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[snappyHexMesh] Problem with snappyhexMesh: modelling a pore chamber and pore throat model

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Old   May 1, 2015, 14:59
Default Problem with snappyhexMesh: modelling a pore chamber and pore throat model
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Saideep
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hi guys.

I am new to the forum and have a doubt regarding the snappyhexmesh.

I am to model a pore chamber and pore throat model.
I developed a (.stl) file in blender and used it over a hexahedron background mesh to snap out the solid portion. however after running the snappyhexmesh i get a wierd problem that instead of removing the required portion, an other model domain is formed and when i apply surface with edges in paraview, it does not show any meshes.

Attached you can view the pictures of background hexahedron (reduced the opacity to view the pores too) and after running the snappyhexmesh utility.

aftersnappyHexMesh.jpg
porethroat+chamber+backgroundhex.jpg

This is my code for snappyhexMesh
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            false;
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
{
   // Exo5.stl
   chamber_throat.stl
    {
        type triSurfaceMesh;
        name fixedWalls;
    }

    /*refinementBox
    {
        type searchableBox;
        min (-1.0 -0.7 0.0);
        max ( 8.0  0.7 2.5);
    }*/
};



// 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 2000000;

    // 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 3;



    // 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 "motorBike.eMesh";
            level 6;
        }*/
    );



    // 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
    {
        fixedWalls
        {
            // Surface-wise min and max refinement level
            level (0 0);

            // Optional specification of patch type (default is wall). No
            // constraint types (cyclic, symmetry) etc. are allowed.
           /* patchInfo
            {
                type wall;
                inGroups (motorBikeGroup);
            }*/
        }
    }

    // Resolve sharp angles
    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
    {
        /*refinementBox
        {
            mode inside;
            levels ((1E15 4));
        }*/
    }


    // 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 (-0.04 0 0);
locationInMesh (15.62 32.51 .02);

    // 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 2.0;

    //- Number of mesh displacement relaxation iterations.
    nSolveIter 30;

    //- 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 false;

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

        //- Detect points on multiple surfaces (only for explicitFeatureSnap)
        multiRegionFeatureSnap false;
}



// 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
    {
        "(lowerWall|motorBike).*"
        {
            nSurfaceLayers 1;
        }
    }

    // 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.
    // 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.
    // 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 60;

    // At non-patched sides allow mesh to slip if extrusion direction makes
    // angle larger than slipFeatureAngle.
    slipFeatureAngle 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
{
    #include "meshQualityDict"


    // Advanced

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


// Advanced

// Write flags
writeFlags
(
    scalarLevels
    layerSets
    layerFields     // write volScalarField for layer coverage
);


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


// ************************************************************************* //
Any help would be reatly be appreciated friends.
Thanks a lot;
Saideep

Last edited by wyldckat; May 1, 2015 at 19:51. Reason: Added [CODE][/CODE] markers
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Old   May 1, 2015, 19:59
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Quick answer:
  1. The snapping step is disabled:
    Code:
    snap            false;
    therefore, snapping is not done.
  2. Please provide specific details on how you've generated the mesh and what dimensions your geometry has got.
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Old   May 3, 2015, 15:01
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Saideep
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Thanks a lot Bruno for your quick response.

Actually the error was with the locationInMesh. I used blender to export my .stl file and later it was not aligned to the origin and I kept on guessing for a random value and therefore it was not snapping out.

however, as per your answer of snapping switch gave me the same result(no difference tough i turned it on.)

however, I learnt a new thing and this could be of use to any others new, incase you are exporting your files make sure you displace your model to the origin so that you can specify the exact location quite easily rather than guessing which is more pain.
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Old   May 3, 2015, 15:10
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Quick answer/tip:
You don't need to completely guess, if you use in ParaView the source Sphere: menu Sources -> Sphere
That way you can see in 3D where the "location in mesh" point should be placed

But yes, it's best to have your geometry centre or at least near the origin of the referential.
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Old   May 10, 2015, 13:58
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Hi Bruno,
Unrelated to this particular question, but Iam still unclear on the concept of locationinmesh. Could you explain which point it should be?
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Old   May 10, 2015, 15:46
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Quote:
Originally Posted by avd28 View Post
Hi Bruno,
Unrelated to this particular question, but Iam still unclear on the concept of locationinmesh. Could you explain which point it should be?
Quick answer:
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