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[snappyHexMesh] snappyHexMesh can't create refimenet region

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Old   August 26, 2016, 09:37
Default snappyHexMesh can't create refimenet region
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gereksiz
Join Date: Mar 2015
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Hello,

I have been creating mesh for a 3d wind turbine analysis with openFoam 2.4.0, but I haven't succeed yet. It is a steady-state analysis so I use periodic boundary conditions and my domain is like a 120 degree pie, domain.jpg.

It is blockMeshDict file that creates this geometry.

Code:
/*--------------------------------*- C++ -*----------------------------------*\
| =========                 |                                                 |
| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
|  \\    /   O peration     | Version:  2.4.0                                 |
|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
|    \\/     M anipulation  |                                                 |
\*---------------------------------------------------------------------------*/
FoamFile
{
    version     2.0;
    format      ascii;
    class       dictionary;
    object      blockMeshDict;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

convertToMeters 1;

vertices
(
    (-100 0 0)
    (100 0 0)
    (-100 -173.20 100)
    (100 -173.20 100)    
    (100 173.20 100)
    (-100 173.20 100)
);

blocks
(
    hex (0 1 1 0 2 3 4 5)(100 100 100) simpleGrading (1 1 100)
);

edges
(
arc 2 5 (-100 0 200)
arc 3 4 (100 0 200)
);

/*defaultPatch
{
    name frontAndBack;
    type wall;
}*/


boundary
(
   /* inlet
    {
        type patch;
        faces
        (
        (0 0 5 2 )
        );
    }*/
    side1
    {
        type cyclic;
        faces
        (
            (0 2 3 1)
        );
        neighbourPatch  side2;
    }
    side2
    {
        type cyclic;
        faces
        (
            (0 1 4 5)
        );
        neighbourPatch  side1;
    }
    inlet
    {
        type patch;
        faces
        (
            (0 0 5 2 )
        );
    }
    outlet
    {
        type patch;
        faces
        (
            (1 3 4 1)
        );
    }
    top
    {
        type patch;
        faces
        (
            (5 2 3 4)
        );
    }
    collapsed
    {
    type empty;
    faces
    (
        (0 1 1 0)
    );
    }
);

mergePatchPairs
(
);

// ************************************************************************* //
I've managed to create the blockmesh without any error. Afterwards I wanted to snappyHexMesh to generate my final mesh contains wind turbine and refinement region, also I would use it as MRF source. However I couldn't do it. snappyHexMesh gives me this error.

Code:

Surface refinement iteration 6
------------------------------

Marked for refinement due to surface intersection          : 1 cells.
Marked for refinement due to curvature/regions             : 22 cells.
Determined cells to refine in = 0.29 s
Selected for refinement : 30 cells (out of 1081578)
Stopping refining since too few cells selected.


Removing mesh beyond surface intersections
------------------------------------------

Found point (8.123 3.9823 10.13123123) in global region 0 out of 2 regions.
Keeping all cells in region 0 containing point (8.123 3.9823 10.13123123)
Selected for keeping : 1075852 cells.
Edge intersection testing:
    Number of edges             : 3275257
    Number of edges to retest   : 12183
    Number of intersected edges : 18589

Shell refinement iteration 0
----------------------------

Marked for refinement due to distance to explicit features : 0 cells.
Marked for refinement due to refinement shells             : 225852 cells.
Determined cells to refine in = 4.46 s
Selected for internal refinement : 225852 cells (out of 1075852)
hexRef8 : Dumping cell as obj to "/home/taygun/Desktop/OpenFOAM/OpenFOAM-2.4.0/run/turbineDesign/turbineGridTest/test_10/cell_40.obj"


--> FOAM FATAL ERROR: 
cell 40 of level 0 does not seem to have 8 points of equal or lower level
cellPoints:6(141 142 40 41 242 243)
pointLevels:6{0}

    From function hexRef8::setRefinement(const labelList&, polyTopoChange&)
    in file polyTopoChange/polyTopoChange/hexRef8.C at line 3775.

FOAM aborting

#0  Foam::error::printStack(Foam::Ostream&) at ??:?
#1  Foam::error::abort() at ??:?
#2  Foam::hexRef8::setRefinement(Foam::List<int> const&, Foam::polyTopoChange&) at ??:?
#3  Foam::meshRefinement::refine(Foam::List<int> const&) at ??:?
#4  Foam::meshRefinement::refineAndBalance(Foam::string const&, Foam::decompositionMethod&, Foam::fvMeshDistribute&, Foam::List<int> const&, double) at ??:?
#5  Foam::autoRefineDriver::shellRefine(Foam::refinementParameters const&, int) at ??:?
#6  Foam::autoRefineDriver::doRefine(Foam::dictionary const&, Foam::refinementParameters const&, Foam::snapParameters const&, bool, Foam::dictionary const&) at ??:?
#7  ? at ??:?
#8  __libc_start_main in "/lib/x86_64-linux-gnu/libc.so.6"
#9  ? at ??:?
Aborted (core dumped)
The cell that gives the error is here error.jpg

This is my snappyHexMeshDict file

Code:
/*--------------------------------*- C++ -*----------------------------------*\
| =========                 |                                                 |
| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
|  \\    /   O peration     | Version:  2.3.1                                 |
|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
|    \\/     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
{
     poyra36_2.stl
    {
        type triSurfaceMesh;
        name blade;
    }
   
     rCylinder
    {
    type searchableCylinder;
       point1 (-20 0 0);    // Height
       point2 (20 0 0);    // Vector
       radius 60;       
    }
/*    rBox
    {
        type searchableCylinder;
        min (-800 -700 0)kkjjjk;
        max (1700 700 80 );
    } */
}





// 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 5000000;

    // 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 25000000;

    // 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 100;

    // Allow a certain level of imbalance during refining
    // (since balancing is quite expensive)
    // Expressed as fraction of perfect balance (= overall number of cells /
    // nProcs). 0=balance always.
    maxLoadUnbalance 0.10;


    // Number of buffer layers between different levels.
    // 1 means normal 2:1 refinement restriction, larger means slower
    // refinement.
    nCellsBetweenLevels 4;



    // 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 "poyra36_2.eMesh";
            level 5;
        }
    );



    // 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
    {

  /*      rCylinder
        {
        mode inside;
            level (2 2);
            faceZone rCylinder;
            cellZone rCylinder;
            cellZoneInside inside;

        }*/


/*       rCylinder
        {
            mode inside;
            level (1 1);
            cellZone    rCylinder;
    }*/

       blade
        {
            // Surface-wise min and max refinement level
            level (3 4);

            // Optional region-wise level specification

            regions
            {

/*       rCylinder
        {
            mode inside;
            level (1 1);
            cellZone    rCylinder;
        }*/


            }

            //- Optional angle to detect small-large cell situation
            //  perpendicular to the surface. Is the angle of face w.r.t.
            //  the local surface normal. Use on flat(ish) surfaces only.
            //  Otherwise leave out or set to negative number.
            //perpendicularAngle 10;


            //- Optional faceZone and (for closed surface) cellZone with
            //  how to select the cells that are in the cellZone
            //  (inside / outside / specified insidePoint)
            //faceZone sphere;
            //cellZone sphere;
            //cellZoneInside inside;  //outside/insidePoint
        } 
    }

    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
    {


    rCylinder
    {
            mode inside;
        levels ((10 15));

            faceZone rCylinder;
            cellZone rCylinder;
            cellZoneInside inside;

    } 

/*
        windTurbine1
        {
            mode inside;
            levels ((6 6));
        }

        windTurbine2
        {
            mode inside;
            levels ((6 6));
        }
*/        //sphere.stl
        //{
        //    mode distance;
        //    levels ((1.0 5) (2.0 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.
    locationInMesh (8.123 3.9823 10.13123123123);

    // 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 4.0;

    //- Number of mesh displacement relaxation iterations.
    nSolveIter 20;

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



// 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
    {
    "blade"
    {
    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.
    // 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 0.1;

    // 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 60;

    // 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
    // Note: changed(corrected) w.r.t 16x! 90 degrees corresponds to 130 in 16x.
    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 3.5;

    //- 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-30;

    //- 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

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


// ************************************************************************* //
I have tried different refinement levels but none of them has worked. At first I had refinement zone as MRFSource as well, but somehow it started to didn't work. I don't remember very well what I changed at that point, but I was trying to create patches and that's why I changed blockMeshDict. That wasn't a big change but I remember very well I changed the orientation of the vertices. Apart from that I don't remember very well, because I wasing paying attention and it was going fine. The best for the wind turbine is quit bad right now, but I didn't do anything for it, I mean you can ignore the snapping quality.

The problem is if I remove the refinement zone or move it to the middle of the domain, it works, at least for some refinement levels, but I need in in the middle. I am completely stacked, I have googled it but I couldn't find much. Any help would be appreciated.

Cheers,
Attached Files
File Type: gz blockmesh-snapphexmeshDict.tar.gz (4.6 KB, 3 views)

Last edited by clktp; August 26, 2016 at 10:42.
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Old   September 14, 2016, 08:33
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Dear Taygun Gungor,

the error that you get is based on the fact, that sHM only can refine cells if they have 8 point (like cubes or any kind of distorted hexaeder). The fact that you have a wedged mesh based on blockMesh, result in non-hexaeder cells. This cells occur/created at the centerline, so there is no way to refine them. Even your mesh is not a nice one (so many cells, compressed closed to the centerline). In any case, if you are using sHM you should always use a pure cube background mesh. Of course you are able to use some distorted guys but the best result is to have cubes. If you are searching for snappyHexMesh tutorials, you should check out the wiki/and/or my website.

Good luck.
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Old   September 14, 2016, 11:08
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Well, that was quite informative. Thanks a lot. I am going to select a different refinement zone which doesn't include the non-hex cells. I guess that will work. Cheers
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