Merge branch 'master' of ssh://noisy/home/noisy3/OpenFOAM/OpenFOAM-dev

applications/utilities/mesh/conversion/tetgenToFoam/beam.1.node

+213  3  0  0
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+  53    1.4998339999999999  1  0
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+  56    0.75044549999999999  0  1
+  57    0.75003524999999993  0  0
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+  69    1.2497509999999998  1  0
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+  71    0  0  0.75
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+  73    0.37522274999999999  0  0.70013946473134281
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+  75    0.31255174452459605  1  0.65638401293888804
+  76    0  0.75  1
+  77    0.249917  1  0
+  78    0  0.70831779089254521  0.29167340665919461
+  79    0.25001174999999998  0  0
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+  81    0.625029375  0.23429805042184107  0
+  82    0  0.24982494999999999  0
+  83    0  0.25008755567468249  0.50008743306175329
+  84    0.33552291795286748  0.37713361953826796  0.37295234921245662
+  85    1.3275022682494733  0.27703395451399626  0
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+  87    1.7393002110516891  0.73944000928409781  0
+  88    2  0.7499999999989998  0.25006298412499983
+  89    0.62528740222670842  0.74964177558619371  1
+  90    0.62465312500000003  1  0.76556323888302447
+  91    0.87551975000000004  0.24985661973700002  1
+  92    0.87551975000000004  0  0.75006834081249996
+  93    1.1922864636768418  1  0.75390684273024755
+  94    1.24958375  0.74986113453803516  1
+  95    1.1698804466514103  0.41956399899988917  1
+  96    1.187959730551635  0  0.74997433471920583
+  97    1.6874419282782818  1  0.68754603555472626
+  98    1.7498612499999999  1  1
+  99    2  0.74999999206099988  0.74999999206099988
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+ 101    1.6597808229817657  0  0.30542952755181008
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+ 103    1.3990667318832528  0.69603906683685635  0
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+ 115    0  1  0.75022814999999998
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+ 120    0  0  0.25
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+ 162    0.52956259724790877  0.46221182650782827  1
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+ 180    1.1620342234529084  0  0.53548179044497457
+ 181    0.77419059143108437  0.35536625456813642  0.76865650139332142
+ 182    0.95600842566592681  0  0.52050427577014857
+ 183    2  0.75  1
+ 184    1.8229055680968635  1  0.82294606919028224
+ 185    1.8124074661770861  0.8124421408239394  1
+ 186    1.6847465495324894  0.55699324455967203  0.74450659675858755
+ 187    1.1945125727535346  0.47020737648361044  0.48501348343009743
+ 188    1.4371531545555845  0.81243056656291324  1
+ 189    1.0230031981183827  0.60745624022002409  0.70905352953001077
+ 190    1.3178218537541635  0.74283221838842173  0.24644567916733129
+ 191    1.2298563370114035  0.23209604059822986  0.27403980288191482
+ 192    1.7289412043422971  0.73378563235104455  0.27218740896208421
+ 193    1.6944192651948711  0.39497422853539144  0.28096087015676863
+ 194    1.719021973042385  0.27206088666699435  0.73925099693622187
+ 195    0.51628118103442489  0.26487001488387318  0.53136856951372224
+ 196    0.22693818747394334  0.22584860839480125  0.50499300132112901
+ 197    0.18870598201308805  1  0.81131589108741564
+ 198    0.18140974929389231  0.81855222162009078  1
+ 199    0.52377345173705003  0.22575111801259504  0.77599180569982884
+ 200    0.44512574719134834  0.82031319413422632  0
+ 201    0.43769402753141229  0  0.18763960779463965
+ 202    0.23194582827732274  0.56348972010969589  0.48517047319960538
+ 203    1.404605953982319  0.2885118284317002  0.71332319773860509
+ 204    0.83285106746651061  0.22679389369216291  0.56316489552371896
+ 205    1.746191712341544  0.57096666984982924  0.48834249131610469
+ 206    1.2698479063322867  0.73902081556323673  0.53223169180184582
+ 207    1.0027339377070847  0.7783240018776667  0.51915438810718473
+ 208    1.1247094999999998  1  0.19525173141898322
+ 209    1.0585177272595161  0.22306568484158776  0.45497453797743681
+ 210    1.5766743500280587  0.62019545180903912  0
+ 211    1.5362846212581589  0.2135856104587727  0
+ 212    1.7956396187713533  0.19223457391785517  0.37621602432494938
+ 213    0.2338562054207384  0.80644498148268706  0.52587899633894741
+# Generated by tetgen -qfa0.005 beam.poly 

applications/utilities/mesh/manipulation/mergeOrSplitBaffles/mergeOrSplitBaffles.C

@@ -154,10 +154,77 @@ void insertDuplicateMerge
 }
 
 
+labelList findBaffles(const polyMesh& mesh, const labelList& boundaryFaces)
+{
+    // Get all duplicate face labels (in boundaryFaces indices!).
+    labelList duplicates = localPointRegion::findDuplicateFaces
+    (
+        mesh,
+        boundaryFaces
+    );
+
+
+    // Check that none are on processor patches
+    const polyBoundaryMesh& patches = mesh.boundaryMesh();
+
+    forAll(duplicates, bFaceI)
+    {
+        if (duplicates[bFaceI] != -1)
+        {
+            label faceI = mesh.nInternalFaces() + bFaceI;
+            label patchI = patches.whichPatch(faceI);
+
+            if (isA<processorPolyPatch>(patches[patchI]))
+            {
+                FatalErrorIn("findBaffles(const polyMesh&, const labelList&)")
+                    << "Duplicate face " << faceI
+                    << " is on a processorPolyPatch."
+                    << "This is not allowed." << nl
+                    << "Face:" << faceI
+                    << " is on patch:" << patches[patchI].name()
+                    << abort(FatalError);
+            }
+        }
+    }
+
+
+    // Write to faceSet for ease of postprocessing.
+    {
+        faceSet duplicateSet
+        (
+            mesh,
+            "duplicateFaces",
+            (mesh.nFaces() - mesh.nInternalFaces())/256
+        );
+
+        forAll(duplicates, bFaceI)
+        {
+            label otherFaceI = duplicates[bFaceI];
+
+            if (otherFaceI != -1 && otherFaceI > bFaceI)
+            {
+                duplicateSet.insert(mesh.nInternalFaces() + bFaceI);
+                duplicateSet.insert(mesh.nInternalFaces() + otherFaceI);
+            }
+        }
+
+        Pout<< "Writing " << duplicateSet.size()
+            << " duplicate faces to faceSet " << duplicateSet.objectPath()
+            << nl << endl;
+        duplicateSet.write();
+    }
+
+    return duplicates;
+}
+
+
+
+
 int main(int argc, char *argv[])
 {
     argList::validOptions.insert("split", "");
     argList::validOptions.insert("overwrite", "");
+    argList::validOptions.insert("detectOnly", "");
 #   include "setRootCase.H"
 #   include "createTime.H"
     runTime.functionObjects().off();
@@ -165,6 +232,7 @@ int main(int argc, char *argv[])
 
     bool split = args.options().found("split");
     bool overwrite = args.options().found("overwrite");
+    bool detectOnly = args.options().found("detectOnly");
 
     // Collect all boundary faces
     labelList boundaryFaces(mesh.nFaces() - mesh.nInternalFaces());
@@ -175,6 +243,15 @@ int main(int argc, char *argv[])
     }
 
 
+    if (detectOnly)
+    {
+        findBaffles(mesh, boundaryFaces);
+
+        return 0;
+    }
+
+
+
     // Read objects in time directory
     IOobjectList objects(mesh, runTime.timeName());
 
@@ -238,62 +315,7 @@ int main(int argc, char *argv[])
             << nl << endl;
 
         // Get all duplicate face labels (in boundaryFaces indices!).
-        labelList duplicates = localPointRegion::findDuplicateFaces
-        (
-            mesh,
-            boundaryFaces
-        );
-
-
-        // Check that none are on processor patches
-        const polyBoundaryMesh& patches = mesh.boundaryMesh();
-
-        forAll(duplicates, bFaceI)
-        {
-            if (duplicates[bFaceI] != -1)
-            {
-                label faceI = mesh.nInternalFaces() + bFaceI;
-                label patchI = patches.whichPatch(faceI);
-
-                if (isA<processorPolyPatch>(patches[patchI]))
-                {
-                    FatalErrorIn(args.executable())
-                        << "Duplicate face " << faceI
-                        << " is on a processorPolyPatch."
-                        << "This is not allowed." << nl
-                        << "Face:" << faceI
-                        << " is on patch:" << patches[patchI].name()
-                        << abort(FatalError);
-                }
-            }
-        }
-
-
-        // Write to faceSet for ease of postprocessing.
-        {
-            faceSet duplicateSet
-            (
-                mesh,
-                "duplicateFaces",
-                (mesh.nFaces() - mesh.nInternalFaces())/256
-            );
-
-            forAll(duplicates, bFaceI)
-            {
-                label otherFaceI = duplicates[bFaceI];
-
-                if (otherFaceI != -1 && otherFaceI > bFaceI)
-                {
-                    duplicateSet.insert(mesh.nInternalFaces() + bFaceI);
-                    duplicateSet.insert(mesh.nInternalFaces() + otherFaceI);
-                }
-            }
-
-            Pout<< "Writing " << duplicateSet.size()
-                << " duplicate faces to faceSet " << duplicateSet.objectPath()
-                << nl << endl;
-            duplicateSet.write();
-        }
+        labelList duplicates(findBaffles(mesh, boundaryFaces));
 
         // Merge into internal faces.
         insertDuplicateMerge(mesh, duplicates, meshMod);

applications/utilities/mesh/manipulation/setSet/setSet.C

@@ -714,9 +714,11 @@ commandStatus parseAction(const word& actionName)
 
 int main(int argc, char *argv[])
 {
+#   include "addRegionOption.H"
+#   include "addTimeOptions.H"
+
     argList::validOptions.insert("noVTK", "");
     argList::validOptions.insert("batch", "file");
-#   include "addTimeOptions.H"
 
 #   include "setRootCase.H"
 #   include "createTime.H"
@@ -730,7 +732,7 @@ int main(int argc, char *argv[])
 
     runTime.setTime(Times[startTime], startTime);
 
-#   include "createPolyMesh.H"
+#   include "createNamedPolyMesh.H"
 
     // Print some mesh info
     printMesh(runTime, mesh);

src/OpenFOAM/meshes/polyMesh/polyMeshIO.C

@@ -284,12 +284,28 @@ Foam::polyMesh::readUpdateState Foam::polyMesh::readUpdate()
             *this
         );
 
+        label oldSize = pointZones_.size();
+
+        if (newPointZones.size() <= pointZones_.size())
+        {
+            pointZones_.setSize(newPointZones.size());
+        }
+
+        // Reset existing ones
+        forAll (pointZones_, czI)
+        {
+            pointZones_[czI] = newPointZones[czI];
+        }
+
+        // Extend with extra ones
         pointZones_.setSize(newPointZones.size());
-        forAll (pointZones_, pzI)
+
+        for (label czI = oldSize; czI < newPointZones.size(); czI++)
         {
-            pointZones_[pzI] = newPointZones[pzI];
+            pointZones_.set(czI, newPointZones[czI].clone(pointZones_));
         }
 
+
         faceZoneMesh newFaceZones
         (
             IOobject
@@ -305,7 +321,14 @@ Foam::polyMesh::readUpdateState Foam::polyMesh::readUpdate()
             *this
         );
 
-        faceZones_.setSize(newFaceZones.size());
+        oldSize = faceZones_.size();
+
+        if (newFaceZones.size() <= faceZones_.size())
+        {
+            faceZones_.setSize(newFaceZones.size());
+        }
+
+        // Reset existing ones
         forAll (faceZones_, fzI)
         {
             faceZones_[fzI].resetAddressing
@@ -315,6 +338,15 @@ Foam::polyMesh::readUpdateState Foam::polyMesh::readUpdate()
             );
         }
 
+        // Extend with extra ones
+        faceZones_.setSize(newFaceZones.size());
+
+        for (label fzI = oldSize; fzI < newFaceZones.size(); fzI++)
+        {
+            faceZones_.set(fzI, newFaceZones[fzI].clone(faceZones_));
+        }
+
+
         cellZoneMesh newCellZones
         (
             IOobject
@@ -330,12 +362,28 @@ Foam::polyMesh::readUpdateState Foam::polyMesh::readUpdate()
             *this
         );
 
-        cellZones_.setSize(newCellZones.size());
+        oldSize = cellZones_.size();
+
+        if (newCellZones.size() <= cellZones_.size())
+        {
+            cellZones_.setSize(newCellZones.size());
+        }
+
+        // Reset existing ones
         forAll (cellZones_, czI)
         {
             cellZones_[czI] = newCellZones[czI];
         }
 
+        // Extend with extra ones
+        cellZones_.setSize(newCellZones.size());
+
+        for (label czI = oldSize; czI < newCellZones.size(); czI++)
+        {
+            cellZones_.set(czI, newCellZones[czI].clone(cellZones_));
+        }
+
+
         if (boundaryChanged)
         {
             return polyMesh::TOPO_PATCH_CHANGE;

src/autoMesh/autoHexMesh/autoHexMeshDriver/autoSnapDriver.C

@@ -218,7 +218,8 @@ Foam::label Foam::autoSnapDriver::getCollocatedPoints
 // Calculate displacement as average of patch points.
 Foam::pointField Foam::autoSnapDriver::smoothPatchDisplacement
 (
-    const motionSmoother& meshMover
+    const motionSmoother& meshMover,
+    const List<labelPair>& baffles
 ) const
 {
     const indirectPrimitivePatch& pp = meshMover.patch();
@@ -253,6 +254,34 @@ Foam::pointField Foam::autoSnapDriver::smoothPatchDisplacement
     const pointField& points = pp.points();
     const polyMesh& mesh = meshMover.mesh();
 
+    // Get labels of faces to count (master of coupled faces and baffle pairs)
+    PackedList<1> isMasterFace(syncTools::getMasterFaces(mesh));
+
+    {
+        forAll(baffles, i)
+        {
+            label f0 = baffles[i].first();
+            label f1 = baffles[i].second();
+
+            if (isMasterFace.get(f0) == 1)
+            {
+                // Make f1 a slave
+                isMasterFace.set(f1, 0);
+            }
+            else if (isMasterFace.get(f1) == 1)
+            {
+                isMasterFace.set(f0, 0);
+            }
+            else
+            {
+                FatalErrorIn("autoSnapDriver::smoothPatchDisplacement(..)")
+                    << "Both sides of baffle consisting of faces " << f0
+                    << " and " << f1 << " are already slave faces."
+                    << abort(FatalError);
+            }
+        }
+    }
+
 
     // Get average position of boundary face centres
     // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -266,9 +295,14 @@ Foam::pointField Foam::autoSnapDriver::smoothPatchDisplacement
 
         forAll(pFaces, pfI)
         {
-            avgBoundary[patchPointI] += pp[pFaces[pfI]].centre(points);
+            label faceI = pFaces[pfI];
+
+            if (isMasterFace.get(pp.addressing()[faceI]) == 1)
+            {
+                avgBoundary[patchPointI] += pp[faceI].centre(points);
+                nBoundary[patchPointI]++;
+            }
         }
-        nBoundary[patchPointI] = pFaces.size();
     }
 
     syncTools::syncPointList
@@ -886,7 +920,7 @@ void Foam::autoSnapDriver::preSmoothPatch
             checkFaces[faceI] = faceI;
         }
 
-        pointField patchDisp(smoothPatchDisplacement(meshMover));
+        pointField patchDisp(smoothPatchDisplacement(meshMover, baffles));
 
         // The current mesh is the starting mesh to smooth from.
         meshMover.setDisplacement(patchDisp);
@@ -1008,9 +1042,11 @@ Foam::vectorField Foam::autoSnapDriver::calcNearestSurface
     // Displacement per patch point
     vectorField patchDisp(localPoints.size(), vector::zero);
 
-
     if (returnReduce(localPoints.size(), sumOp<label>()) > 0)
     {
+        // Current surface snapped to
+        labelList snapSurf(localPoints.size(), -1);
+
         // Divide surfaces into zoned and unzoned
         labelList zonedSurfaces;
         labelList unzonedSurfaces;
@@ -1039,16 +1075,9 @@ Foam::vectorField Foam::autoSnapDriver::calcNearestSurface
                     patchDisp[pointI] =
                         hitInfo[pointI].hitPoint()
                       - localPoints[pointI];
+
+                    snapSurf[pointI] = hitSurface[pointI];
                 }
-                //else
-                //{
-                //   WarningIn("autoSnapDriver::calcNearestSurface(..)")
-                //        << "For point:" << pointI
-                //        << " coordinate:" << localPoints[pointI]
-                //        << " did not find any surface within:"
-                //        << 4*snapDist[pointI]
-                //        << " meter." << endl;
-                //}
             }
         }
 
@@ -1060,6 +1089,7 @@ Foam::vectorField Foam::autoSnapDriver::calcNearestSurface
         // Surfaces with zone information
         const wordList& faceZoneNames = surfaces.faceZoneNames();
 
+        // Current best snap distance