CFD Online Discussion Forums - [snappyHexMesh] snappyHexMesh does not remove internal cells

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snappyHexMesh does not remove internal cells

Hi everyone. I would really appreciate your help.
I use snappyHexMesh to create a grid around a pile. The pile is in stl format. But when I apply castellatedMesh it does not remove the cells inside. The geometry doesn't have any holes and I have execute the checkmesh, it seems eveything is OK.

Here is my snappyHexMeshDict:

Quote:

/*--------------------------------*- C++ -*----------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 4.1 |
| \\ / 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 true;

// 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
{
big.stl
{
type triSurfaceMesh;
name big;

refinementBox
{
type searchableBox;
min (-0.1 -0.1 0);
max (0.2 0.1 0.09);
}
}
};

// 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 1;

// 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 "big.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
{
big.stl
{
// Surface-wise min and max refinement level
level (5 6);

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

// 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 (-0.19001 0 0.002);

// 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;

//- 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
{
"(lower|big).*"
{
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.
// 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;

// 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 20;
}

// 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
);

// 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 0;

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

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

Attachment 56512

This is the results of surfaceCheck command:

Quote:

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Reading surface from "big.stl" ...

Statistics:
Triangles : 382
Vertices : 193
Bounding Box : (-0.028575 -0.0285426 0) (0.028575 0.0285426 0.07715)

Region Size
------ ----
nopiece 382

Surface has no illegal triangles.

Triangle quality (equilateral=1, collapsed=0):
0 .. 0.05 : 0.115183
0.05 .. 0.1 : 0.0628272
0.1 .. 0.15 : 0.253927
0.15 .. 0.2 : 0.0314136
0.2 .. 0.25 : 0.384817
0.25 .. 0.3 : 0.0235602
0.3 .. 0.35 : 0.0366492
0.35 .. 0.4 : 0.0287958
0.4 .. 0.45 : 0.0026178
0.45 .. 0.5 : 0.0157068
0.5 .. 0.55 : 0
0.55 .. 0.6 : 0.0104712
0.6 .. 0.65 : 0.0078534
0.65 .. 0.7 : 0.0078534
0.7 .. 0.75 : 0
0.75 .. 0.8 : 0.0026178
0.8 .. 0.85 : 0.0026178
0.85 .. 0.9 : 0.0052356
0.9 .. 0.95 : 0.0078534
0.95 .. 1 : 0

min 1.34849e-06 for triangle 86
max 0.943943 for triangle 18

Edges:
min 0.000247049 for edge 48 points (0.0163586 0.0231575 0.02)(0.0165751 0.0232765 0.02)
max 0.0574076 for edge 282 points (0.0224615 -0.0176639 0.02)(0.0187126 -0.0215956 0.07715)

Checking for points less than 1e-6 of bounding box ((0.05715 0.0570852 0.07715) metre) apart.
Found 0 nearby points.

Surface is closed. All edges connected to two faces.

Number of unconnected parts : 1

Number of zones (connected area with consistent normal) : 1

End

1) Is your stl geometry fully closed?

2) Is the locationInMesh coordinate inside the domain but out of the box?

3) Are you viewing the latest time step in paraview?

Sent from my LG-H818 using CFD Online Forum mobile app

Thank you sooo much, I just made a silly mistake. The refinementSurfaces should be "big" but not "big.stl".

Quote:

Originally Posted by hokhay (Post 652255)

Thx a lot！I've fixed it.

I would like to also thank the contributors to this entry. I had a similar issue and came across the following techniques to resolve it:

1- Always make sure of the quality of the surface before running snappyHexMesh. Under the triSurface directory, run:

surfaceCheck object.stl

This should confirm the following:

a: surface must be close
b: all edges must be connected to two faces
c: number of unconnected parts = 1
d: number of zones = 1

2- In snappyHexMeshDict and under refinementSurfaces, you must have the name of the surface e.g. object, NOT the filename of the surface object.stl.

3- Make sure you use locationInMesh with a coordinate that is NOT on a face or edge even after refinement, but always inside a cell.

Hello Amir,

Thank you for your valuable addition.
Is there a way before meshing to make sure that locationInMeeesh is within the cell rather than on face or on the edge of the cell.

Regards

SnappyHexMesh does not remove cells

Hello everyone,

I have the same problem. However, I multiple stl files. They are not closed individually but all of them together closes all the boundaries. I need your help.

Hello Jalil,

Little information about your case and problem would be beneficial to give some suggestions. In general, if overall body is closed, then there should not be any problem.
Open your all stl files in paraview and check again if they are water tight.

Regards

Quote:

Originally Posted by Jalil786 (Post 726986)

Hello everyone,

I have the same problem. However, I multiple stl files. They are not closed individually but all of them together closes all the boundaries. I need your help.

I have the same problem. I have two geometries both withmultiple stl files, non of stl files are "closed" when I run surfaceCheck. when I run snappyHexMesh, one gives good mesh with correctly snapped area the other one no. The locationInMesh is correct.
I dont know how I can check if the whole geometry is "water tight" or not, should I do that visually or there is a way to do it properly?

Quote:

Originally Posted by Jalil786 (Post 726986)

Hello everyone,

I have the same problem. However, I multiple stl files. They are not closed individually but all of them together closes all the boundaries. I need your help.

hello jalil,
this is not a problem,
you should do the following:
create a folder that contains only your muliple stls (no other stls files at least) I am assuming they a re assci stls (and not binary)
1. you open terminal $ cat *.stl >> model.stl (this will create a only stl that if your surface meshes are correct, this should give a water tight mesh you can check it with surfaceChek command.)
2. you use a region stl configuration in snappy hex inside the geometry dict. example bellow.
3. one really important thing to take in accound is that you should give a refiment level, even if it is (0 0) to each region in castellated if you dont do this snappy will have problems.

Code:

/*--------------------------------*- C++ -*----------------------------------*\

| =========                 |                                                 |

| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |

|  \\    /   O peration     | Version:  v2012                                 |

|   \\  /    A nd           | Website:  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

{

    model.stl // name of the file in the constant/triSurface/

    {

        type            triSurfaceMesh;

                name InnerCylinder; // name that it will be called thought the simulation (it is also used in the castellatedMeshDict)

        regions //if the stl is divided in region the regions can be used to create patchs

                {

                        regionSTL_i //this is the name of the different regions in the stl, if the workflow will be with stl with regions create a patch for each region, do not leave

                                                // a regionSTL without a name. if thats the case, snappy will create a patch named nameOfModel_regionSTL_i.

                                {

                                        name patchNameOfRegion_i; // this is the name of the patch that snappy will create for the regionSTL_i (the type of patch/boundary can be assigned in the castellatedMeshDict)

                                }

                        Inlet

                                {

                                        name Inlet;

                                }

                        Outlet

                                {

                                        name Outlet;

                                }

                        Walls

                                {

                                        name Walls;

                                }

                        sym_1

                                {

                                        name symm_1;

                                }

                        sym_2

                                {

                                        name symm_2;

                                }

                }

    }

};





// 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 2000000000;



    // 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 200000000;



    // 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 5;



    // 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 1;



    // 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 "model.extendedFeatureEdgeMesh"; //this should be created using the surfaceFeatureExtract application (combined with system/surfaceFeatureExtractDict)

            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

    {



                InnerCylinder //here we use the name designated to the stl in the geometryDict section

                {

                        level (1 1); // This is the min and maximum refiment of the background mesh that intersect the geometry at the boundaries of the stl the minimum refiment

                                                 // is the refiment over a surface (boundary of the stl) and the maximum is the refiment over a feature (corner/wire of the stl)

                        regions

                        {

                                regionSTL_i // Here we need to use the regionSTL_i name, and not the name assignated in the geometryDict section!

                                {

                                        level ( 1 2 ); // Same as before the min and max refiment but only over this boundary, so in this way we can refine over a boundary if necessary

                                        patchInfo

                                        {

                                                type        patch; // Here we define the boundary type patch, wall, etc, be aware snappy does not accept contrainst type boundaries

                                                                                   // so, no: symmetry, symmetryPlane, cyclic, clyclicAMI, etc. For these type of boundaries or they are carried out from the backgroundMesh (from the blockMeshDict)

                                                                                   // or it should be created after the snappyHexMesh with createPatch application (combined with system/createPatchDict)

                                        }

                                }        

                                Inlet

                                {

                                        level ( 1 2 );

                                        patchInfo

                                        {

                                                type        patch;

                                        }

                                }                        

                                Outlet

                                {

                                        level ( 1 2 );

                                        patchInfo

                                        {

                                                type        patch;

                                        }

                                }

                                sym_1

                                {

                                        level ( 1 2 );

                                        patchInfo

                                        {

                                                type        patch;

                                        }

                                }

                                sym_2

                                {

                                        level ( 1 2 );

                                        patchInfo

                                        {

                                                type        patch;

                                        }

                                }

                                Walls

                                {

                                        level ( 1 2 );

                                        patchInfo

                                        {

                                                type        wall;

                                        }

                                }

                        }

                }

    }

in this way you will have a boundary for each stl.
best regards.

Quote:

Originally Posted by mhsadafi (Post 804976)

surfaceCheck gives the information around 8 th last line:
surfaceCheck model.stl | tail -9 | head -1 should give you as output only that line, but in any case you will see this in surfaceCheck.
as I menioned in my previous post, when using multiple stls you should fuse it into one and then use surfaceCheck to see it is waterthight. (2 separate stls can be not waterthight but their fussion can be)

best regards.

Quote:

Originally Posted by otaolafr (Post 805197)

Thank you @otaolafr, I execute surfaceCheck on a single stl file which was the merge of all surfaces and the result was: Surface is closed. All edges connected to two faces.
If I am not mistaken, for snappyHexMesh and simualation, I need to have separated stl file for each boundary condition. When I give the separated stl files, snappyHexMesh does not snap the outer part (I am interested in the inner part). I am sure about the locationInMesh. Do you have any advice?

Quote:

Originally Posted by mhsadafi (Post 805218)

hello,
you dont need separate stls files, you need an stl with regions (one file). following the step 1. in https://www.cfd-online.com/Forums/op...tml#post805195 will give you exactly that, an stl with a region for each stl that you used to create them.
imagine you have 1.stl, 2.stl & 3.stl , you use cat *.stl >>model.stl you will have 4 stls in total the three originals that you will not use, and model.stl that will be separated in regions inside of the file (each region will be each of original stls). you should use the 4th stl (model.stl) for snappy, have a look at the geometryDict inside the example in snappy that I post in the post I mentionned previously. here you indicate one file, with regions inside of it.
Franco

Quote:

Originally Posted by otaolafr (Post 805223)

Great! it works now, thank you.
just one more question, to add boundary layers, I modified the dictionary as below, but it didnt create the boundary layers.

addLayersControls
{

relativeSizes true;
layers
{
InnerCylinder
{
regions
{
"wall1"
{
nSurfaceLayers 3;
}
}
}
}

I have also tried this, but no luck!

addLayersControls
{

relativeSizes true;
layers
{
"wall1"
{
nSurfaceLayers 3;
}

}

Quote:

Originally Posted by mhsadafi (Post 805228)

I can not help you without the rest of the snappyHexMeshDict. in any case, I will answer taking the example the geometry definition in the snappyHexMeshDict that I menitonned previously.
the layers you have to define them like this:

Code:

    layers

    {



                patchNameOfRegion_i // Here in difference with the castellatedMeshDict section, we should use the patchNameOfRegion_i! and not the regionSTL_i!

                {

                            nSurfaceLayers 3; // here we define the number of layers over the patchNameOfRegion_i

        }



                

    }

have a look at this ppt: http://www.wolfdynamics.com/wiki/meshing_OF_SHM.pdf
also take in accound that if snappy does not achive the 100% of the meshQuality, it will not create layers.
so in my opinion from the little info, or you defined wrong in the layer dictionary or you are not achiving the quality so snappy is able to add the layer

ps please use CODE mode when posting part of dictionaries so it is easier to read.

Quote:

Originally Posted by otaolafr (Post 805232)

Code:

    layers

    {



                patchNameOfRegion_i // Here in difference with the castellatedMeshDict section, we should use the patchNameOfRegion_i! and not the regionSTL_i!

                {

                            nSurfaceLayers 3; // here we define the number of layers over the patchNameOfRegion_i

        }



                

    }

Thank you very much. It was indeed becasue of low quality of mesh. After refining, I got the boundary layers. The pdf is also very useful.