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Old   January 6, 2013, 13:04
Default Confused About SnappyHexMesh Error (solved)
  #1
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Tom
Join Date: Nov 2011
Location: Atlanta, Ga
Posts: 21
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Irish09 is on a distinguished road
Hello Friends,

I have been working with SHM lately to make a mesh of a diesel injector have become confused about an error I receive under certain conditions.

The error I receive is:

Code:
/home/tfurlong/OpenFOAM/OpenFOAM-2.1.x/bin/tools/RunFunctions: line 37: 32254 Aborted                 $APP_RUN $* > log.$APP_NAME 2>&1
First as an illustration, this is an example of a slice of the mesh I am creating (from a working case):
injector.jpg

Created utilizing a SHMdict:
Code:
/*--------------------------------*- C++ -*----------------------------------*\
| =========                 |                                                 |
| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
|  \\    /   O peration     | Version:  2.0.0                                 |
|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
|    \\/     M anipulation  |                                                 |
\*---------------------------------------------------------------------------*/
FoamFile
{
    version     2.1;
    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
{
    assembly.stl
    {
        type triSurfaceMesh;
        regions
        {
          inlet
          {
            name inlet;
          }
          needle
          {
            name needle;
          }
          orifice
          {
            name orifice;
          }
          outlet
          {
            name outlet;
          }
          wall
          {
            name wall;
          }
        }
    }

    courseregion
    {
      type searchableBox;
      min (-0.5 -0.45 -0.1);
      max (0.4 0.43 1.85);
    }

};

// 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 1000000;

    // 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 10000000;

    // 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 20;

    // 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 "SprayA_210675_meanDiaZ_inlet.eMesh";
            level 2;
        }
        {
            file "SprayA_210675_meanDiaZ_outlet.eMesh";
            level 2;
        }
        {
            file "SprayA_210675_meanDiaZ_wall.eMesh";
            level 2;
        }
        {
            file "SprayA_210675_meanDiaZ_needle.eMesh";
            level 2;
        }
        {
            file "SprayA_210675_meanDiaZ_orifice.eMesh";
            level 2;
        }
    );



    // 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
    {
      assembly.stl
      {
        level (1 1);
        regions
        {
          inlet
          {
            // Surface-wise min and max refinement level
            level (4 4);
          }
         needle
         {
            // Surface-wise min and max refinement level
            level (4 4);
         }
         orifice
         {
            // Surface-wise min and max refinement level
            level (4 4);
         }
         outlet
         {
            // Surface-wise min and max refinement level
            level (4 4);
         }
         wall
         {
            // Surface-wise min and max refinement level
            level (4 4);
         }
       }
     }
    }

    // Resolve sharp angles
    resolveFeatureAngle 180;


    // 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
    {
      courseregion
       {
          mode inside;
          levels ((1e15 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 (0.071278423 0.000093273 1.302938462);


    // 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 10;

    //- Relative distance for points to be attracted by surface feature point
    //  or edge. True distance is this factor times local
    //  maximum edge length.
    tolerance 1.0;

    //- Number of mesh displacement relaxation iterations.
    nSolveIter 10;

    //- Maximum number of snapping relaxation iterations. Should stop
    //  before upon reaching a correct mesh.
    nRelaxIter 10;

    //- Highly experimental and wip: number of feature edge snapping
    //  iterations. Leave out altogether to disable.
    //  Do not use here since mesh resolution too low and baffles present
    nFeatureSnapIter 10;
}



// 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
    {
        "orifice_*"
        {
           nSurfaceLayers 3;
        }

    }

    // Expansion factor for layer mesh
    expansionRatio 2.0;

    //- 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.
    //  is the thickness of the layer furthest away from the wall.
    //  See relativeSizes parameter.
    finalLayerThickness 5.0;

    //- 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 0.5;

    //- 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
    //  make straight angle.
    featureAngle 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;

    // 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 3.5;
    maxInternalSkewness 2.5;

    //- 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-30;

    //- 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 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 0.02;

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

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

    //- 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;
}


// Advanced

// Flags for optional output
// 0 : only write final meshes
// 1 : write intermediate meshes
// 2 : write volScalarField with cellLevel for postprocessing
// 4 : write current intersections as .obj files
debug 1;


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


// ************************************************************************* //
The SHMdict works just fine as I have it, but I have been attempting to increase the number of cells of the mesh overall and in doing so I ran into the above stated error. The error seems to appear when the initial blockmesh is refined beyond a critical point creating an initial mesh that has relatively small cells initially.

From what I understand of the error, it is being caused by the STL file within the blockmesh region not allowing the local mesh to snap to it. The cases that run into this error refine the entire blockmesh region to the specified level as if the supplied STL file were not a closed region. This is where my confusion comes in as I have not been able to reconcile why refining the initial mesh would cause the snapping to not occur.

Before running into this error I had been under the impression that when I am creating the initial blockmesh that it was most efficient to start with a cell size equivalent to the maximum cell size you desired in order to limit the amount of refinement necessary during SHM. My real question comes down to this, should I be trying to either:

1) Create a very fine blockmesh initially to reduce SHM refinement, which leads to this error.

or

2) Create a course blockmesh initially, increasing SHM refinement and then stipulating a refinementregion inside the entire STL flile via (which is what seems to be working):
Code:
    refinementRegions
    {
      courseregion
       {
          mode inside;
          levels ((1e15 3));
       }
    }
As an additional note, and further confusing note, is that based on my forum searching before creating this post the only other place I can find this error referenced is:

motorbike tutorial error in snappy hex

Which was apparently solved by performing a fresh install of OpenFOAM on their machine.

Any thoughts on this are appreciated. Thanks in advance.

Last edited by Irish09; January 7, 2013 at 10:56. Reason: Changed title to reflect solution
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Old   January 7, 2013, 10:55
Default Solution
  #2
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Tom
Join Date: Nov 2011
Location: Atlanta, Ga
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Irish09 is on a distinguished road
The answer to this problem was much simpler than I had imagined in that my machine was just running out of memory and couldn't handle the amount of nodes that were being created before removing the excess regions not associated with the region of interest.

I will now just have to adapt the starting blockmesh to be more appropriately dimensioned to start.
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