Merge branch 'master' into cvm

Conflicts:
	applications/utilities/surface/surfaceFeatureExtract/surfaceFeatureExtract.C

tutorials/mesh/snappyHexMesh/flange/Allclean

@@ -0,0 +1,15 @@
+#!/bin/sh
+cd ${0%/*} || exit 1    # run from this directory
+
+# Source tutorial clean functions
+. $WM_PROJECT_DIR/bin/tools/CleanFunctions
+
+rm -rf 0 > /dev/null 2>&1
+rm -f ./*.obj > /dev/null 2>&1
+rm -rf constant/extendedFeatureEdgeMesh > /dev/null 2>&1
+rm -f constant/triSurface/flange.eMesh > /dev/null 2>&1
+rm -f constant/polyMesh/boundary
+
+cleanCase
+
+# ----------------------------------------------------------------- end-of-file

tutorials/mesh/snappyHexMesh/flange/Allrun

@@ -0,0 +1,7 @@
+#!/bin/sh
+# Source tutorial run functions
+. $WM_PROJECT_DIR/bin/tools/RunFunctions
+
+runApplication blockMesh
+runApplication surfaceFeatureExtract -includedAngle 150 -writeObj constant/triSurface/flange.stl flange
+runApplication snappyHexMesh -overwrite

tutorials/mesh/snappyHexMesh/flange/constant/polyMesh/blockMeshDict

@@ -0,0 +1,53 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    object      blockMeshDict;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+convertToMeters 1;
+
+vertices
+(
+    ( -0.03 -0.03 -0.03)
+    (  0.03 -0.03 -0.03)
+    (  0.03  0.03 -0.03)
+    ( -0.03  0.03 -0.03)
+    ( -0.03 -0.03 0.01)
+    (  0.03 -0.03 0.01)
+    (  0.03  0.03 0.01)
+    ( -0.03  0.03 0.01)
+);
+
+blocks
+(
+    hex (0 1 2 3 4 5 6 7) (20 16 12) simpleGrading (1 1 1)
+);
+
+edges
+(
+);
+
+patches
+(
+    patch allBoundary
+    (
+        (3 7 6 2)
+        (0 4 7 3)
+        (2 6 5 1)
+        (1 5 4 0)
+        (0 3 2 1)
+        (4 5 6 7)
+    )
+);
+
+// ************************************************************************* //

tutorials/mesh/snappyHexMesh/flange/system/controlDict

@@ -0,0 +1,49 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    location    "system";
+    object      controlDict;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+application     icoFoam;
+
+startFrom       startTime;
+
+startTime       0;
+
+stopAt          endTime;
+
+endTime         50;
+
+deltaT          1;
+
+writeControl    timeStep;
+
+writeInterval   20;
+
+purgeWrite      0;
+
+writeFormat     ascii;
+
+writePrecision  6;
+
+writeCompression uncompressed;
+
+timeFormat      general;
+
+timePrecision   6;
+
+runTimeModifiable yes;
+
+
+// ************************************************************************* //

tutorials/mesh/snappyHexMesh/flange/system/decomposeParDict

@@ -0,0 +1,50 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    location    "system";
+    object      decomposeParDict;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+numberOfSubdomains 4;
+
+method          ptscotch; //simple;
+
+simpleCoeffs
+{
+    n               ( 2 2 1 );
+    delta           0.001;
+}
+
+hierarchicalCoeffs
+{
+    n               ( 1 1 1 );
+    delta           0.001;
+    order           xyz;
+}
+
+metisCoeffs
+{
+    processorWeights ( 1 1 1 1 );
+}
+
+manualCoeffs
+{
+    dataFile        "";
+}
+
+distributed     no;
+
+roots           ( );
+
+
+// ************************************************************************* //

tutorials/mesh/snappyHexMesh/flange/system/fvSchemes

@@ -0,0 +1,30 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    location    "system";
+    object      fvSchemes;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+gradSchemes
+{
+}
+
+divSchemes
+{
+}
+
+laplacianSchemes
+{
+}
+
+// ************************************************************************* //

tutorials/mesh/snappyHexMesh/flange/system/fvSolution

@@ -0,0 +1,18 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    location    "system";
+    object      fvSolution;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+// ************************************************************************* //

tutorials/mesh/snappyHexMesh/flange/system/snappyHexMeshDict

@@ -0,0 +1,358 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| =========                 |                                                 |
+| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
+|  \\    /   O peration     | Version:  dev                                   |
+|   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
+|    \\/     M anipulation  |                                                 |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+    version     2.0;
+    format      ascii;
+    class       dictionary;
+    object      autoHexMeshDict;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+// Which of the steps to run
+castellatedMesh true;
+snap            true;
+addLayers       false;
+
+
+// Geometry. Definition of all surfaces. All surfaces are of class
+// searchableSurface.
+// Surfaces are used
+// - to specify refinement for any mesh cell intersecting it
+// - to specify refinement for any mesh cell inside/outside/near
+// - to 'snap' the mesh boundary to the surface
+geometry
+{
+    flange.stl
+    {
+        type triSurfaceMesh;
+        name flange;
+    }
+
+    //- Refine a bit extra around the small centre hole
+    refineHole
+    {
+        type searchableSphere;
+        centre (0 0 -0.012);
+        radius 0.003;
+    }
+};
+
+
+
+// Settings for the castellatedMesh generation.
+castellatedMeshControls
+{
+
+    // Refinement parameters
+    // ~~~~~~~~~~~~~~~~~~~~~
+
+    // While refining maximum number of cells per processor. This is basically
+    // the number of cells that fit on a processor. If you choose this too small
+    // it will do just more refinement iterations to obtain a similar mesh.
+    maxLocalCells 1000000;
+
+    // Overall cell limit (approximately). Refinement will stop immediately
+    // upon reaching this number so a refinement level might not complete.
+    // Note that this is the number of cells before removing the part which
+    // is not 'visible' from the keepPoint. The final number of cells might
+    // actually be a lot less.
+    maxGlobalCells 2000000;
+
+    // The surface refinement loop might spend lots of iterations refining just a
+    // few cells. This setting will cause refinement to stop if <= minimumRefine
+    // are selected for refinement. Note: it will at least do one iteration
+    // (unless the number of cells to refine is 0)
+    minRefinementCells 0;
+
+    // Number of buffer layers between different levels.
+    // 1 means normal 2:1 refinement restriction, larger means slower
+    // refinement.
+    nCellsBetweenLevels 1;
+
+
+
+    // Explicit feature edge refinement
+    // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+    // Specifies a level for any cell intersected by its edges.
+    // This is a featureEdgeMesh, read from constant/triSurface for now.
+    features
+    (
+        {
+            file "flange.eMesh";
+            level 0;
+        }
+    );
+
+
+
+    // Surface based refinement
+    // ~~~~~~~~~~~~~~~~~~~~~~~~
+
+    // Specifies two levels for every surface. The first is the minimum level,
+    // every cell intersecting a surface gets refined up to the minimum level.
+    // The second level is the maximum level. Cells that 'see' multiple
+    // intersections where the intersections make an
+    // angle > resolveFeatureAngle get refined up to the maximum level.
+
+    refinementSurfaces
+    {
+        flange
+        {
+            // Surface-wise min and max refinement level
+            level (2 2);
+        }
+    }
+
+    resolveFeatureAngle 30;
+
+
+    // Region-wise refinement
+    // ~~~~~~~~~~~~~~~~~~~~~~
+
+    // Specifies refinement level for cells in relation to a surface. One of
+    // three modes
+    // - distance. 'levels' specifies per distance to the surface the
+    //   wanted refinement level. The distances need to be specified in
+    //   descending order.
+    // - inside. 'levels' is only one entry and only the level is used. All
+    //   cells inside the surface get refined up to the level. The surface
+    //   needs to be closed for this to be possible.
+    // - outside. Same but cells outside.
+
+    refinementRegions
+    {
+        refineHole
+        {
+            mode inside;
+            levels ((1E15 3));
+        }
+    }
+
+
+    // Mesh selection
+    // ~~~~~~~~~~~~~~
+
+    // After refinement patches get added for all refinementSurfaces and
+    // all cells intersecting the surfaces get put into these patches. The
+    // section reachable from the locationInMesh is kept.
+    // NOTE: This point should never be on a face, always inside a cell, even
+    // after refinement.
+    // This is an outside point locationInMesh (-0.033 -0.033 0.0033);
+    locationInMesh (-9.23149e-05 -0.0025 -0.0025); // Inside point
+
+    // Whether any faceZones (as specified in the refinementSurfaces)
+    // are only on the boundary of corresponding cellZones or also allow
+    // free-standing zone faces. Not used if there are no faceZones.
+    allowFreeStandingZoneFaces true;
+}
+
+
+
+// Settings for the snapping.
+snapControls
+{
+    //- Number of patch smoothing iterations before finding correspondence
+    //  to surface
+    nSmoothPatch 3;
+
+    //- Relative distance for points to be attracted by surface feature point
+    //  or edge. True distance is this factor times local
+    //  maximum edge length.
+    tolerance 1.0;
+
+    //- Number of mesh displacement relaxation iterations.
+    nSolveIter 300;
+
+    //- Maximum number of snapping relaxation iterations. Should stop
+    //  before upon reaching a correct mesh.
+    nRelaxIter 5;
+
+    //- Highly experimental and wip: number of feature edge snapping
+    //  iterations. Leave out altogether to disable.
+    nFeatureSnapIter 10;
+}
+
+
+
+// Settings for the layer addition.
+addLayersControls
+{
+    // Are the thickness parameters below relative to the undistorted
+    // size of the refined cell outside layer (true) or absolute sizes (false).
+    relativeSizes true;
+
+    // Per final patch (so not geometry!) the layer information
+    layers
+    {
+        "flange_.*"
+        {
+            nSurfaceLayers 1;
+        }
+    }
+
+    // Expansion factor for layer mesh
+    expansionRatio 1.0;
+
+
+    //- Wanted thickness of final added cell layer. If multiple layers
+    //  is the thickness of the layer furthest away from the wall.
+    //  See relativeSizes parameter.
+    finalLayerThickness 0.3;
+
+    //- Minimum thickness of cell layer. If for any reason layer
+    //  cannot be above minThickness do not add layer.
+    //  See relativeSizes parameter.
+    minThickness 0.25;
+
+    //- If points get not extruded do nGrow layers of connected faces that are
+    //  also not grown. This helps convergence of the layer addition process
+    //  close to features.
+    nGrow 0;
+
+
+    // Advanced settings
+
+    //- When not to extrude surface. 0 is flat surface, 90 is when two faces
+    //  make straight angle.
+    featureAngle 30;
+
+    //- Maximum number of snapping relaxation iterations. Should stop
+    //  before upon reaching a correct mesh.
+    nRelaxIter 5;
+
+    // Number of smoothing iterations of surface normals
+    nSmoothSurfaceNormals 1;
+
+    // Number of smoothing iterations of interior mesh movement direction
+    nSmoothNormals 3;
+
+    // Smooth layer thickness over surface patches
+    nSmoothThickness 10;
+
+    // Stop layer growth on highly warped cells
+    maxFaceThicknessRatio 0.5;
+
+    // Reduce layer growth where ratio thickness to medial
+    // distance is large
+    maxThicknessToMedialRatio 0.3;
+
+    // Angle used to pick up medial axis points
+    minMedianAxisAngle 90;
+
+    // Create buffer region for new layer terminations
+    nBufferCellsNoExtrude 0;
+
+
+    // Overall max number of layer addition iterations. The mesher will exit
+    // if it reaches this number of iterations; possibly with an illegal
+    // mesh.
+    nLayerIter 50;
+
+    // Max number of iterations after which relaxed meshQuality controls
+    // get used. Up to nRelaxIter it uses the settings in meshQualityControls,
+    // after nRelaxIter it uses the values in meshQualityControls::relaxed.
+    nRelaxedIter 20;
+}
+
+
+
+// Generic mesh quality settings. At any undoable phase these determine
+// where to undo.
+meshQualityControls
+{
+    //- Maximum non-orthogonality allowed. Set to 180 to disable.
+    maxNonOrtho 65;
+
+    //- Max skewness allowed. Set to <0 to disable.
+    maxBoundarySkewness 20;
+    maxInternalSkewness 4;
+
+    //- Max concaveness allowed. Is angle (in degrees) below which concavity
+    //  is allowed. 0 is straight face, <0 would be convex face.
+    //  Set to 180 to disable.
+    maxConcave 80;
+
+    //- Minimum pyramid volume. Is absolute volume of cell pyramid.
+    //  Set to a sensible fraction of the smallest cell volume expected.
+    //  Set to very negative number (e.g. -1E30) to disable.
+    minVol 1e-13;
+
+    //- Minimum quality of the tet formed by the face-centre
+    //  and variable base point minimum decomposition triangles and
+    //  the cell centre.  Set to very negative number (e.g. -1E30) to
+    //  disable.
+    //     <0 = inside out tet,
+    //      0 = flat tet
+    //      1 = regular tet
+    minTetQuality 1e-9;
+
+    //- Minimum face area. Set to <0 to disable.
+    minArea -1;
+
+    //- Minimum face twist. Set to <-1 to disable. dot product of face normal
+    //- and face centre triangles normal
+    minTwist 0.05;
+
+    //- minimum normalised cell determinant
+    //- 1 = hex, <= 0 = folded or flattened illegal cell
+    minDeterminant 0.001;
+
+    //- minFaceWeight (0 -> 0.5)
+    minFaceWeight 0.05;
+
+    //- minVolRatio (0 -> 1)
+    minVolRatio 0.01;
+
+    //must be >0 for Fluent compatibility
+    minTriangleTwist -1;
+
+    //- if >0 : preserve single cells with all points on the surface if the
+    //  resulting volume after snapping (by approximation) is larger than
+    //  minVolCollapseRatio times old volume (i.e. not collapsed to flat cell).
+    //  If <0 : delete always.
+    //minVolCollapseRatio 0.5;
+
+
+    // Advanced
+
+    //- Number of error distribution iterations
+    nSmoothScale 4;
+    //- amount to scale back displacement at error points
+    errorReduction 0.75;
+
+
+
+    // Optional : some meshing phases allow usage of relaxed rules.
+    // See e.g. addLayersControls::nRelaxedIter.
+    relaxed
+    {
+        //- Maximum non-orthogonality allowed. Set to 180 to disable.
+        maxNonOrtho 75;
+    }
+}
+
+
+// Advanced
+
+// Flags for optional output
+// 0 : only write final meshes
+// 1 : write intermediate meshes
+// 2 : write volScalarField with cellLevel for postprocessing
+// 4 : write current intersections as .obj files
+debug 0;
+
+
+// Merge tolerance. Is fraction of overall bounding box of initial mesh.
+// Note: the write tolerance needs to be higher than this.
+mergeTolerance 1E-6;
+
+
+// ************************************************************************* //