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snappyhexmesh remove blockmesh geometry

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Old   March 19, 2014, 03:41
Default snappyhexmesh remove blockmesh geometry
  #1
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Philipp Reinhold
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Hi there,

i have a small question again. since i'm working just once per week on openfoam and snappyhexmesh, you've got to excuse, that these questions are sometimes a little bit stupid.

here we go:

i have created a geometry via snappyhexmesh, but the geometry or the faces from the blockmesh geometry do not seem to be removed. how do i do that? is this a setting in the snappyhexmeshdict?

Thank you,

PR
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Old   March 19, 2014, 05:39
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Philipp Reinhold
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okay, i think i,ve got the right settings in the snappyhexmeshdict now, but i get a floating point exception now after 2 timesteps.. can anybody help me?
i have to finish this study in a few weeks

Quote:
Code:
Iteration 2
Moving mesh using displacement scaling : min:0.5625  max:0.5625
Checking faces in error :
    non-orthogonality >  65 degrees                        : 0
    faces with face pyramid volume < 1e-13                 : 6
    faces with face-decomposition tet quality < 1e-30      : 0
    faces with concavity >  80 degrees                     : 0
    faces with skewness >   4 (internal) or  20 (boundary) : 0
    faces with interpolation weights (0..1)  <  0.02       : 0
    faces with volume ratio of neighbour cells <  0.01     : 0
    faces with face twist <  0.02                          : 0
    faces on cells with determinant < 0.001                : 0

Iteration 3
Moving mesh using displacement scaling : min:0.421875  max:0.421875
Checking faces in error :
    non-orthogonality >  65 degrees                        : 0
    faces with face pyramid volume < 1e-13                 : 6
    faces with face-decomposition tet quality < 1e-30      : 0
    faces with concavity >  80 degrees                     : 0
    faces with skewness >   4 (internal) or  20 (boundary) : 0
    faces with interpolation weights (0..1)  <  0.02       : 0
    faces with volume ratio of neighbour cells <  0.01     : 0
    faces with face twist <  0.02                          : 0
    faces on cells with determinant < 0.001                : 0

Iteration 4
Moving mesh using displacement scaling : min:0.316406  max:0.316406
Checking faces in error :
    non-orthogonality >  65 degrees                        : 0
    faces with face pyramid volume < 1e-13                 : 6
    faces with face-decomposition tet quality < 1e-30      : 0
    faces with concavity >  80 degrees                     : 0
    faces with skewness >   4 (internal) or  20 (boundary) : 0
    faces with interpolation weights (0..1)  <  0.02       : 0
    faces with volume ratio of neighbour cells <  0.01     : 0
    faces with face twist <  0.02                          : 0
    faces on cells with determinant < 0.001                : 0

Iteration 5
Displacement scaling for error reduction set to 0.
Moving mesh using displacement scaling : min:0.237305  max:0.237305
Checking faces in error :
    non-orthogonality >  65 degrees                        : 0
    faces with face pyramid volume < 1e-13                 : 6
    faces with face-decomposition tet quality < 1e-30      : 0
    faces with concavity >  80 degrees                     : 0
    faces with skewness >   4 (internal) or  20 (boundary) : 0
    faces with interpolation weights (0..1)  <  0.02       : 0
    faces with volume ratio of neighbour cells <  0.01     : 0
    faces with face twist <  0.02                          : 0
    faces on cells with determinant < 0.001                : 0

Iteration 6
Moving mesh using displacement scaling : min:0  max:0
Checking faces in error :
    non-orthogonality >  65 degrees                        : 0
    faces with face pyramid volume < 1e-13                 : 0
    faces with face-decomposition tet quality < 1e-30      : 0
    faces with concavity >  80 degrees                     : 0
    faces with skewness >   4 (internal) or  20 (boundary) : 0
    faces with interpolation weights (0..1)  <  0.02       : 0
    faces with volume ratio of neighbour cells <  0.01     : 0
    faces with face twist <  0.02                          : 0
    faces on cells with determinant < 0.001                : 0
Successfully moved mesh
Moved mesh in = 0 s



Morph iteration 9
-----------------
Calculating patchDisplacement as distance to nearest surface point ...
Wanted displacement : average:0.000209065 min:0.000173982 max:0.000234267
Calculated surface displacement in = 0 s


Overriding displacement on features :
   implicit features    : false
   explicit features    : true
   multi-patch features : false

Stringing feature edges : changed 2 points
Stringing feature edges : changed 0 points
Attraction:
     linear   : max:(4.33681e-19 1.84314e-17 -0.000173982) avg:(5.42101e-20 5.50233e-18 -0.000209065)
     feature  : max:(0 1.47451e-17 0) avg:(-0.000360237 1.55854e-18 -6.80867e-05)
Feature analysis : total points:8 attraction to :
    feature point   : 0
    feature edge    : 4
    nearest surface : 0
    rest            : 4

--> FOAM Warning : Displacement (-0.000540986 -5.52943e-18 -9.83649e-05) at mesh point 0 coord (0.00108197 0.00190512 0.00019673) points through the surrounding patch faces
Smoothing displacement ...
Iteration 0
Iteration 10
Iteration 20
Displacement smoothed in = 0 s


Moving mesh ...

Iteration 0
Moving mesh using displacement scaling : min:1  max:1
Checking faces in error :
    non-orthogonality >  65 degrees                        : 0
    faces with face pyramid volume < 1e-13                 : 6
    faces with face-decomposition tet quality < 1e-30      : 0
    faces with concavity >  80 degrees                     : 0
    faces with skewness >   4 (internal) or  20 (boundary) : 0
    faces with interpolation weights (0..1)  <  0.02       : 0
    faces with volume ratio of neighbour cells <  0.01     : 0
    faces with face twist <  0.02                          : 0
    faces on cells with determinant < 0.001                : 0

Iteration 1
Moving mesh using displacement scaling : min:0.75  max:0.75
Checking faces in error :
    non-orthogonality >  65 degrees                        : 0
    faces with face pyramid volume < 1e-13                 : 6
    faces with face-decomposition tet quality < 1e-30      : 0
    faces with concavity >  80 degrees                     : 0
    faces with skewness >   4 (internal) or  20 (boundary) : 0
    faces with interpolation weights (0..1)  <  0.02       : 0
    faces with volume ratio of neighbour cells <  0.01     : 0
    faces with face twist <  0.02                          : 0
    faces on cells with determinant < 0.001                : 0

Iteration 2
Moving mesh using displacement scaling : min:0.5625  max:0.5625
Checking faces in error :
    non-orthogonality >  65 degrees                        : 0
    faces with face pyramid volume < 1e-13                 : 6
    faces with face-decomposition tet quality < 1e-30      : 0
    faces with concavity >  80 degrees                     : 0
    faces with skewness >   4 (internal) or  20 (boundary) : 0
    faces with interpolation weights (0..1)  <  0.02       : 0
    faces with volume ratio of neighbour cells <  0.01     : 0
    faces with face twist <  0.02                          : 0
    faces on cells with determinant < 0.001                : 0

Iteration 3
Moving mesh using displacement scaling : min:0.421875  max:0.421875
Checking faces in error :
    non-orthogonality >  65 degrees                        : 0
    faces with face pyramid volume < 1e-13                 : 6
    faces with face-decomposition tet quality < 1e-30      : 0
    faces with concavity >  80 degrees                     : 0
    faces with skewness >   4 (internal) or  20 (boundary) : 0
    faces with interpolation weights (0..1)  <  0.02       : 0
    faces with volume ratio of neighbour cells <  0.01     : 0
    faces with face twist <  0.02                          : 0
    faces on cells with determinant < 0.001                : 0

Iteration 4
Moving mesh using displacement scaling : min:0.316406  max:0.316406
Checking faces in error :
    non-orthogonality >  65 degrees                        : 0
    faces with face pyramid volume < 1e-13                 : 6
    faces with face-decomposition tet quality < 1e-30      : 0
    faces with concavity >  80 degrees                     : 0
    faces with skewness >   4 (internal) or  20 (boundary) : 0
    faces with interpolation weights (0..1)  <  0.02       : 0
    faces with volume ratio of neighbour cells <  0.01     : 0
    faces with face twist <  0.02                          : 0
    faces on cells with determinant < 0.001                : 0

Iteration 5
Displacement scaling for error reduction set to 0.
Moving mesh using displacement scaling : min:0.237305  max:0.237305
Checking faces in error :
    non-orthogonality >  65 degrees                        : 0
    faces with face pyramid volume < 1e-13                 : 6
    faces with face-decomposition tet quality < 1e-30      : 0
    faces with concavity >  80 degrees                     : 0
    faces with skewness >   4 (internal) or  20 (boundary) : 0
    faces with interpolation weights (0..1)  <  0.02       : 0
    faces with volume ratio of neighbour cells <  0.01     : 0
    faces with face twist <  0.02                          : 0
    faces on cells with determinant < 0.001                : 0

Iteration 6
Moving mesh using displacement scaling : min:0  max:0
Checking faces in error :
    non-orthogonality >  65 degrees                        : 0
    faces with face pyramid volume < 1e-13                 : 0
    faces with face-decomposition tet quality < 1e-30      : 0
    faces with concavity >  80 degrees                     : 0
    faces with skewness >   4 (internal) or  20 (boundary) : 0
    faces with interpolation weights (0..1)  <  0.02       : 0
    faces with volume ratio of neighbour cells <  0.01     : 0
    faces with face twist <  0.02                          : 0
    faces on cells with determinant < 0.001                : 0
Successfully moved mesh
Moved mesh in = 0 s


Repatching faces according to nearest surface ...
Repatched 0 faces in = 0 s


Edge intersection testing:
    Number of edges             : 6
    Number of edges to retest   : 6
    Number of intersected edges : 0
Merging 0 sets of faces.

No faces merged ...

Merging all points on surface that
- are used by only two boundary faces and
- make an angle with a cosine of more than 0.866025.

No straight edges simplified and no points removed ...
Snapped mesh : cells:1  faces:6  points:8
Cells per refinement level:
    0    0
    1    0
    2    0
    3    0
    4    0
    5    0
    6    1
Writing mesh to time 2
Wrote mesh in = 0 s.
Mesh snapped in = 0.05 s.
Layer thickness specified as final layer and expansion ratio.

Shrinking and layer addition phase
----------------------------------

Using mesh parameters 
{
    maxNonOrtho     65;
    maxBoundarySkewness 20;
    maxInternalSkewness 4;
    maxConcave      80;
    minVol          1e-13;
    minTetQuality   1e-30;
    minArea         -1;
    minTwist        0.02;
    minDeterminant  0.001;
    minFaceWeight   0.02;
    minVolRatio     0.01;
    minTriangleTwist -1;
    nSmoothScale    4;
    errorReduction  0.75;
}



Merging all faces of a cell
---------------------------
    - which are on the same patch
    - which make an angle < 60 degrees
      (cos:0.5)
    - as long as the resulting face doesn't become concave by more than 90 degrees
      (0=straight, 180=fully concave)

Merging 0 sets of faces.

No faces merged ...

Merging all points on surface that
- are used by only two boundary faces and
- make an angle with a cosine of more than 0.5.

No straight edges simplified and no points removed ...

Checking mesh manifoldness ...

Checking initial mesh ...
Checking faces in error :
    non-orthogonality >  65 degrees                        : 0
    faces with face pyramid volume < 1e-13                 : 0
    faces with face-decomposition tet quality < 1e-30      : 0
    faces with concavity >  80 degrees                     : 0
    faces with skewness >   4 (internal) or  20 (boundary) : 0
    faces with interpolation weights (0..1)  <  0.02       : 0
    faces with volume ratio of neighbour cells <  0.01     : 0
    faces with face twist <  0.02                          : 0
    faces on cells with determinant < 0.001                : 0
Detected 0 illegal faces (concave, zero area or negative cell pyramid volume)

Adding in total 0 inter-processor patches to handle extrusion of non-manifold processor boundaries.
Constructing mesh displacer ...

Handling points with inconsistent layer specification ...

Handling non-manifold points ...

Checking patch manifoldness ...
Outside of local patch is multiply connected across edges or points at 0 points.
Set displacement to zero for all 0 non-manifold points

Handling feature edges ...

Handling cells with warped patch faces ...
Set displacement to zero on 0 warped faces since layer would be > 0.5 of the size of the bounding box.

patch                            faces    layers avg thickness[m]
                                                 near-wall overall
-----                            -----    ------ --------- -------
lowerWall                        0        1      0         0       
runde_rueckfoerderstruktur_ascii 6        1      4.07e-06  4.07e-06

medialAxisSmoothingInfo : Calculate distance to Medial Axis ...
shrinkMeshDistance : Smoothing normals ...
    Iteration 0   residual 0.553
Inserting points on patch frontAndBack if angle to nearest layer patch > 30 degrees.
Inserting points on patch inlet if angle to nearest layer patch > 30 degrees.
Inserting points on patch outlet if angle to nearest layer patch > 30 degrees.
Inserting points on patch upperWall if angle to nearest layer patch > 30 degrees.
shrinkMeshDistance : Smoothing normals ...
shrinkMeshDistance : Smoothing normals in interior ...
    Iteration 0   residual 0.361

Layer addition iteration 0
--------------------------
Prevented extrusion on 0 coupled patch points during syncPatchDisplacement.

Determining displacement for added points according to pointNormal ...
No valid normal for point 0 (0.00108 0.00191 0.000197); setting displacement to (2.8e-06 -2.85e-06 7.59e-07)
No valid normal for point 4 (0.00108 0.00214 0.000197); setting displacement to (2.8e-06 2.85e-06 7.59e-07)
No valid normal for point 3 (0.0009 0.00191 0.000174); setting displacement to (-2.02e-06 -3.17e-06 1.55e-06)
No valid normal for point 5 (0.0009 0.00214 0.000174); setting displacement to (-2.02e-06 3.17e-06 1.55e-06)
Displacement at illegal point (0.00108 0.00191 0.000197) set to (-7.06e-05 8.69e-05 6.93e-06)
Displacement at illegal point (0.00108 0.00214 0.000197) set to (-9.51e-05 -5.7e-05 8.98e-06)
Displacement at illegal point (0.0009 0.00191 0.000174) set to (6.41e-05 0.000119 3.07e-05)
Displacement at illegal point (0.0009 0.00214 0.000174) set to (7.79e-05 -6.86e-05 4.12e-05)
Prevented extrusion on 0 coupled patch points during syncPatchDisplacement.

shrinkMeshMedialDistance : Smoothing using Medial Axis ...
#0  Foam::error::printStack(Foam::Ostream&) in "/opt/openfoam221/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
#1  Foam::sigFpe::sigHandler(int) in "/opt/openfoam221/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
#2   in "/lib/x86_64-linux-gnu/libc.so.6"
#3  Foam::autoLayerDriver::shrinkMeshMedialDistance(Foam::motionSmoother&, Foam::dictionary const&, Foam::List<Foam::Pair<int> > const&, int, double, int, int, double, Foam::Field<double> const&, Foam::Field<double> const&, Foam::GeometricField<Foam::Vector<double>, Foam::pointPatchField, Foam::pointMesh> const&, Foam::GeometricField<double, Foam::pointPatchField, Foam::pointMesh> const&, Foam::GeometricField<double, Foam::pointPatchField, Foam::pointMesh> const&, Foam::GeometricField<Foam::Vector<double>, Foam::pointPatchField, Foam::pointMesh> const&, Foam::List<Foam::autoLayerDriver::extrudeMode>&, Foam::Field<Foam::Vector<double> >&, Foam::List<int>&) const in "/opt/openfoam221/platforms/linux64GccDPOpt/lib/libautoMesh.so"
#4  Foam::autoLayerDriver::addLayers(Foam::layerParameters const&, Foam::dictionary const&, Foam::List<int> const&, int, Foam::decompositionMethod&, Foam::fvMeshDistribute&) in "/opt/openfoam221/platforms/linux64GccDPOpt/lib/libautoMesh.so"
#5  Foam::autoLayerDriver::doLayers(Foam::dictionary const&, Foam::dictionary const&, Foam::layerParameters const&, bool, Foam::decompositionMethod&, Foam::fvMeshDistribute&) in "/opt/openfoam221/platforms/linux64GccDPOpt/lib/libautoMesh.so"
#6  
 in "/opt/openfoam221/platforms/linux64GccDPOpt/bin/snappyHexMesh"
#7  __libc_start_main in "/lib/x86_64-linux-gnu/libc.so.6"
#8  
 in "/opt/openfoam221/platforms/linux64GccDPOpt/bin/snappyHexMesh"
thank you
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Old   December 12, 2014, 11:58
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Petr Furmanek
Join Date: Jan 2012
Location: Faenza, Italy
Posts: 65
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Hi Philipp,

I'm constantly facing very similar problem - snappy blows out during layer addition phase when moving mesh using displacement scaling. Usually I get something like

Moving mesh using displacement scaling : min:0.5625 max:1
[3] #0 Foam::error:rintStack(Foam::Ostream&) in "/opt/OpenFOAM/OpenFOAM-2.3.x/platforms/linux64Gcc48DPOpt/lib/libOpenFOAM.so"
[3] #1 Foam::sigFpe::sigHandler(int) in "/opt/OpenFOAM/OpenFOAM-2.3.x/platforms/linux64Gcc48DPOpt/lib/libOpenFOAM.so"
[3] #2
[3] at sigaction.c:0
...

So far the only thing that helped me was:
1) using different snappyHexMeshDict for snap and addLayers phases,
2) decreasing the featureAngle and/or
3) increasing number of smoothing iterations, e.g.
nSmoothSurfaceNormals 50;
nSmoothNormals 30;
nSmoothThickness 50;
4) AND increasing the error reduction e.g.
errorReduction 0.9;

Good luck.
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