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Old   January 6, 2011, 05:14
Default underdeterminedCells
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Robert Ong
Join Date: Aug 2010
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Dear All,

I keep encounter the underdeterminedCells problem and really appreciate if you can help me with this.

Here is the checkMesh output at SHM -latestTime folder:

Time = 0.003

Mesh stats
points: 634900
faces: 1536336
internal faces: 1358718
cells: 470885
boundary patches: 9
point zones: 0
face zones: 0
cell zones: 0

Overall number of cells of each type:
hexahedra: 330057
prisms: 32100
wedges: 0
pyramids: 0
tet wedges: 1841
tetrahedra: 18
polyhedra: 106869

Checking topology...
Boundary definition OK.
Point usage OK.
Upper triangular ordering OK.
Face vertices OK.
Number of regions: 1 (OK).

Checking patch topology for multiply connected surfaces ...
Patch Faces Points Surface topology Bounding box
inlet 277 346 ok (non-closed singly connected) (-4.72261 -2.45232 -10.0353) (-4.59171 6.63503 1.74641)
patient_Outlet7 280 469 ok (non-closed singly connected) (-10.1504 -55.2556 -112.911) (-7.43396 -52.0717 -110.325)
patient_Outlet6 96 148 ok (non-closed singly connected) (-68.4308 11.8798 -164.197) (-67.262 13.2621 -162.795)
patient_Outlet5 331 436 ok (non-closed singly connected) (-103.498 1.02312 -130.839) (-100.359 2.27901 -128.027)
patient_Outlet4 22 38 ok (non-closed singly connected) (-103.626 -11.5322 -104.36) (-102.943 -11.0494 -103.605)
patient_Outlet3 174 261 ok (non-closed singly connected) (-75.9318 4.84919 -20.7391) (-74.3726 7.82684 -18.8701)
patient_Outlet2 72 132 ok (non-closed singly connected) (-90.9039 76.1677 -53.2535) (-89.7788 77.6239 -51.9731)
patient_Outlet1 164 223 ok (non-closed singly connected) (-64.8448 129.496 -98.3191) (-61.9272 130.703 -97.6571)
patient_Patient2 176202 214951 multiply connected (shared edge) (-103.626 -64.5097 -166.667) (-4.59171 130.703 5.02298)
<<Writing 4 conflicting points to set nonManifoldPoints

Checking geometry...
Overall domain bounding box (-103.626 -64.5097 -166.667) (-4.59171 130.703 5.02298)
Mesh (non-empty, non-wedge) directions (1 1 1)
Mesh (non-empty) directions (1 1 1)
Boundary openness (-3.86952e-17 1.71227e-16 3.76657e-17) OK.
Max cell openness = 3.13562e-16 OK.
Max aspect ratio = 7.75377 OK.
Minumum face area = 0.00112404. Maximum face area = 7.71469. Face area magnitudes OK.
Min volume = 0.000432306. Max volume = 11.2818. Total volume = 20464.4. Cell volumes OK.
Mesh non-orthogonality Max: 64.8085 average: 14.498
Non-orthogonality check OK.
Face pyramids OK.
Max skewness = 3.78346 OK.
Min/max edge length = 0.0316528 1.5 OK.
*There are 4325 faces with concave angles between consecutive edges. Max concave angle = 78.5315 degrees.
<<Writing 4325 faces with concave angles to set concaveFaces
Face flatness (1 = flat, 0 = butterfly) : average = 0.995389 min = 0.115482
*There are 21 faces with ratio between projected and actual area < 0.8
Minimum ratio (minimum flatness, maximum warpage) = 0.115482
<<Writing 21 warped faces to set warpedFaces
Cell determinant (wellposedness) : minimum: 0 average: 14.9775
***Cells with small determinant found, number of cells: 7
<<Writing 7 under-determined cells to set underdeterminedCells

Failed 1 mesh checks.

End

The SHM setting:
/*--------------------------------*- C++ -*----------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.6 |
| \\ / A nd | Web: http://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
{
patient.stl
{
type triSurfaceMesh;
name patient;
}
};



// Settings for the castellatedMesh generation.
castellatedMeshControls
{

// Refinement parameters
// ~~~~~~~~~~~~~~~~~~~~~

// While refining maximum number of cells per processor. This is basically
// the number of cells that fit on a processor. If you choose this too small
// it will do just more refinement iterations to obtain a similar mesh.
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 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;

// 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 "someLine.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
{
patient
{
// Surface-wise min and max refinement level
level (3 4);
}
}

// 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 (-6 0 0);
}



// 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;
}



// Settings for the layer addition.
addLayersControls
{
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.
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.
nGrow 1;


// Advanced settings

//- When not to extrude surface. 0 is flat surface, 90 is when two faces
// make straight angle.
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
minMedianAxisAngle 130;

// Create buffer region for new layer terminations
nBufferCellsNoExtrude 0;

// Overall max number of layer addition iterations
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 projected area v.s. actual area. Set to -1 to disable.
minFlatness 0.5;

//- Minimum pyramid volume. Is absolute volume of cell pyramid.
// Set to very negative number (e.g. -1E30) to disable.
minVol 1e-13;

//- 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 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;


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

Here is what the underdeterminedCells and mesh in paraview looks like
underdeterminedCells.jpg

mesh.jpg

Thanks for your time and attention.

Kind Regards,
Robert
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Old   January 17, 2011, 14:24
Default
  #2
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bruce
Join Date: May 2009
Location: Germany
Posts: 42
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Hi

Do you add layers? I don't see this in the "addLayersControls"

If you added, It seems you might have bad mesh after layer addition. Have you done checkMesh for snapped mesh ( time = 2 ) ? Do you still have concave, warped faces ? if that is the case try to tight your quality settings , of course that will make approximations to real cad !

na
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Old   January 17, 2011, 22:12
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  #3
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Robert Ong
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Hi Bruce,

Thanks for the reply.

I didn't add any layers.

Below is the checkMesh output:
================================================== ========
Create time

Create polyMesh for time = 0

Time = 0

Mesh stats
points: 357911
faces: 1043700
internal faces: 1014300
cells: 343000
boundary patches: 1
point zones: 0
face zones: 0
cell zones: 0

Overall number of cells of each type:
hexahedra: 343000
prisms: 0
wedges: 0
pyramids: 0
tet wedges: 0
tetrahedra: 0
polyhedra: 0

Checking topology...
Boundary definition OK.
Point usage OK.
Upper triangular ordering OK.
Face vertices OK.
Number of regions: 1 (OK).

Checking patch topology for multiply connected surfaces ...
Patch Faces Points Surface topology
inlet 29400 29402 ok (closed singly connected)

Checking geometry...
Overall domain bounding box (-107 -70 -170) (-4.5 140 10)
Mesh (non-empty, non-wedge) directions (1 1 1)
Mesh (non-empty) directions (1 1 1)
Boundary openness (-1.90981e-16 -1.51374e-17 5.27562e-15) OK.
Max cell openness = 1.20272e-16 OK.
Max aspect ratio = 2.08926 OK.
Minumum face area = 3.69236. Maximum face area = 7.71476. Face area magnitudes OK.
Min volume = 11.0771. Max volume = 11.2943. Total volume = 3.8367e+06. Cell volumes OK.
Mesh non-orthogonality Max: 0.632047 average: 0.299557
Non-orthogonality check OK.
Face pyramids OK.
Max skewness = 0.0197593 OK.

Mesh OK.

--> FOAM Warning :
From function polyMesh::readUpdateState polyMesh::readUpdate()
in file meshes/polyMesh/polyMeshIO.C at line 205
Number of patches has changed. This may have unexpected consequences. Proceed with care.
Time = 0.001

Mesh stats
points: 659397
faces: 1517757
internal faces: 1240017
cells: 430694
boundary patches: 9
point zones: 0
face zones: 0
cell zones: 0

Overall number of cells of each type:
hexahedra: 388746
prisms: 0
wedges: 0
pyramids: 0
tet wedges: 0
tetrahedra: 0
polyhedra: 41948

Checking topology...
Boundary definition OK.
Point usage OK.
Upper triangular ordering OK.
Face vertices OK.
Number of regions: 1 (OK).

Checking patch topology for multiply connected surfaces ...
Patch Faces Points Surface topology
inlet 277 374 ok (non-closed singly connected)
patient_Outlet7 536 623 ok (non-closed singly connected)
patient_Outlet6 159 189 ok (non-closed singly connected)
patient_Outlet5 503 586 ok (non-closed singly connected)
patient_Outlet4 34 50 ok (non-closed singly connected)
patient_Outlet3 283 341 ok (non-closed singly connected)
patient_Outlet2 150 181 ok (non-closed singly connected)
patient_Outlet1 193 237 ok (non-closed singly connected)
patient_Patient2 275605 277293 multiply connected (shared edge)
<<Writing 4 conflicting points to set nonManifoldPoints

Checking geometry...
Overall domain bounding box (-103.565 -64.375 -166.625) (-4.59286 130.625 5.17859)
Mesh (non-empty, non-wedge) directions (1 1 1)
Mesh (non-empty) directions (1 1 1)
Boundary openness (8.42463e-17 -1.9502e-16 -1.76402e-15) OK.
Max cell openness = 2.11325e-16 OK.
Max aspect ratio = 2.0903 OK.
Minumum face area = 0.014352. Maximum face area = 7.71469. Face area magnitudes OK.
Min volume = 0.002691. Max volume = 11.2818. Total volume = 20490.5. Cell volumes OK.
Mesh non-orthogonality Max: 42.6624 average: 11.4072
Non-orthogonality check OK.
Face pyramids OK.
Max skewness = 1.01276 OK.

Mesh OK.

Time = 0.002

Mesh stats
points: 659397
faces: 1517757
internal faces: 1240017
cells: 430694
boundary patches: 9
point zones: 0
face zones: 0
cell zones: 0

Overall number of cells of each type:
hexahedra: 388746
prisms: 0
wedges: 0
pyramids: 0
tet wedges: 0
tetrahedra: 0
polyhedra: 41948

Checking topology...
Boundary definition OK.
Point usage OK.
Upper triangular ordering OK.
Face vertices OK.
Number of regions: 1 (OK).

Checking patch topology for multiply connected surfaces ...
Patch Faces Points Surface topology
inlet 277 374 ok (non-closed singly connected)
patient_Outlet7 526 608 ok (non-closed singly connected)
patient_Outlet6 159 188 ok (non-closed singly connected)
patient_Outlet5 468 545 ok (non-closed singly connected)
patient_Outlet4 28 42 ok (non-closed singly connected)
patient_Outlet3 296 355 ok (non-closed singly connected)
patient_Outlet2 146 172 ok (non-closed singly connected)
patient_Outlet1 200 243 ok (non-closed singly connected)
patient_Patient2 275640 277311 multiply connected (shared edge)
<<Writing 4 conflicting points to set nonManifoldPoints

Checking geometry...
Overall domain bounding box (-103.626 -64.5097 -166.667) (-4.59171 130.703 5.02362)
Mesh (non-empty, non-wedge) directions (1 1 1)
Mesh (non-empty) directions (1 1 1)
Boundary openness (-3.67117e-16 5.83083e-16 4.88723e-16) OK.
Max cell openness = 3.15439e-16 OK.
Max aspect ratio = 7.6818 OK.
Minumum face area = 0.00112404. Maximum face area = 7.71469. Face area magnitudes OK.
Min volume = 0.000523331. Max volume = 11.2818. Total volume = 20478.5. Cell volumes OK.
Mesh non-orthogonality Max: 64.1816 average: 14.1079
Non-orthogonality check OK.
Face pyramids OK.
Max skewness = 3.82228 OK.

Mesh OK.

Time = 0.003

Mesh stats
points: 659382
faces: 1517673
internal faces: 1240017
cells: 430694
boundary patches: 9
point zones: 0
face zones: 0
cell zones: 0

Overall number of cells of each type:
hexahedra: 388682
prisms: 0
wedges: 0
pyramids: 0
tet wedges: 0
tetrahedra: 0
polyhedra: 42012

Checking topology...
Boundary definition OK.
Point usage OK.
Upper triangular ordering OK.
Face vertices OK.
Number of regions: 1 (OK).

Checking patch topology for multiply connected surfaces ...
Patch Faces Points Surface topology
inlet 277 374 ok (non-closed singly connected)
patient_Outlet7 505 605 ok (non-closed singly connected)
patient_Outlet6 154 187 ok (non-closed singly connected)
patient_Outlet5 444 541 ok (non-closed singly connected)
patient_Outlet4 28 42 ok (non-closed singly connected)
patient_Outlet3 281 354 ok (non-closed singly connected)
patient_Outlet2 134 168 ok (non-closed singly connected)
patient_Outlet1 193 241 ok (non-closed singly connected)
patient_Patient2 275640 277311 multiply connected (shared edge)
<<Writing 4 conflicting points to set nonManifoldPoints

Checking geometry...
Overall domain bounding box (-103.626 -64.5097 -166.667) (-4.59171 130.703 5.02362)
Mesh (non-empty, non-wedge) directions (1 1 1)
Mesh (non-empty) directions (1 1 1)
Boundary openness (-3.67117e-16 5.83083e-16 4.88723e-16) OK.
Max cell openness = 3.15439e-16 OK.
Max aspect ratio = 7.6818 OK.
Minumum face area = 0.00112404. Maximum face area = 7.71469. Face area magnitudes OK.
Min volume = 0.000523331. Max volume = 11.2818. Total volume = 20478.5. Cell volumes OK.
Mesh non-orthogonality Max: 64.1816 average: 14.1079
Non-orthogonality check OK.
Face pyramids OK.
Max skewness = 3.82228 OK.

Mesh OK.

End
==================================================

I think I've played around with the qualityControl settings before, but this setting gave me a slightly better checkMesh output.

Thanks for your time and attention.

Kind Regards,
Robert
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