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[snappyHexMesh] Mesh not updating after increasing refinement

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Old   May 11, 2021, 16:12
Default Mesh not updating after increasing refinement
  #1
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Santi Parera
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Hey there,


I'm using snappyHexMesh in an AWS instance (using the CFDDFC command line interface) and after doing checkMeshs it seems the number of cells keeps to be the same.


As this is a complicated 3D geometry I started with a not so high refinement level and controlled the mesh with maxGlobalCells. The method was, set 2000000 max cells and lower the refinement levels till it does not reach this max level. After that take a close look and see with what specific refinement type I had to go on and do the same.


I reached 6000000 cells and still getting some errors in checkMesh, but all the parameters are getting better. Now I have raised the max to 6500000 and put a little more of refinement, but the results of ALL chechMesh data are EXACTLY the same than the previous.


SnappyHexMesh log informs as the refining has reached the max level, but it has finished the meshing process properly. It also agrees with checkMesh with the statistics.


How can the mesh be the same after increasing the max level and some refinements!!


Thanks.
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Old   May 12, 2021, 06:36
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Jack B
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Hi Kalabagh,
Could you post your checkMesh, snappyHexMeshDict and your geometry to get a better idea of what's going on? Also It would be beneficial to check where these problem cells are by using the foamToVTK command.

If I am not mistaken increasing the the refinement isn't necessarily going to fix all your problems. A bad input geometry or the wrong snappyHexMesh settings can be the issue but its hard to help without seeing the checkMesh output and snappyHexMeshDict.
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Old   May 13, 2021, 15:09
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The zip folder with the geometry and blockMesh exceeds the maximum, so here's the link: https://drive.google.com/file/d/1wm6...ew?usp=sharing

This is checkMesh for the 3rt mesh:

Code:
Build  : 8-340defec456f
Exec   : checkMesh -allGeometry -allTopology -writeSets vtk
Date   : May 05 2021
Time   : 18:50:01
Host   : "ip-172-31-27-198"
PID    : 8442
I/O    : uncollated
Case   : /home/ubuntu/OXIRIS_REV
nProcs : 1
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster (fileModificationSkew 10)
allowSystemOperations : Allowing user-supplied system call operations

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time

--> FOAM Warning : 
    From function static Foam::instantList Foam::timeSelector::select0(Foam::Time&, const Foam::argList&)
    in file db/Time/timeSelector.C at line 269
    No time specified or available, selecting 'constant'
Create polyMesh for time = constant

Enabling all (cell, face, edge, point) topology checks.

Enabling all geometry checks.

Reconstructing and writing vtk representation of all faceSets and cellSets.

Time = constant

Mesh stats
    points:           6515840
    faces:            16161800
    internal faces:   14760764
    cells:            4860137
    faces per cell:   6.36249
    boundary patches: 4
    point zones:      0
    face zones:       1
    cell zones:       3

Overall number of cells of each type:
    hexahedra:     3842957
    prisms:        194516
    wedges:        0
    pyramids:      0
    tet wedges:    2065
    tetrahedra:    0
    polyhedra:     820599
    Breakdown of polyhedra by number of faces:
        faces   number of cells
            4   48696
            5   60452
            6   200339
            7   3226
            8   1273
            9   354803
           10   801
           11   764
           12   109374
           13   121
           14   397
           15   34452
           16   16
           17   118
           18   5757
           21   10

Checking topology...
    Boundary definition OK.
    Cell to face addressing OK.
    Point usage OK.
    Upper triangular ordering OK.
    Face vertices OK.
    Topological cell zip-up check OK.
  <<Number of duplicate (not baffle) faces found: 7. This might indicate a problem.
  <<Number of faces with non-consecutive shared points: 8. This might indicate a problem.
  <<Writing 23 faces with non-standard edge connectivity to set edgeFaces
  <<Writing 4 cells with zero or one non-boundary face to set oneInternalFaceCells
  <<Writing 23 cells with two non-boundary faces to set twoInternalFacesCells
   *Number of regions: 2
    The mesh has multiple regions which are not connected by any face.
  <<Writing region information to "constant/cellToRegion"
  <<Writing region 0 (fully disconnected) with 4566597 cells to cellSet region0
  <<Writing region 1 (fully disconnected) with 293540 cells to cellSet region1

Checking patch topology for multiply connected surfaces...
                   Patch    Faces   Points                  Surface topology Bounding box
                 TURBINA    64402    69427      ok (closed singly connected) (-0.450157 -0.2275 -0.600122) (0.450157 4.1725 0.600122)
                 REACTOR  1230010  1305069      ok (closed singly connected) (-0.964995 -0.9236 -0.963344) (0.959343 4.22713 0.963345)
                   ROTOR    53555    57797      ok (closed singly connected) (-0.700728 -0.240026 -0.699433) (0.695518 4.18647 0.699128)
             ROTOR_slave    53069    57406      ok (closed singly connected) (-0.700003 -0.240562 -0.698775) (0.695267 4.18645 0.699006)

Checking geometry...
    Overall domain bounding box (-0.964995 -0.9236 -0.963344) (0.959343 4.22713 0.963345)
    Mesh has 3 geometric (non-empty/wedge) directions (1 1 1)
    Mesh has 3 solution (non-empty) directions (1 1 1)
    Boundary openness (-4.84183e-16 -4.5411e-17 1.20272e-15) OK.
    Max cell openness = 4.18834e-16 OK.
    Max aspect ratio = 50.8108 OK.
    Minimum face area = 2.02074e-08. Maximum face area = 0.00893745.  Face area magnitudes OK.
    Min volume = 4.33648e-09. Max volume = 0.000565624.  Total volume = 12.8158.  Cell volumes OK.
    Mesh non-orthogonality Max: 64.999 average: 15.7927
    Non-orthogonality check OK.
    Face pyramids OK.
 ***Max skewness = 7.83481, 133 highly skew faces detected which may impair the quality of the results
  <<Writing 133 skew faces to set skewFaces
    Coupled point location match (average 0) OK.
 ***Error in face tets: 2562 faces with low quality or negative volume decomposition tets.
  <<Writing 2379 faces with low quality or negative volume decomposition tets to set lowQualityTetFaces
    Min/max edge length = 8.09615e-06 0.136443 OK.
  <<Writing 4 near (closer than 5.82625e-06 apart) points to set nearPoints
   *There are 33202 faces with concave angles between consecutive edges. Max concave angle = 79.9951 degrees.
  <<Writing 33202 faces with concave angles to set concaveFaces
    Face flatness (1 = flat, 0 = butterfly) : min = 0.0529411  average = 0.999035
   *There are 938 faces with ratio between projected and actual area < 0.8
    Minimum ratio (minimum flatness, maximum warpage) = 0.0529411
  <<Writing 938 warped faces to set warpedFaces
    Cell determinant (wellposedness) : minimum: 0 average: 12.3539
 ***Cells with small determinant (< 0.001) found, number of cells: 104
  <<Writing 104 under-determined cells to set underdeterminedCells
 ***Concave cells (using face planes) found, number of cells: 358423
  <<Writing 358423 concave cells to set concaveCells
    Face interpolation weight : minimum: 0.0500341 average: 0.455345
    Face interpolation weight check OK.
    Face volume ratio : minimum: 0.0100194 average: 0.771984
    Face volume ratio check OK.

Failed 4 mesh checks.

End
And this is checkMesh for the 4th mesh:


Code:
/*---------------------------------------------------------------------------*\
  =========                 |
  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
   \\    /   O peration     | Website:  https://openfoam.org
    \\  /    A nd           | Version:  8
     \\/     M anipulation  |
\*---------------------------------------------------------------------------*/
Build  : 8-340defec456f
Exec   : checkMesh -allGeometry -allTopology -writeSets vtk
Date   : May 11 2021
Time   : 18:53:51
Host   : "ip-172-31-27-198"
PID    : 1175931
I/O    : uncollated
Case   : /home/ubuntu/OXIRIS_REV
nProcs : 1
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster (fileModificationSkew 10)
allowSystemOperations : Allowing user-supplied system call operations

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time

--> FOAM Warning : 
    From function static Foam::instantList Foam::timeSelector::select0(Foam::Time&, const Foam::argList&)
    in file db/Time/timeSelector.C at line 269
    No time specified or available, selecting 'constant'
Create polyMesh for time = constant

Enabling all (cell, face, edge, point) topology checks.

Enabling all geometry checks.

Reconstructing and writing vtk representation of all faceSets and cellSets.

Time = constant

Mesh stats
    points:           6515840
    faces:            16161800
    internal faces:   14760764
    cells:            4860137
    faces per cell:   6.36249
    boundary patches: 4
    point zones:      0
    face zones:       1
    cell zones:       3

Overall number of cells of each type:
    hexahedra:     3842957
    prisms:        194516
    wedges:        0
    pyramids:      0
    tet wedges:    2065
    tetrahedra:    0
    polyhedra:     820599
    Breakdown of polyhedra by number of faces:
        faces   number of cells
            4   48696
            5   60452
            6   200339
            7   3226
            8   1273
            9   354803
           10   801
           11   764
           12   109374
           13   121
           14   397
           15   34452
           16   16
           17   118
           18   5757
           21   10

Checking topology...
    Boundary definition OK.
    Cell to face addressing OK.
    Point usage OK.
    Upper triangular ordering OK.
    Face vertices OK.
    Topological cell zip-up check OK.
  <<Number of duplicate (not baffle) faces found: 7. This might indicate a problem.
  <<Number of faces with non-consecutive shared points: 8. This might indicate a problem.
  <<Writing 23 faces with non-standard edge connectivity to set edgeFaces
  <<Writing 4 cells with zero or one non-boundary face to set oneInternalFaceCells
  <<Writing 23 cells with two non-boundary faces to set twoInternalFacesCells
   *Number of regions: 2
    The mesh has multiple regions which are not connected by any face.
  <<Writing region information to "constant/cellToRegion"
  <<Writing region 0 (fully disconnected) with 4566597 cells to cellSet region0
  <<Writing region 1 (fully disconnected) with 293540 cells to cellSet region1

Checking patch topology for multiply connected surfaces...
                   Patch    Faces   Points                  Surface topology Bounding box
                 TURBINA    64402    69427      ok (closed singly connected) (-0.450157 -0.2275 -0.600122) (0.450157 4.1725 0.600122)
                 REACTOR  1230010  1305069      ok (closed singly connected) (-0.964995 -0.9236 -0.963344) (0.959343 4.22713 0.963345)
                   ROTOR    53555    57797      ok (closed singly connected) (-0.700728 -0.240026 -0.699433) (0.695518 4.18647 0.699128)
             ROTOR_slave    53069    57406      ok (closed singly connected) (-0.700003 -0.240562 -0.698775) (0.695267 4.18645 0.699006)

Checking geometry...
    Overall domain bounding box (-0.964995 -0.9236 -0.963344) (0.959343 4.22713 0.963345)
    Mesh has 3 geometric (non-empty/wedge) directions (1 1 1)
    Mesh has 3 solution (non-empty) directions (1 1 1)
    Boundary openness (-4.84183e-16 -4.5411e-17 1.20272e-15) OK.
    Max cell openness = 4.18834e-16 OK.
    Max aspect ratio = 50.8108 OK.
    Minimum face area = 2.02074e-08. Maximum face area = 0.00893745.  Face area magnitudes OK.
    Min volume = 4.33648e-09. Max volume = 0.000565624.  Total volume = 12.8158.  Cell volumes OK.
    Mesh non-orthogonality Max: 64.999 average: 15.7927
    Non-orthogonality check OK.
    Face pyramids OK.
 ***Max skewness = 7.83481, 133 highly skew faces detected which may impair the quality of the results
  <<Writing 133 skew faces to set skewFaces
    Coupled point location match (average 0) OK.
 ***Error in face tets: 2562 faces with low quality or negative volume decomposition tets.
  <<Writing 2379 faces with low quality or negative volume decomposition tets to set lowQualityTetFaces
    Min/max edge length = 8.09615e-06 0.136443 OK.
  <<Writing 4 near (closer than 5.82625e-06 apart) points to set nearPoints
   *There are 33202 faces with concave angles between consecutive edges. Max concave angle = 79.9951 degrees.
  <<Writing 33202 faces with concave angles to set concaveFaces
    Face flatness (1 = flat, 0 = butterfly) : min = 0.0529411  average = 0.999035
   *There are 938 faces with ratio between projected and actual area < 0.8
    Minimum ratio (minimum flatness, maximum warpage) = 0.0529411
  <<Writing 938 warped faces to set warpedFaces
    Cell determinant (wellposedness) : minimum: 0 average: 12.3539
 ***Cells with small determinant (< 0.001) found, number of cells: 104
  <<Writing 104 under-determined cells to set underdeterminedCells
 ***Concave cells (using face planes) found, number of cells: 358423
  <<Writing 358423 concave cells to set concaveCells
    Face interpolation weight : minimum: 0.0500341 average: 0.455345
    Face interpolation weight check OK.
    Face volume ratio : minimum: 0.0100194 average: 0.771984
    Face volume ratio check OK.

Failed 4 mesh checks.

End
This is snappyHexMeshDict (the only difference between meshes is the maxGlobalCells):
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Old   May 13, 2021, 15:33
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Also, here is the last snappyHexMesh log: https://drive.google.com/file/d/1wun...ew?usp=sharing


I've have been doing exactly what you say. With the vtk format I tried to search where the different wrong cells were and think what kind of refinement should be done.
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Old   May 13, 2021, 15:37
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Sorry,


The snnapyHexMeshDict:


Code:
/*--------------------------------*- C++ -*----------------------------------*\
| =========                 |                                                 |
| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
|  \\    /   O peration     | Version:  5                                     |
|   \\  /    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
{
    TURBINA
    {
        type        triSurfaceMesh;
        file        "TURBINA_SCALED.stl";
    }

    REACTOR
    {
        type        triSurfaceMesh;
        file        "REACTOR_SCALED.stl";
    }

    ROTOR
    {
        type        triSurfaceMesh;
        file        "ROTOR_SCALED.stl";
    }
};



// 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 6500000;//6000000;//5000000;//4000000;//3500000;//3000000;

    // 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 10;

    // 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 2;



    // 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        "TURBINA_SCALED.eMesh";
            level       4;//5;
        }
        {
            file        "REACTOR_SCALED.eMesh";
            level       3;//4;
        }
        {
            file        "ROTOR_SCALED.eMesh";
            level       0;//1;
    }
    );



    // 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
    {
        TURBINA
        {
            level       (3 3);//(3 4);//(2 3);
        }
        
    REACTOR
        {
            level       (3 4);//(2 3);
        }
        
    ROTOR
        {
            level       (1 2);//(1 1);

            faceType    boundary;
            cellZone    ROTOR;
            faceZone    ROTOR;
            cellZoneInside  inside;
        }
    }

    // Resolve sharp angles
    resolveFeatureAngle 25;//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
    {
        REACTOR
        {
            mode        inside;
            levels      ((0 0));
        }
        ROTOR
        {
            mode        inside;
            levels      ((0 1));
        }
    }


    // 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 (0.00 -0.50 0.00);


    // 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 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; // 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;

    // Feature snapping

        // Number of feature edge snapping iterations.
        // Leave out altogether to disable.
        nFeatureSnapIter 10;

        // Detect (geometric only) features by sampling the surface
        // (default=false).
        implicitFeatureSnap true;

        // Use castellatedMeshControls::features (default = true)
        explicitFeatureSnap false;

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



// 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
    {
    }

    // 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.
    // Relative to undistorted size of cell outside layer.
    // See relativeSizes parameter.
    finalLayerThickness 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 0.1;

    // 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 3;

    // 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 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 50;
}



// 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. This has to be a positive number for tracking
    //  to work. Set to very negative number (e.g. -1E30) to
    //  disable.
    //     <0 = inside out tet,
    //      0 = flat tet
    //      1 = regular tet
    minTetQuality -1; // 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 0.01;

    //- 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;


    // 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;
    }
}



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


// ************************************************************************* //
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Old   May 18, 2021, 13:30
Default
  #6
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Santi Parera
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Location: BARCELONA
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Hey Jack,

I have posted the information you required. Have you been able to take a look?

Thanks.
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