Merge branch 'master' of ssh://opencfd:8007/home/dm4/OpenFOAM/OpenFOAM-dev

applications/utilities/parallelProcessing/reconstructParMesh/reconstructParMesh.C

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2011-2012 OpenFOAM Foundation
+    \\  /    A nd           | Copyright (C) 2011-2013 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -48,6 +48,7 @@ Description
 #include "faceCoupleInfo.H"
 #include "fvMeshAdder.H"
 #include "polyTopoChange.H"
+#include "zeroGradientFvPatchFields.H"
 
 using namespace Foam;
 
@@ -297,6 +298,12 @@ int main(int argc, char *argv[])
         "fullMatch",
         "do (slower) geometric matching on all boundary faces"
     );
+    argList::addBoolOption
+    (
+        "cellDist",
+        "write cell distribution as a labelList - for use with 'manual' "
+        "decomposition method or as a volScalarField for post-processing."
+    );
 
     #include "addTimeOptions.H"
     #include "addRegionOption.H"
@@ -362,6 +369,7 @@ int main(int argc, char *argv[])
             << nl << "This assumes a correct decomposition." << endl;
     }
 
+    bool writeCellDist = args.optionFound("cellDist");
 
 
     int nProcs = 0;
@@ -507,7 +515,7 @@ int main(int argc, char *argv[])
     {
         // Construct empty mesh.
         Info<< "Constructing empty mesh to add to." << nl << endl;
-        polyMesh masterMesh
+        fvMesh masterMesh
         (
             IOobject
             (
@@ -528,7 +536,7 @@ int main(int argc, char *argv[])
                 << " for time = " << databases[procI].timeName()
                 << nl << endl;
 
-            polyMesh meshToAdd
+            fvMesh meshToAdd
             (
                 IOobject
                 (
@@ -560,7 +568,7 @@ int main(int argc, char *argv[])
             // Add elements to mesh
             Info<< "Adding to master mesh" << nl << endl;
 
-            autoPtr<mapAddedPolyMesh> map = polyMeshAdder::add
+            autoPtr<mapAddedPolyMesh> map = fvMeshAdder::add
             (
                 masterMesh,
                 meshToAdd,
@@ -608,6 +616,67 @@ int main(int argc, char *argv[])
                 << "Failed writing polyMesh."
                 << exit(FatalError);
         }
+
+
+
+        if (writeCellDist)
+        {
+            // Write the decomposition as labelList for use with 'manual'
+            // decomposition method.
+            labelIOList cellDecomposition
+            (
+                IOobject
+                (
+                    "cellDecomposition",
+                    masterMesh.facesInstance(),
+                    masterMesh,
+                    IOobject::NO_READ,
+                    IOobject::NO_WRITE,
+                    false
+                ),
+                masterMesh.nCells()
+            );
+
+            forAll(cellProcAddressing, procI)
+            {
+                const labelList& pCells = cellProcAddressing[procI];
+                UIndirectList<label>(cellDecomposition, pCells) = procI;
+            }
+
+            cellDecomposition.write();
+
+            Info<< nl << "Wrote decomposition to "
+                << cellDecomposition.objectPath()
+                << " for use in manual decomposition." << endl;
+
+
+            // Write as volScalarField for postprocessing.
+            volScalarField cellDist
+            (
+                IOobject
+                (
+                    "cellDist",
+                    runTime.timeName(),
+                    masterMesh,
+                    IOobject::NO_READ,
+                    IOobject::AUTO_WRITE
+                ),
+                masterMesh,
+                dimensionedScalar("cellDist", dimless, 0),
+                zeroGradientFvPatchScalarField::typeName
+            );
+
+            forAll(cellDecomposition, cellI)
+            {
+                cellDist[cellI] = cellDecomposition[cellI];
+            }
+
+            cellDist.write();
+
+            Info<< nl << "Wrote decomposition as volScalarField to "
+                << cellDist.name() << " for use in postprocessing."
+                << endl;
+        }
     }
 
 
@@ -770,6 +839,7 @@ int main(int argc, char *argv[])
         Info<< endl;
     }
 
+
     Info<< "End.\n" << endl;
 
     return 0;

applications/utilities/surface/surfaceFeatureExtract/surfaceFeatureExtract.C

@@ -974,28 +974,6 @@ int main(int argc, char *argv[])
         const word extractionMethod = surfaceDict.lookup("extractionMethod");
 
 
-#ifndef ENABLE_CURVATURE
-        if (curvature)
-        {
-            WarningIn(args.executable())
-                << "Curvature calculation has been requested but "
-                << args.executable() << " has not " << nl
-                << "    been compiled with CGAL. "
-                << "Skipping the curvature calculation." << endl;
-        }
-#else
-        if (curvature && env("FOAM_SIGFPE"))
-        {
-            WarningIn(args.executable())
-                << "Detected floating point exception trapping (FOAM_SIGFPE)."
-                << " This might give" << nl
-                << "    problems when calculating curvature on straight angles"
-                << " (infinite curvature)" << nl
-                << "    Switch it off in case of problems." << endl;
-        }
-#endif
-
-
         Info<< nl << "Feature line extraction is only valid on closed manifold "
             << "surfaces." << endl;
 

src/OpenFOAM/containers/Lists/CompactListList/CompactListListI.H

@@ -223,11 +223,7 @@ inline Foam::UList<T> Foam::CompactListList<T, Container>::operator[]
 )
 {
     label start = offsets_[i];
-    return UList<T>
+    return UList<T>(m_.begin() + start, offsets_[i+1] - start);
-    (
-        (m_.size() ? m_.begin() + start : NULL),
-        offsets_[i+1] - start
-    );
 }
 
 
@@ -241,7 +237,7 @@ Foam::CompactListList<T, Container>::operator[]
     label start = offsets_[i];
     return UList<T>
     (
-        (m_.size() ? const_cast<T*>(m_.begin() + start) : NULL),
+        const_cast<T*>(m_.begin() + start),
         offsets_[i+1] - start
     );
 }

src/OpenFOAM/meshes/primitiveMesh/PatchTools/PatchTools.H

@@ -34,10 +34,11 @@ SourceFiles
     PatchToolsCheck.C
     PatchToolsEdgeOwner.C
     PatchToolsGatherAndMerge.C
+    PatchToolsMatch.C
+    PatchToolsNormals.C
     PatchToolsSearch.C
     PatchToolsSortEdges.C
-    PatchToolsNormals.C
+    PatchToolsSortPoints.C
-    PatchToolsMatch.C
 
 \*---------------------------------------------------------------------------*/
 

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

@@ -1047,7 +1047,12 @@ void Foam::autoRefineDriver::splitAndMergeBaffles
         }
 
         // Remove any now dangling parts
-        meshRefiner_.splitMeshRegions(refineParams.keepPoints()[0]);
+        meshRefiner_.splitMeshRegions
+        (
+            globalToMasterPatch_,
+            globalToSlavePatch_,
+            refineParams.keepPoints()[0]
+        );
 
         if (debug)
         {

src/mesh/autoMesh/autoHexMesh/meshRefinement/meshRefinement.C

@@ -131,7 +131,7 @@ void Foam::meshRefinement::calcNeighbourData
                     // Other cell more refined. Adjust normal distance
                     d *= 0.5;
                 }
-                neiLevel[bFaceI] = cellLevel[ownLevel];
+                neiLevel[bFaceI] = faceLevel;
                 // Calculate other cell centre by extrapolation
                 neiCc[bFaceI] = faceCentres[i] + d*fn;
                 bFaceI++;
@@ -1901,8 +1901,6 @@ void Foam::meshRefinement::selectSeparatedCoupledFaces(boolList& selected) const
 
     forAll(patches, patchI)
     {
-        const polyPatch& pp = patches[patchI];
-
         // Check all coupled. Avoid using .coupled() so we also pick up AMI.
         if (isA<coupledPolyPatch>(patches[patchI]))
         {
@@ -1913,9 +1911,9 @@ void Foam::meshRefinement::selectSeparatedCoupledFaces(boolList& selected) const
 
             if (cpp.separated() || !cpp.parallel())
             {
-                forAll(pp, i)
+                forAll(cpp, i)
                 {
-                    selected[pp.start()+i] = true;
+                    selected[cpp.start()+i] = true;
                 }
             }
         }
@@ -1925,6 +1923,8 @@ void Foam::meshRefinement::selectSeparatedCoupledFaces(boolList& selected) const
 
 Foam::autoPtr<Foam::mapPolyMesh> Foam::meshRefinement::splitMeshRegions
 (
+    const labelList& globalToMasterPatch,
+    const labelList& globalToSlavePatch,
     const point& keepPoint
 )
 {
@@ -1933,7 +1933,11 @@ Foam::autoPtr<Foam::mapPolyMesh> Foam::meshRefinement::splitMeshRegions
 
     // Determine connected regions. regionSplit is the labelList with the
     // region per cell.
-    regionSplit cellRegion(mesh_);
+
+    boolList blockedFace(mesh_.nFaces(), false);
+    selectSeparatedCoupledFaces(blockedFace);
+
+    regionSplit cellRegion(mesh_, blockedFace);
 
     label regionI = -1;
 
@@ -1985,22 +1989,39 @@ Foam::autoPtr<Foam::mapPolyMesh> Foam::meshRefinement::splitMeshRegions
     removeCells cellRemover(mesh_);
 
     labelList exposedFaces(cellRemover.getExposedFaces(cellsToRemove));
+    labelList exposedPatch;
 
-    if (exposedFaces.size())
+    label nExposedFaces = returnReduce(exposedFaces.size(), sumOp<label>());
+    if (nExposedFaces)
     {
-        FatalErrorIn
+        //FatalErrorIn
+        //(
+        //    "meshRefinement::splitMeshRegions(const point&)"
+        //)   << "Removing non-reachable cells should only expose"
+        //    << " boundary faces" << nl
+        //    << "ExposedFaces:" << exposedFaces << abort(FatalError);
+
+        // Patch for exposed faces for lack of anything sensible.
+        label defaultPatch = 0;
+        if (globalToMasterPatch.size())
+        {
+            defaultPatch = globalToMasterPatch[0];
+        }
+
+        WarningIn
         (
             "meshRefinement::splitMeshRegions(const point&)"
-        )   << "Removing non-reachable cells should only expose boundary faces"
+        )   << "Removing non-reachable cells exposes "
-            << nl
+            << nExposedFaces << " internal or coupled faces." << endl
-            << "ExposedFaces:" << exposedFaces << abort(FatalError);
+            << "    These get put into patch " << defaultPatch << endl;
+        exposedPatch.setSize(exposedFaces.size(), defaultPatch);
     }
 
     return doRemoveCells
     (
         cellsToRemove,
         exposedFaces,
-        labelList(exposedFaces.size(),-1),  // irrelevant since 0 size.
+        exposedPatch,
         cellRemover
     );
 }

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

@@ -868,7 +868,12 @@ public:
             void selectSeparatedCoupledFaces(boolList&) const;
 
             //- Split mesh. Keep part containing point.
-            autoPtr<mapPolyMesh> splitMeshRegions(const point& keepPoint);
+            autoPtr<mapPolyMesh> splitMeshRegions
+            (
+                const labelList& globalToMasterPatch,
+                const labelList& globalToSlavePatch,
+                const point& keepPoint
+            );
 
             //- Update local numbering for mesh redistribution
             void distribute(const mapDistributePolyMesh&);

src/mesh/autoMesh/autoHexMesh/meshRefinement/meshRefinementBaffles.C

@@ -1411,6 +1411,7 @@ void Foam::meshRefinement::findCellZoneInsideWalk
 {
     // Analyse regions. Reuse regionsplit
     boolList blockedFace(mesh_.nFaces());
+    //selectSeparatedCoupledFaces(blockedFace);
 
     forAll(namedSurfaceIndex, faceI)
     {
@@ -2055,7 +2056,7 @@ void Foam::meshRefinement::baffleAndSplitMesh
         runTime++;
     }
 
-    splitMeshRegions(keepPoint);
+    splitMeshRegions(globalToMasterPatch, globalToSlavePatch, keepPoint);
 
     if (debug)
     {