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[snappyHexMesh] SHM doesn't create cellZones for one region

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Old   January 22, 2018, 03:39
Default SHM doesn't create cellZones for one region
  #1
Eko
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Hey guys,

I have a problem using snappyHexMesh. I am trying to mesh a geometry with 7 regions but one region doesn't get meshed.
I once had the same problem and solved it somehow but now I have no clue. Tried changing parameters in SHM dict file - without any success.
Does anyone have the same problem or an idea how to solve it?

Code:
Introducing zones for interfaces
--------------------------------

Setting cellZones according to named surfaces:
Surface : B1600-12
    faceZone : B1600-12
    cellZone : B1600-12
Surface : Block-1
    faceZone : Block-1
    cellZone : Block-1
Surface : Block-2
    faceZone : Block-2
    cellZone : Block-2
Surface : Block-3
    faceZone : Block-3
    cellZone : Block-3
Surface : Block-4
    faceZone : Block-4
    cellZone : Block-4
Surface : Block-5
    faceZone : Block-5
    cellZone : Block-5
Surface : Air
    faceZone : Air
    cellZone : Air

Setting cellZones according to locationsInMesh:
Location : (0 0 0)
    cellZone : none

For cellZone none found point (0 0 0) in global region 0 out of 1 regions.
Found 7 closed, named surfaces. Assigning cells in/outside these surfaces to the corresponding cellZone.

Walking from known cellZones; crossing a faceZone face changes cellZone

Only keeping zone faces inbetween different cellZones.

Setting faceZones according to neighbouring cellZones:

CellZones:
    Umgebung    size:7246
    B1600-12   size:0
    Block-1     size:8
    Block-2     size:4
    Block-3     size:8
    Block-4     size:7
    Block-5     size:8
    Air size:733

FaceZones:
    B1600-12   size:122
    Block-1     size:8
    Block-2     size:4
    Block-3     size:9
    Block-4     size:13
    Block-5     size:11
    Air size:377

Edge intersection testing:
    Number of edges             : 25589
    Number of edges to retest   : 0
    Number of intersected edges : 733

And my Dict file

Code:
/*--------------------------------*- C++ -*----------------------------------*\
| =========                 |                                                 |
| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
|  \\    /   O peration     | Version:  plus                                  |
|   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
|    \\/     M anipulation  |                                                 |
\*---------------------------------------------------------------------------*/
FoamFile
{
    version     2.0;
    format      ascii;
    class       dictionary;
    object      snappyHexMeshDict;
}

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

// 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
{

    B-1600-klein-1.stl
    {
        type triSurfaceMesh;
        name B1600-12;
	scale 0.001;
    }

    Block-klein-1.stl
    {
        type triSurfaceMesh;
        name Block-1;
	scale 0.001;
    }

    Block-klein-2.stl
    {
        type triSurfaceMesh;
        name Block-2;
	scale 0.001;
    }

    Block-klein-3.stl
    {
        type triSurfaceMesh;
        name Block-3;
	scale 0.001;
    }

    Block-klein-4.stl
    {
        type triSurfaceMesh;
        name Block-4;
	scale 0.001;
    }

    Block-klein-5.stl
    {
        type triSurfaceMesh;
        name Block-5;
	scale 0.001;
    }
 
    Air-klein.stl
    {
	type triSurfaceMesh;
	name Air;
	scale 0.001;
    }
};



// 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 100000;

    // 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 300000;

    // 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 3;

    // Number of buffer layers between different levels.
    // 1 means normal 2:1 refinement restriction, larger means slower
    // refinement.
    nCellsBetweenLevels 6;



    // 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
    (
    );



    // 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
    {

        B1600-12
        {
            level ( 1 3 );

            cellZone B1600-12;
            faceZone B1600-12;           
	    cellZoneInside inside;
        }

        Block-1
        {
            level ( 1 1 );

            cellZone Block-1;
            faceZone Block-1;
            cellZoneInside inside;
        }

        Block-2
        {
            level ( 1 1 );

            cellZone Block-2;
            faceZone Block-2;
            cellZoneInside inside;
        }

        Block-3
        {
            level ( 1 1 );

            cellZone Block-3;
            faceZone Block-3;
            cellZoneInside inside;
        }

        Block-4
        {
            level ( 1 1 );

            cellZone Block-4;
            faceZone Block-4;
            cellZoneInside inside;
        }

        Block-5
        {
            level ( 1 1 );

            cellZone Block-5;
            faceZone Block-5;
            cellZoneInside inside;
        }
	
	Air
	{
	    level ( 1 3 );
	    
	    cellZone Air;
	    faceZone Air;
            cellZoneInside inside;
         }

    }

    // Resolve sharp angles
    resolveFeatureAngle 60;


    // 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.
    locationInMesh 
    (0.02 0.02 0.05);


    // 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 false;
}



// Settings for the snapping.
snapControls
{
    //- Number of patch smoothing iterations before finding correspondence
    //  to surface
    nSmoothPatch 4;

    //- Relative distance for points to be attracted by surface feature point
    //  or edge. True distance is this factor times local
    //  maximum edge length.
    tolerance 1.5;

    //- Number of mesh displacement relaxation iterations.
    nSolveIter 150;

    //- Maximum number of snapping relaxation iterations. Should stop
    //  before upon reaching a correct mesh.
    nRelaxIter 5;

    // Feature snapping

        //- Number of feature edge snapping iterations.
        //  Leave out altogether to disable.
        nFeatureSnapIter 4;

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

        //- Use castellatedMeshControls::features
        explicitFeatureSnap false;

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



// Settings for the layer addition.
addLayersControls
{
    relativeSizes true;

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

    // Expansion factor for layer mesh
    expansionRatio 1.3;

    // 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 1;

    // 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 0.1;

    // 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.
    // Note: changed(corrected) w.r.t 17x! (didn't do anything in 17x)
    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 6;

    // 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 2;

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

    // Reduce layer growth where ratio thickness to medial
    // distance is large
    maxThicknessToMedialRatio 1;

    // Angle used to pick up medial axis points
    // Note: changed(corrected) w.r.t 17x! 90 degrees corresponds to 130 in 17x.
    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;
}



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

    // Advanced

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


// Advanced

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


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

Last edited by Eko; January 22, 2018 at 04:50.
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Old   January 22, 2018, 04:31
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Hi,

Maybe I am wrong, but you seem to be assigning it to a different cellZone name for B1600-12 ("cellZone LichtbandB1600-12;"), no? Maybe the error comes from that?

Cheers,
Antimony
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Old   January 22, 2018, 04:54
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Quote:
Originally Posted by Antimony View Post
Hi,

Maybe I am wrong, but you seem to be assigning it to a different cellZone name for B1600-12 ("cellZone LichtbandB1600-12;"), no? Maybe the error comes from that?

Cheers,
Antimony
I saw that too and changed it. But that wasn't the problem. Still not meshing
In my other task it worked after I changed refinement level and maxGlobal and MaxLocalCells but this ain't working for the current task.
Is there something like a minimum cell size (e.g. 1m*1m*1m)? I would like to have as less cells as possible.

Last edited by Eko; January 23, 2018 at 03:53.
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Old   January 22, 2018, 21:44
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Hi,

Yes it is possible that there is a size mismatch.

Can you post your blockMeshDict as well?

As an alternative, you can try with the foundation version of snappyHexMesh instead of the ESI version. It has a different approach to the snappy process...

Cheers,
Antimony
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Old   January 23, 2018, 02:38
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Quote:
Originally Posted by Antimony View Post
Hi,

Yes it is possible that there is a size mismatch.

Can you post your blockMeshDict as well?

As an alternative, you can try with the foundation version of snappyHexMesh instead of the ESI version. It has a different approach to the snappy process...

Cheers,
Antimony
Hey Antimony,

Thanks for your answer and my blockMeshDict looks like this:

Code:
/*--------------------------------*- C++ -*----------------------------------*\
| =========                 |                                                 |
| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
|  \\    /   O peration     | Version:  plus                                  |
|   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
|    \\/     M anipulation  |                                                 |
\*---------------------------------------------------------------------------*/
FoamFile
{
    version     2.0;
    format      ascii;
    class       dictionary;
    object      blockMeshDict;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

convertToMeters 1;

vertices
(
    (-4  -3  0)
    (12  -3  0)
    (12   5  0)
    (-4   5  0)
    (-4  -3  4)
    (12  -3  4)
    (12   5  4)
    (-4   5  4)
);

blocks
(
    hex (0 1 2 3 4 5 6 7) Umgebung (32 16 8) simpleGrading (1 1 1)
);

edges
(
);

boundary
(
    inlet
    {
        type patch;
        faces
        (
            (0 4 7 3)
        );
    }

    outlet
    {
        type patch;
        faces
        (
            (2 6 5 1)
        );
    }

    floor
    {
        type wall;
        faces
        (
            (0 3 2 1)
        );
    }

    ceiling
    {
        type wall;
        faces
        (
            (4 5 6 7)
        );
    }

    frontAndBack
    {
        type wall;
        faces
        (
            (1 5 4 0)
	    (3 7 6 2)
        );
    }
);

mergePatchPairs
(
);

// ************************************************************************* //
I think this should be alright.
My current guess is that it has to do with the geometry of the B1600-12 region since it has openings/holes in it.
Could this be an issue? The other parts work without any problem and have closed surfaces.
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Old   January 23, 2018, 11:04
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If the STL itself is not closed, how you would expect sHM to build a cellZone. For that purpose the application needs a closed STL file based on the fact to check what is inside and outside. Use surfaceCheck to proof that your STL is waterproof.
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Old   January 23, 2018, 11:31
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Quote:
Originally Posted by Tobi View Post
If the STL itself is not closed, how you would expect sHM to build a cellZone. For that purpose the application needs a closed STL file based on the fact to check what is inside and outside. Use surfaceCheck to proof that your STL is waterproof.
I get your point and am trying to make a waterproof stl as well.
But I noticed that if I change up the sHMDict file a bit the region gets fully meshed and looks good.
I don't understand why it works sometimes and sometimes doesn't.
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Old   January 23, 2018, 12:38
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If you cell size is fine enough to detect holes in your STL, then it is not working. If the cell size is large enough to overcome it, then you have no problems. I refer you to watch my tutorials videos about snappyHexMesh and meshing. If one is following these steps (I know it is not always possible because one gets a bad STL file from others), you have no problems and you will not get any unexpected results. Actually, the unexpected results are only a lack of knowledge and expertise in the application itself. If you work long enough with snappy and you know how it works, than the mistakes are obvious.
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Old   January 24, 2018, 02:40
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Quote:
Originally Posted by Tobi View Post
If you cell size is fine enough to detect holes in your STL, then it is not working. If the cell size is large enough to overcome it, then you have no problems. I refer you to watch my tutorials videos about snappyHexMesh and meshing. If one is following these steps (I know it is not always possible because one gets a bad STL file from others), you have no problems and you will not get any unexpected results. Actually, the unexpected results are only a lack of knowledge and expertise in the application itself. If you work long enough with snappy and you know how it works, than the mistakes are obvious.
Thanks a lot. I am currently rewatching your tutorials and trying to fix the problem. I'm new to OpenFOAM so I don't have much knowledge or expertise
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Old   January 24, 2018, 02:50
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Hi,

Just one further point to add - sometimes you want snappy to mesh through some opening (for example, a building with a window open). In such a case, you will need to include the thickness of the building so that snappy does a good job through the "hole"/opening.

Cheers,
Antimony
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Old   January 24, 2018, 03:03
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To further increase the content of information here. To get a closed surface one can use blender. However, one simple way is to mesh with sHM in a coarse manner and extracting the new generated boundaries as STL which can be used in a subsequent new meshing step.
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