[otaolafr]

hello,
I am facing an strange behavior with SHM, when snappy adds the boundary layers, the last step, there are holes that shows up in the surface of the internal mesh when I look at it in paraview via .foam file.


here is an image of the surface mesh and the three times saved by snappy, castellated, snappying and boundary addition and aditionally a zoom to the two holes.
this holes show up only in the internal mesh and not in the surface mesh that shows as boundary of the .foam file.
snappyLayersHoles.jpg


OFv8
ubuntu 20.04
paravew 5.6.0
the surface mesh was created with salome 9.6 netgen 1d-2d and checkSurface does not throw any error.



also attaching the snappyHexDict

/*--------------------------------*- C++ -*----------------------------------*\
  =========                 |
  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
   \\    /   O peration     | Website:  https://openfoam.org
    \\  /    A nd           | Version:  7
     \\/     M anipulation  |
\*---------------------------------------------------------------------------*/
FoamFile
{
    version     2.0;
    format      ascii;
    class       dictionary;
    object      snappyHexMeshDict;
}

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

// Which of the steps to run
castellatedMesh true;
snap            true;
addLayers       true;


// 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
{
    model
    {
        type triSurfaceMesh;
        file "model.stl";
        regions
        {
            inlet // Named region in the STL file
            {
                name inlet;// User-defined patch name
            }
            outlet 
            {
                name outlet;
            }
            walls
            {
                name walls;
            }
            /*
            sym_1
            {
                name sym_1;
            }
            sym_2
            {
                name sym_2;
            }
            */
        }
    }
};



// Settings for the castellatedMesh generation.
castellatedMeshControls
{

    // Refinement parameters
    // ~~~~~~~~~~~~~~~~~~~~~

    // If local number of cells is >= maxLocalCells on any processor
    // switches from from refinement followed by balancing
    // (current method) to (weighted) balancing before refinement.
    maxLocalCells 2000000;

    // 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 13000000;

    // 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 2;

    // 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 "model.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
    {
        model
        {
            level (5 5);
            
            regions
            {
                inlet    { level (5 5); patchInfo { type patch; }}
                outlet    { level (5 5); patchInfo { type patch; }}
                walls    { level (5 5); patchInfo { type walls; }}
                /*
                sym_1    { level (3 3); patchInfo { type symmetry; }}
                sym_2    { level (3 3); patchInfo { type symmetry; }}
                */
            }
            
        }
    }

    resolveFeatureAngle 20;


    // 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
    {
    }


    // 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 (0.00025 0.00025 0.0005); // 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 5;

    //- Relative distance for points to be attracted by surface feature point
    //  or edge. True distance is this factor times local
    //  maximum edge length.
    tolerance 1.05;

    //- Number of mesh displacement relaxation iterations.
    nSolveIter 300;

    //- Maximum number of snapping relaxation iterations. Should stop
    //  before upon reaching a correct mesh.
    nRelaxIter 4;

    // Feature snapping

        //- Number of feature edge snapping iterations.
        //  Leave out altogether to disable.
        nFeatureSnapIter 30;

        //- Detect (geometric) features by sampling the surface
        implicitFeatureSnap false;

        //- Use castellatedMeshControls::features
        explicitFeatureSnap true;

        //- Detect features between multiple surfaces
        //  (only for explicitFeatureSnap, default = false)
        multiRegionFeatureSnap false;
}



// 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
    {
    walls
    {
            nSurfaceLayers 3;
        }
    }

    // Expansion factor for layer mesh
    expansionRatio 1.1;


    // Wanted thickness of final added cell layer. If multiple layers
    // is the thickness of the layer furthest away from the wall.
    // Relative to undistorted size of cell outside layer.
    // See relativeSizes parameter.
    finalLayerThickness 0.9;

    // Minimum thickness of cell layer. If for any reason layer
    // cannot be above minThickness do not add layer.
    // See relativeSizes parameter.
    minThickness 0.05;

    // 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
    // are perpendicular
    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 30;

    // 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 10;
}



// Generic mesh quality settings. At any undoable phase these determine
// where to undo.
meshQualityControls
{
    #include "meshQualityDict"

    // 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

// Write flags
writeFlags
(
    scalarLevels    // write volScalarField with cellLevel for postprocessing
    layerSets       // write cellSets, faceSets of faces in layer
    layerFields     // write volScalarField for layer coverage
);


// Merge tolerance. Is fraction of overall bounding box of initial mesh.
// Note: the write tolerance needs to be higher than this.
mergeTolerance 1E-6;


// ************************************************************************* //

[Tobi]

What does checkMesh give you? And did you decompose the polyhedral on your ParaView program?


Seems more to be a display-problem rather than a real "hole"

[otaolafr]

Originally Posted by Tobi

What does checkMesh give you? And did you decompose the polyhedral on your ParaView program?


Seems more to be a display-problem rather than a real "hole"

sorry I forgot to upload the log of checkMesh, effectly the "holes" are coming from the decompose polyhedral! you where right, anyway there is still a lot to work to do, as it can be seen in the following image evethought it is a periodic geometry i finish with some bizarre surfaces collapsed (in red lines the trinagulated surface cutted by a slice and the final mesh) and with the quantity of fails in the checkMesh i would think that in anycase it is not a good mesh ^^


log.checkMesh.txt

[Tobi]

Nice mesh ... make your background mesh double as fine as it is now and things will look much better