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[snappyHexMesh] SHM is not extruding/adding Layers everywhere

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Old   October 13, 2016, 17:52
Default SHM is not extruding/adding Layers everywhere
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Matthias D
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Hi everybody,

I am trying to mesh a terrain surface with snappyHexMesh (SHM).
As far as I can tell, the steps of castellating and snapping the mesh are working fine. I have included the output of checkMesh for the different steps. The only slightly wired thing is the bounding box of the mesh after the snapping:
Code:
Checking geometry...
    Overall domain bounding box (-2.80928364337e-11 -2.86651979204e-11 -1.91131555027e-09) (83300 76950 10000)
Those very small values should be zero. But I am not sure if that is a problem here.


The bigger problem seems to be the layer addition:
Code:
Layer addition iteration 0
--------------------------

Determining displacement for added points according to pointNormal ...
Detected 0 points with point normal pointing through faces.
Reset displacement at 0 points to average of surrounding points.

displacementMedialAxis : Smoothing using Medial Axis ...
displacementMedialAxis : Reducing layer thickness at 0 nodes where thickness to medial axis distance is large 
displacementMedialAxis : Removing isolated regions ...
displacementMedialAxis : Number of isolated points extrusion stopped : 0
displacementMedialAxis : Smoothing field ...
    Iteration 0   residual 2.74267968847e-16
displacementMedialAxis : Moving mesh ...
displacementMedialAxis : Iteration 0
Moving mesh using displacement scaling : min:1  max:1
Checking faces in error :
    non-orthogonality > 70  degrees                        : 1
    faces with face pyramid volume < 1e-30                 : 0
    faces with face-decomposition tet quality < -1         : 0
    faces with concavity > 80  degrees                     : 0
    faces with area < 1e-30 m^2                            : 0
    faces with skewness > 4   (internal) or 20  (boundary) : 0
displacementMedialAxis : Iteration 1
Moving mesh using displacement scaling : min:0.75  max:1
Checking faces in error :
    non-orthogonality > 70  degrees                        : 1
    faces with face pyramid volume < 1e-30                 : 0
    faces with face-decomposition tet quality < -1         : 0
    faces with concavity > 80  degrees                     : 0
    faces with area < 1e-30 m^2                            : 0
    faces with skewness > 4   (internal) or 20  (boundary) : 0
displacementMedialAxis : Iteration 2
Moving mesh using displacement scaling : min:0.5625  max:1
Checking faces in error :
    non-orthogonality > 70  degrees                        : 1
    faces with face pyramid volume < 1e-30                 : 0
    faces with face-decomposition tet quality < -1         : 0
    faces with concavity > 80  degrees                     : 0
    faces with area < 1e-30 m^2                            : 0
    faces with skewness > 4   (internal) or 20  (boundary) : 0
displacementMedialAxis : Iteration 3
Moving mesh using displacement scaling : min:0.421875  max:1
Checking faces in error :
    non-orthogonality > 70  degrees                        : 1
    faces with face pyramid volume < 1e-30                 : 0
    faces with face-decomposition tet quality < -1         : 0
    faces with concavity > 80  degrees                     : 0
    faces with area < 1e-30 m^2                            : 0
    faces with skewness > 4   (internal) or 20  (boundary) : 0
displacementMedialAxis : Iteration 4
Moving mesh using displacement scaling : min:0.31640625  max:1
Checking faces in error :
    non-orthogonality > 70  degrees                        : 1
    faces with face pyramid volume < 1e-30                 : 0
    faces with face-decomposition tet quality < -1         : 0
    faces with concavity > 80  degrees                     : 0
    faces with area < 1e-30 m^2                            : 0
    faces with skewness > 4   (internal) or 20  (boundary) : 0
displacementMedialAxis : Iteration 5
displacementMedialAxis : Displacement scaling for error reduction set to 0.
Moving mesh using displacement scaling : min:0.2373046875  max:1
Checking faces in error :
    non-orthogonality > 70  degrees                        : 1
    faces with face pyramid volume < 1e-30                 : 0
    faces with face-decomposition tet quality < -1         : 0
    faces with concavity > 80  degrees                     : 0
    faces with area < 1e-30 m^2                            : 0
    faces with skewness > 4   (internal) or 20  (boundary) : 0
displacementMedialAxis : Iteration 6
Moving mesh using displacement scaling : min:0  max:1
Checking faces in error :
    non-orthogonality > 70  degrees                        : 0
    faces with face pyramid volume < 1e-30                 : 0
    faces with face-decomposition tet quality < -1         : 0
    faces with concavity > 80  degrees                     : 0
    faces with area < 1e-30 m^2                            : 0
    faces with skewness > 4   (internal) or 20  (boundary) : 0
displacementMedialAxis : Successfully moved mesh
displacementMedialAxis : Finished moving mesh ...
truncateDisplacement : Unextruded 0 faces due to non-consecutive vertices being extruded.
truncateDisplacement : Unextruded 1 faces due to stringed edges with inconsistent extrusion.
truncateDisplacement : Unextruded 0 faces due to non-consecutive vertices being extruded.
truncateDisplacement : Unextruded 0 faces due to stringed edges with inconsistent extrusion.

Setting up information for layer truncation ...

Checking mesh with layer ...
Checking faces in error :
    non-orthogonality > 70  degrees                        : 0
    faces with face pyramid volume < 1e-30                 : 0
    faces with face-decomposition tet quality < -1         : 0
    faces with concavity > 80  degrees                     : 0
    faces with area < 1e-30 m^2                            : 0
    faces with skewness > 4   (internal) or 20  (boundary) : 0
Detected 0 illegal faces (concave, zero area or negative cell pyramid volume)
Extruding 2557541 out of 2557543 faces (99.9999217999%). Removed extrusion at 0 faces.
Added 2557541 out of 2557543 cells (99.9999217999%).
Edge intersection testing:
    Number of edges             : 38571469
    Number of edges to retest   : 0
    Number of intersected edges : 5101041

patch  faces    layers   overall thickness
                         [m]       [%]
-----  -----    ------   ---       ---
domain 2557543  1        15        10
The layer addition iteration clears the orthogonal faces and it states "Successfully moved mesh". But there is first 1 unextruded face due to stringed edges. What does that even mean?
And in the end it is only extruding 2557541 out of 2557543 faces, missing two faces. Which is kind of close, but unfortunately not good enough for my case...

Here are the layer and the quality settings of the snappyHexMeshDict:
Code:
// 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;

    nMedialAxisIter 10;

    // Per final patch (so not geometry!) the layer information
    layers
    {
        domain
        {
            nSurfaceLayers 1;
        }
    }

    // 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.
    //  See relativeSizes parameter.
    //finalLayerThickness 0.8; 
    firstLayerThickness 0.3;

    //- Minimum thickness of cell layer. If for any reason layer
    //  cannot be above minThickness do not add layer.
    //  Relative to undistorted size of cell outside layer.
    minThickness 0.001;

    //- 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 180; // 60

    //slipFeatureAngel 90;

    //- 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; //5;

    // Number of smoothing iterations of interior mesh movement direction
    nSmoothNormals 3; // 10

    // Stop layer growth on highly warped cells
    maxFaceThicknessRatio 0.6; // 0.5

    // Reduce layer growth where ratio thickness to medial
    // distance is large
    maxThicknessToMedialRatio 0.6; // 0.3

    // Smooth layer thickness over surface patches
    nSmoothThickness 10;

    // Angle used to pick up medial axis points
    minMedianAxisAngle 130; // 90

    // Create buffer region for new layer terminations
    nBufferCellsNoExtrude 0;

    // Overall max number of layer addition iterations
    nLayerIter 1;

}



// Generic mesh quality settings. At any undoable phase these determine
// where to undo.
meshQualityControls
{
    //- Maximum non-orthogonality allowed. Set to 180 to disable.
    maxNonOrtho 70; // 65;

    //- Max skewness allowed. Set to <0 to disable.
    maxBoundarySkewness 20; //20
    maxInternalSkewness 4;  //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; // 80;

    //- Minimum projected area v.s. actual area. Set to -1 to disable.
    minFlatness 0.5; // 0.5;

    //- 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-30;

    //- Minimum face area. Set to <0 to disable.
    minArea 1e-30;

    //- Minimum face twist. Set to <-1 to disable. dot product of face normal
    //- and face centre triangles normal
    //minTwist 0.02;
    minTwist -1;

    //- minimum normalised cell determinant
    //- 1 = hex, <= 0 = folded or flattened illegal cell
    minDeterminant  -1; //0.001;

    //- minFaceWeight (0 -> 0.5)
    minFaceWeight -1; //0.02;

    //- minVolRatio (0 -> 1)
    minVolRatio -1; //0.01;

    //must be >0 for Fluent compatibility
    minTriangleTwist -1;

    //Added for 2.1.x, no clue what should be used here...
    minTetQuality -1; //1e-30; // -1

    // Advanced

    //- Number of error distribution iterations
    nSmoothScale 4;
    //- amount to scale back displacement at error points
    errorReduction 0.75;

    relaxed
    {
 	maxNonOrtho 75;
    }

}
I will also attache the complete snappyHexMeshDict and the output of snappyHexMesh. I appreciate every hint! I am not very experienced at all, so it might also be that I am missing something really stupid...

Thanks a lot and let me know if you need any further information.
Matthias
Attached Files
File Type: txt checkMesh_0.001.txt (3.9 KB, 0 views)
File Type: txt checkMesh_0.002.txt (4.0 KB, 0 views)
File Type: txt checkMesh_0.003.txt (4.0 KB, 4 views)
File Type: txt logsnappy.txt (32.3 KB, 3 views)
File Type: txt snappyHexMeshDict.txt (9.2 KB, 4 views)
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Old   October 15, 2016, 19:46
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I'm sorry, could you be clearer on what exactly the problem is? Does your mesh look wrong or something?
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Old   October 16, 2016, 16:45
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Matthias D
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Quote:
Originally Posted by KarenRei View Post
I'm sorry, could you be clearer on what exactly the problem is? Does your mesh look wrong or something?

Hi,

thanks for your response! And sorry if I made a bad job explaining my problem.

My problem is: SnappyHexMesh does not extrude and add a layer for every face.
I only miss a few faces, but this is a problem in my case, as I need two perfectly parallel faces at the surface in order to calculate surface layer fluxes. Without those layers my solver will crash.

Thank you in advance for every hint and help!
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