Merge branch 'feature_shm_zoning' into develop

Conflicts:
	src/mesh/autoMesh/autoHexMesh/autoHexMeshDriver/refinementParameters/refinementParameters.C
	src/mesh/autoMesh/autoHexMesh/meshRefinement/meshRefinement.H
	src/mesh/autoMesh/autoHexMesh/meshRefinement/meshRefinementBaffles.C

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

@@ -58,6 +58,7 @@ Description
 #include "globalIndex.H"
 #include "IOmanip.H"
 #include "decompositionModel.H"
+#include "fvMeshTools.H"
 
 using namespace Foam;
 
@@ -813,6 +814,7 @@ int main(int argc, char *argv[])
         readScalar(meshDict.lookup("mergeTolerance"))
     );
 
+    const Switch keepPatches(meshDict.lookupOrDefault("keepPatches", false));
 
 
     // Read decomposePar dictionary
@@ -1517,6 +1519,12 @@ int main(int argc, char *argv[])
             motionDict
         );
 
+        // Remove zero sized patches originating from faceZones
+        if (!keepPatches && !wantSnap && !wantLayers)
+        {
+            fvMeshTools::removeEmptyPatches(mesh, true);
+        }
+
         writeMesh
         (
             "Refined mesh",
@@ -1559,6 +1567,12 @@ int main(int argc, char *argv[])
             snapParams
         );
 
+        // Remove zero sized patches originating from faceZones
+        if (!keepPatches && !wantLayers)
+        {
+            fvMeshTools::removeEmptyPatches(mesh, true);
+        }
+
         writeMesh
         (
             "Snapped mesh",
@@ -1609,6 +1623,12 @@ int main(int argc, char *argv[])
             distributor
         );
 
+        // Remove zero sized patches originating from faceZones
+        if (!keepPatches)
+        {
+            fvMeshTools::removeEmptyPatches(mesh, true);
+        }
+
         writeMesh
         (
             "Layer mesh",
@@ -1622,6 +1642,7 @@ int main(int argc, char *argv[])
     }
 
 
+
     {
         // Check final mesh
         Info<< "Checking final mesh ..." << endl;

applications/utilities/mesh/generation/snappyHexMesh/snappyHexMeshDict

@@ -296,8 +296,18 @@ castellatedMeshControls
         locationInMesh (5 0.28 0.43);
 
         // Whether any faceZones (as specified in the refinementSurfaces)
-        // are only on the boundary of corresponding cellZones or also allow
+        // are only on the boundary of corresponding cellZones.
-        // free-standing zone faces. Not used if there are no faceZones.
+        // Not used if there are no faceZones. The behaviour has changed
+        // with respect to previous versions:
+        //  true  : all intersections with surface are put in faceZone
+        //          (same behaviour as before)
+        //  false : depending on the type of surface intersected:
+        //      - if intersecting surface has faceZone only (so no cellZone)
+        //        leave in faceZone (so behave as if set to true) (= changed
+        //        behaviour)
+        //      - if intersecting surface has faceZone and cellZone
+        //        remove if inbetween same cellZone or if on boundary
+        //        (same behaviour as before)
         allowFreeStandingZoneFaces true;
 
 

src/dynamicMesh/fvMeshTools/fvMeshTools.C

@@ -355,6 +355,69 @@ void Foam::fvMeshTools::reorderPatches
 }
 
 
+Foam::labelList Foam::fvMeshTools::removeEmptyPatches
+(
+    fvMesh& mesh,
+    const bool validBoundary
+)
+{
+    const polyBoundaryMesh& pbm = mesh.boundaryMesh();
+
+    labelList newToOld(pbm.size());
+    labelList oldToNew(pbm.size(), -1);
+    label newI = 0;
+
+
+    // Assumes all non-coupled boundaries are on all processors!
+    forAll(pbm, patchI)
+    {
+        const polyPatch& pp = pbm[patchI];
+
+        if (!isA<processorPolyPatch>(pp))
+        {
+            label nFaces = pp.size();
+            if (validBoundary)
+            {
+                reduce(nFaces, sumOp<label>());
+            }
+
+            if (nFaces > 0)
+            {
+                newToOld[newI] = patchI;
+                oldToNew[patchI] = newI++;
+            }
+        }
+    }
+
+    // Same for processor patches (but need no reduction)
+    forAll(pbm, patchI)
+    {
+        const polyPatch& pp = pbm[patchI];
+
+        if (isA<processorPolyPatch>(pp) && pp.size())
+        {
+            newToOld[newI] = patchI;
+            oldToNew[patchI] = newI++;
+        }
+    }
+
+    newToOld.setSize(newI);
+
+    // Move all deleteable patches to the end
+    forAll(oldToNew, patchI)
+    {
+        if (oldToNew[patchI] == -1)
+        {
+            oldToNew[patchI] = newI++;
+        }
+    }
+
+    reorderPatches(mesh, oldToNew, newToOld.size(), validBoundary);
+
+    return newToOld;
+}
+
+
 Foam::autoPtr<Foam::fvMesh> Foam::fvMeshTools::newMesh
 (
     const IOobject& io,

src/dynamicMesh/fvMeshTools/fvMeshTools.H

@@ -113,7 +113,7 @@ public:
     static void zeroPatchFields(fvMesh& mesh, const label patchI);
 
     //- Reorder and remove trailing patches. If validBoundary call is parallel
-    //  synced and all add the same patch with same settings
+    //  synced
     static void reorderPatches
     (
         fvMesh&,
@@ -122,6 +122,11 @@ public:
         const bool validBoundary
     );
 
+    //- Remove zero sized patches. All but processor patches are
+    //  assumed to be present on all processors (so size will be reduced
+    //  if validBoundary). Return map from new
+    //  to old patches
+    static labelList removeEmptyPatches(fvMesh&, const bool validBoundary);
 
     //- Read mesh or create dummy mesh (0 cells, >0 patches). Works in two
     //  modes according to masterOnlyReading:
@@ -133,7 +138,6 @@ public:
         const IOobject& io,
         const bool masterOnlyReading
     );
-
 };
 
 

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

@@ -74,14 +74,7 @@ Foam::refinementParameters::refinementParameters(const dictionary& dict)
     if (dict.readIfPresent("locationInMesh", locationInMesh))
     {
         locationsInMesh_.append(locationInMesh);
-        zonesInMesh_.append("noneIfNotSet");// special name for no cellZone
+        zonesInMesh_.append("none");    // special name for no cellZone
-
-        if (dict.found("locationsInMesh"))
-        {
-            FatalIOErrorInFunction(dict)
-                << "Cannot both specify 'locationInMesh' and 'locationsInMesh'"
-                << exit(FatalIOError);
-        }
     }
 
     List<Tuple2<point, word> > pointsToZone;
@@ -95,6 +88,10 @@ Foam::refinementParameters::refinementParameters(const dictionary& dict)
         {
             locationsInMesh_[nZones] = pointsToZone[i].first();
             zonesInMesh_[nZones] = pointsToZone[i].second();
+            if (zonesInMesh_[nZones] == word::null)
+            {
+                zonesInMesh_[nZones] = "none";
+            }
             nZones++;
         }
     }
@@ -152,12 +149,7 @@ Foam::labelList Foam::refinementParameters::addCellZonesToMesh
     labelList zoneIDs(zonesInMesh_.size(), -1);
     forAll(zonesInMesh_, i)
     {
-        if
+        if (zonesInMesh_[i] != word::null && zonesInMesh_[i] != "none")
-        (
-            zonesInMesh_[i] != word::null
-         && zonesInMesh_[i] != "none"
-         && zonesInMesh_[i] != "noneIfNotSet"
-        )
         {
             zoneIDs[i] = surfaceZonesInfo::addCellZone
             (
@@ -242,8 +234,8 @@ Foam::labelList Foam::refinementParameters::zonedLocations
     {
         if
         (
-            zonesInMesh[i] == word::null
+            zonesInMesh[i] != word::null
-        ||  zonesInMesh[i] != "noneIfNotSet"
+         && zonesInMesh[i] != "none"
         )
         {
             indices.append(i);
@@ -264,8 +256,8 @@ Foam::labelList Foam::refinementParameters::unzonedLocations
     {
         if
         (
-            zonesInMesh[i] != word::null
+            zonesInMesh[i] == word::null
-        &&  zonesInMesh[i] == "noneIfNotSet"
+         || zonesInMesh[i] == "none"
         )
         {
             indices.append(i);

src/mesh/autoMesh/autoHexMesh/meshRefinement/meshRefinement.H

@@ -507,7 +507,6 @@ private:
             void getIntersections
             (
                 const labelList& surfacesToTest,
-                const labelList& neiLevel,
                 const pointField& neiCc,
                 const labelList& testFaces,
 
@@ -515,7 +514,19 @@ private:
                 labelList& globalRegion2
             ) const;
 
-            //- Determine patches for baffles on all intersected unnamed faces
+            //- Calculate intersections on zoned faces. Return per face -1
+            // or the index of the surface and the orientation w.r.t. surface
+            void getIntersections
+            (
+                const labelList& surfacesToTest,
+                const pointField& neiCc,
+                const labelList& testFaces,
+
+                labelList& namedSurfaceIndex,
+                PackedBoolList& posOrientation
+            ) const;
+
+            //- Determine patches for baffles
             void getBafflePatches
             (
                 const labelList& globalToMasterPatch,
@@ -635,13 +646,13 @@ private:
                 labelList& cellToZone
             ) const;
 
-            //- Finds zone per cell for cells inside named surfaces that have
+            //- Finds zone per cell for cells inside region for which name
-            //  an inside point specified.
+            //  is specified.
             void findCellZoneInsideWalk
             (
-                const labelList& locationSurfaces,
+                const pointField& locationsInMesh,
-                const labelList& namedSurfaceIndex,
+                const labelList& zonesInMesh,
-                const labelList& surfaceToCellZone,
+                const labelList& blockedFace, // per face -1 or some index >= 0
                 labelList& cellToZone
             ) const;
 
@@ -650,8 +661,8 @@ private:
             void findCellZoneInsideWalk
             (
                 const pointField& locationsInMesh,
-                const wordList& regionsInMesh,
+                const wordList& zoneNamesInMesh,
-                const labelList& blockedFace, // per face -1 or some index >= 0
+                const labelList& faceToZone, // per face -1 or some index >= 0
                 labelList& cellToZone
             ) const;
 
@@ -670,6 +681,7 @@ private:
             void findCellZoneTopo
             (
                 const pointField& locationsInMesh,
+                const labelList& allSurfaceIndex,
                 const labelList& namedSurfaceIndex,
                 const labelList& surfaceToCellZone,
                 labelList& cellToZone
@@ -679,10 +691,23 @@ private:
             //  - clear out any blocked faces inbetween same cell zone.
             void makeConsistentFaceIndex
             (
+                const labelList& zoneToNamedSurface,
                 const labelList& cellToZone,
                 labelList& namedSurfaceIndex
             ) const;
 
+            //- Calculate cellZone allocation
+            void zonify
+            (
+                const bool allowFreeStandingZoneFaces,
+                const pointField& locationsInMesh,
+                const wordList& zonesInMesh,
+
+                labelList& cellToZone,
+                labelList& namedSurfaceIndex,
+                PackedBoolList& posOrientation
+            ) const;
+
             //- Put cells into cellZone, faces into faceZone
             void zonify
             (

src/mesh/autoMesh/autoHexMesh/refinementSurfaces/surfaceZonesInfo.C

@@ -226,6 +226,32 @@ Foam::labelList Foam::surfaceZonesInfo::getNamedSurfaces
 }
 
 
+Foam::labelList Foam::surfaceZonesInfo::getStandaloneNamedSurfaces
+(
+    const PtrList<surfaceZonesInfo>& surfList
+)
+{
+   labelList namedSurfaces(surfList.size());
+
+    label namedI = 0;
+    forAll(surfList, surfI)
+    {
+        if
+        (
+            surfList.set(surfI)
+        &&  surfList[surfI].faceZoneName().size()
+        && !surfList[surfI].cellZoneName().size()
+        )
+        {
+            namedSurfaces[namedI++] = surfI;
+        }
+    }
+    namedSurfaces.setSize(namedI);
+
+    return namedSurfaces;
+}
+
+
 Foam::labelList Foam::surfaceZonesInfo::getClosedNamedSurfaces
 (
     const PtrList<surfaceZonesInfo>& surfList,

src/mesh/autoMesh/autoHexMesh/refinementSurfaces/surfaceZonesInfo.H

@@ -191,6 +191,12 @@ public:
                 const PtrList<surfaceZonesInfo>& surfList
             );
 
+            //- Get indices of named surfaces without a cellZone
+            static labelList getStandaloneNamedSurfaces
+            (
+                const PtrList<surfaceZonesInfo>& surfList
+            );
+
             //- Get indices of surfaces with a cellZone that are closed and
             //  have 'inside' or 'outside' selection.
             static labelList getClosedNamedSurfaces