
+            if (pp.coupled())
+            {
+                forAll(pp, i)
                 {
-                    // Jump. Change one of the sides to my type.
+                    label faceI = pp.start()+i;
+                    neiCellRegion[faceI-mesh_.nInternalFaces()] =
+                        cellRegion[mesh_.faceOwner()[faceI]];
+                }
+            }
+        }
+        syncTools::swapBoundaryFaceList(mesh_, neiCellRegion, false);
 
-                    // 1. Interface between my type and unset region.
-                    // Set region to keepRegion
+        // Calculate region to zone from cellRegions on either side of coupled
+        // face.
+        forAll(patches, patchI)
+        {
+            const polyPatch& pp = patches[patchI];
 
-                    if (regionToCellZone[ownRegion] == -2)
+            if (pp.coupled())
+            {
+                forAll(pp, i)
+                {
+                    label faceI = pp.start()+i;
+
+                    label surfI = namedSurfaceIndex[faceI];
+
+                    if (surfI != -1)
                     {
-                        if (regionToCellZone[neiRegion] == surfZoneI)
-                        {
-                            // Face between unset and my region. Put unset
-                            // region into keepRegion
-                            regionToCellZone[ownRegion] = -1;
-                            changed = true;
-                        }
-                        else if (regionToCellZone[neiRegion] != -2)
-                        {
-                            // Face between unset and other region.
-                            // Put unset region into my region
-                            regionToCellZone[ownRegion] = surfZoneI;
-                            changed = true;
-                        }
-                    }
-                    else if (regionToCellZone[neiRegion] == -2)
-                    {
-                        if (regionToCellZone[ownRegion] == surfZoneI)
-                        {
-                            // Face between unset and my region. Put unset
-                            // region into keepRegion
-                            regionToCellZone[neiRegion] = -1;
-                            changed = true;
-                        }
-                        else if (regionToCellZone[ownRegion] != -2)
-                        {
-                            // Face between unset and other region.
-                            // Put unset region into my region
-                            regionToCellZone[neiRegion] = surfZoneI;
-                            changed = true;
-                        }
+                        bool changedCell = calcRegionToZone
+                        (
+                            surfaceToCellZone[surfI],
+                            cellRegion[mesh_.faceOwner()[faceI]],
+                            neiCellRegion[faceI-mesh_.nInternalFaces()],
+                            regionToCellZone
+                        );
+
+                        changed = changed | changedCell;
                     }
                 }
             }
@@ -1258,6 +1338,88 @@ void Foam::meshRefinement::findCellZoneTopo
 }
 
 
+// Make namedSurfaceIndex consistent with cellToZone - clear out any blocked
+// faces inbetween same cell zone.
+void Foam::meshRefinement::makeConsistentFaceIndex
+(
+    const labelList& cellToZone,
+    labelList& namedSurfaceIndex
+) const
+{
+    const labelList& faceOwner = mesh_.faceOwner();
+    const labelList& faceNeighbour = mesh_.faceNeighbour();
+
+    for (label faceI = 0; faceI < mesh_.nInternalFaces(); faceI++)
+    {
+        label ownZone = cellToZone[faceOwner[faceI]];
+        label neiZone = cellToZone[faceNeighbour[faceI]];
+
+        if (ownZone == neiZone && namedSurfaceIndex[faceI] != -1)
+        {
+            namedSurfaceIndex[faceI] = -1;
+        }
+        else if (ownZone != neiZone && namedSurfaceIndex[faceI] == -1)
+        {
+            FatalErrorIn("meshRefinement::zonify()")
+                << "Different cell zones on either side of face " << faceI
+                << " at " << mesh_.faceCentres()[faceI]
+                << " but face not marked with a surface."
+                << abort(FatalError);
+        }
+    }
+
+    const polyBoundaryMesh& patches = mesh_.boundaryMesh();
+
+    // Get coupled neighbour cellZone
+    labelList neiCellZone(mesh_.nFaces()-mesh_.nInternalFaces());
+    forAll(patches, patchI)
+    {
+        const polyPatch& pp = patches[patchI];
+
+        if (pp.coupled())
+        {
+            forAll(pp, i)
+            {
+                label faceI = pp.start()+i;
+                neiCellZone[faceI-mesh_.nInternalFaces()] =
+                    cellToZone[mesh_.faceOwner()[faceI]];
+            }
+        }
+    }
+    syncTools::swapBoundaryFaceList(mesh_, neiCellZone, false);
+
+    // Use coupled cellZone to do check
+    forAll(patches, patchI)
+    {
+        const polyPatch& pp = patches[patchI];
+
+        if (pp.coupled())
+        {
+            forAll(pp, i)
+            {
+                label faceI = pp.start()+i;
+
+                label ownZone = cellToZone[faceOwner[faceI]];
+                label neiZone = neiCellZone[faceI-mesh_.nInternalFaces()];
+
+                if (ownZone == neiZone && namedSurfaceIndex[faceI] != -1)
+                {
+                    namedSurfaceIndex[faceI] = -1;
+                }
+                else if (ownZone != neiZone && namedSurfaceIndex[faceI] == -1)
+                {
+                    FatalErrorIn("meshRefinement::zonify()")
+                        << "Different cell zones on either side of face "
+                        << faceI << " at " << mesh_.faceCentres()[faceI]
+                        << " but face not marked with a surface."
+                        << abort(FatalError);
+                }
+            }
+        }
+    }
+}
+
+
 // * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
 
 // Split off unreachable areas of mesh.
@@ -2166,36 +2328,6 @@ Foam::autoPtr<Foam::mapPolyMesh> Foam::meshRefinement::zonify
         );
     }
 
-    //{
-    //    Pout<< "** finding out blocked faces." << endl;
-    //
-    //    cellSet zonedCellsGeom(mesh_, "zonedCellsGeom", 100);
-    //    forAll(cellToZone, cellI)
-    //    {
-    //        if (cellToZone[cellI] >= 0)
-    //        {
-    //            zonedCellsGeom.insert(cellI);
-    //        }
-    //    }
-    //    Pout<< "Writing zoned cells to " << zonedCellsGeom.objectPath()
-    //        << endl;
-    //    zonedCellsGeom.write();
-    //
-    //
-    //    faceSet zonedFaces(mesh_, "zonedFaces", 100);
-    //    forAll(namedSurfaceIndex, faceI)
-    //    {
-    //        label surfI = namedSurfaceIndex[faceI];
-    //
-    //        if (surfI != -1)
-    //        {
-    //            zonedFaces.insert(faceI);
-    //        }
-    //    }
-    //    Pout<< "Writing zoned faces to " << zonedFaces.objectPath() << endl;
-    //    zonedFaces.write();
-    //}
-
     // Set using walking
     // ~~~~~~~~~~~~~~~~~
 
@@ -2212,6 +2344,10 @@ Foam::autoPtr<Foam::mapPolyMesh> Foam::meshRefinement::zonify
     }
 
 
+    // Make sure namedSurfaceIndex is unset inbetween same cell cell zones.
+    makeConsistentFaceIndex(cellToZone, namedSurfaceIndex);
+
+
     // Topochange container
     polyTopoChange meshMod(mesh_);
 
@@ -2314,6 +2450,9 @@ Foam::autoPtr<Foam::mapPolyMesh> Foam::meshRefinement::zonify
         mesh_.clearOut();
     }
 
+    // None of the faces has changed, only the zones. Still...
+    updateMesh(map, labelList());
+
     return map;
 }
 

From 0bab1aa06876c0b22e6dfb4e83be937bdd7c882c Mon Sep 17 00:00:00 2001
From: mattijs <mattijs@hunt.opencfd.co.uk>
Date: Tue, 27 Jan 2009 20:25:05 +0000
Subject: [PATCH 7/7] face surface data consistent with cell

---
 src/autoMesh/autoHexMesh/meshRefinement/meshRefinementBaffles.C | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/autoMesh/autoHexMesh/meshRefinement/meshRefinementBaffles.C b/src/autoMesh/autoHexMesh/meshRefinement/meshRefinementBaffles.C
index c27c74abb2..2423f05f19 100644
--- a/src/autoMesh/autoHexMesh/meshRefinement/meshRefinementBaffles.C
+++ b/src/autoMesh/autoHexMesh/meshRefinement/meshRefinementBaffles.C
@@ -1029,8 +1029,6 @@ void Foam::meshRefinement::findCellZoneGeometric
     }
     syncTools::swapBoundaryFaceList(mesh_, neiCellZone, false);
 
-    const polyBoundaryMesh& patches = mesh_.boundaryMesh();
-
     forAll(patches, patchI)
     {
         const polyPatch& pp = patches[patchI];