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-   -   Problem with skew faces in simpleFoam... (https://www.cfd-online.com/Forums/openfoam/75985-problem-skew-faces-simplefoam.html)

HelloWorld May 11, 2010 06:41
Problem with skew faces in simpleFoam...
 
Hello Foamers,

I'm running in a problem with simpleFoam here which is caused by highly skewed faces in my mesh after snappyHexMesh. But since this is my second model ever I'm simulating on I just can't figure out how to fix the problem.

so here's the detailed description of my problem:
I have an STL-model of a car which I'm meshing with snappyHexMesh. After meshing I've run the checkMesh-utility on it (see the result below). As shown in the checkMesh-report I have to deal with some highly skewed faces. Please note that I had a number about 190 highly skewed faces after my first run, so I increased the number of iterations in the snappyHexMeshDict for smoothing and solving to approx. 100, which actually took loads of time to mesh (about 9.5 hours only for meshing, is that normal?). As I said the result is shown below.

So I decided to give the simulation a try because the results after meshing for 2nd looked better than the results from the first time (Max skewness > 7 there). I first ran the potentialFoam solver on the case to calculate the potential flow (in parallel with writep-option) and started to run the simpleFoam-solver. It begins quite fine and the residuals also look good but after the it produces an error which I don't understand what it wants to tell me (see log-output below) and the simulation stops.

So, for now, I am a little confused on how to get that problem solved, because I don't really understand what's happening. Should I further increase the number of iterations in solving and smoothing in snappyHexMesh?

Any ideas on this issue would be greatly appreciated. Thanks in advance, regards
Yasar


checkMesh-report:
Quote:
Create time

Create polyMesh for time = 0

Time = 0

Mesh stats
points: 7789696
faces: 19507504
internal faces: 17853716
cells: 5889441
boundary patches: 6
point zones: 0
face zones: 0
cell zones: 0

Overall number of cells of each type:
hexahedra: 5181607
prisms: 0
wedges: 0
pyramids: 0
tet wedges: 0
tetrahedra: 0
polyhedra: 707834

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
frontAndBack 32256 32786 ok (non-closed singly connected)
inlet 9216 9409 ok (non-closed singly connected)
outlet 9216 9409 ok (non-closed singly connected)
lowerWall 39202 40974 ok (non-closed singly connected)
upperWall 16128 16393 ok (non-closed singly connected)
body_ascii 1547770 1616044 multiply connected (shared edge)
<<Writing 6 conflicting points to set nonManifoldPoints

Checking geometry...
Overall domain bounding box (-7 -4 -2.19444e-05) (7 4 8)
Mesh (non-empty, non-wedge) directions (1 1 1)
Mesh (non-empty) directions (1 1 1)
Boundary openness (7.1503e-16 -1.75172e-15 -2.08081e-14) OK.
Max cell openness = 3.4668e-16 OK.
Max aspect ratio = 13.7502 OK.
Minumum face area = 1.17455e-08. Maximum face area = 0.00694556. Face area magnitudes OK.
Min volume = 1.09199e-11. Max volume = 0.000578843. Total volume = 895.944. Cell volumes OK.
Mesh non-orthogonality Max: 65.5369 average: 11.097
Non-orthogonality check OK.
Face pyramids OK.
***Max skewness = 5.00251, 28 highly skew faces detected which may impair the quality of the results
<<Writing 28 skew faces to set skewFaces

Failed 1 mesh checks.

End
simpleFoam-report:
Quote:
Time = 1

DILUPBiCG: Solving for Ux, Initial residual = 0.0470019, Final residual = 0.00159451, No Iterations 1
DILUPBiCG: Solving for Uy, Initial residual = 0.016735, Final residual = 0.000794285, No Iterations 1
DILUPBiCG: Solving for Uz, Initial residual = 0.00512888, Final residual = 0.000209387, No Iterations 1
GAMG: Solving for p, Initial residual = 0.533966, Final residual = 0.0521085, No Iterations 5
GAMG: Solving for p, Initial residual = 6.32435e-05, Final residual = 6.1552e-06, No Iterations 5
GAMG: Solving for p, Initial residual = 5.9373e-06, Final residual = 4.10853e-07, No Iterations 6
GAMG: Solving for p, Initial residual = 4.09881e-07, Final residual = 7.06244e-08, No Iterations 4
time step continuity errors : sum local = 0.000203317, global = -4.61929e-07, cumulative = -4.61929e-07
DILUPBiCG: Solving for omega, Initial residual = 0.00155999, Final residual = 0.000146049, No Iterations 1
DILUPBiCG: Solving for k, Initial residual = 1, Final residual = 0.0113172, No Iterations 2
ExecutionTime = 52.6 s ClockTime = 52 s

Time = 2

DILUPBiCG: Solving for Ux, Initial residual = 0.149428, Final residual = 0.0113072, No Iterations 1
DILUPBiCG: Solving for Uy, Initial residual = 0.117821, Final residual = 0.0093268, No Iterations 1
DILUPBiCG: Solving for Uz, Initial residual = 0.106949, Final residual = 0.0070286, No Iterations 1
GAMG: Solving for p, Initial residual = 0.00210953, Final residual = 0.00016236, No Iterations 3
GAMG: Solving for p, Initial residual = 0.000120218, Final residual = 7.7692e-06, No Iterations 6
GAMG: Solving for p, Initial residual = 7.5233e-06, Final residual = 5.19068e-07, No Iterations 6
GAMG: Solving for p, Initial residual = 5.18458e-07, Final residual = 8.13884e-08, No Iterations 4
time step continuity errors : sum local = 8.77645e-05, global = -1.32735e-06, cumulative = -1.78927e-06
DILUPBiCG: Solving for omega, Initial residual = 0.000656903, Final residual = 5.00807e-06, No Iterations 2
DILUPBiCG: Solving for k, Initial residual = 0.0293622, Final residual = 0.00282563, No Iterations 1
ExecutionTime = 91.23 s ClockTime = 91 s

Time = 3

DILUPBiCG: Solving for Ux, Initial residual = 0.203513, Final residual = 0.014925, No Iterations 1
DILUPBiCG: Solving for Uy, Initial residual = 0.138747, Final residual = 0.0110201, No Iterations 1
DILUPBiCG: Solving for Uz, Initial residual = 0.124262, Final residual = 0.00813135, No Iterations 1
GAMG: Solving for p, Initial residual = 0.0042347, Final residual = 0.000315632, No Iterations 3
GAMG: Solving for p, Initial residual = 0.027243, Final residual = 0.00228496, No Iterations 6
GAMG: Solving for p, Initial residual = 0.000232067, Final residual = 1.93698e-05, No Iterations 11
GAMG: Solving for p, Initial residual = 1.77123e-05, Final residual = 1.68434e-06, No Iterations 10
time step continuity errors : sum local = 0.000132953, global = 1.22741e-06, cumulative = -5.61861e-07
DILUPBiCG: Solving for omega, Initial residual = 0.000526977, Final residual = 5.19195e-05, No Iterations 1
DILUPBiCG: Solving for k, Initial residual = 0.0175695, Final residual = 0.0016615, No Iterations 1
ExecutionTime = 140.46 s ClockTime = 140 s

Time = 4

DILUPBiCG: Solving for Ux, Initial residual = 0.142828, Final residual = 0.0099319, No Iterations 1
DILUPBiCG: Solving for Uy, Initial residual = 0.0910163, Final residual = 0.00705615, No Iterations 1
DILUPBiCG: Solving for Uz, Initial residual = 0.0430176, Final residual = 0.00261685, No Iterations 1
GAMG: Solving for p, Initial residual = 0.00562449, Final residual = 0.000403218, No Iterations 4
GAMG: Solving for p, Initial residual = 0.000298234, Final residual = 2.85729e-05, No Iterations 5
GAMG: Solving for p, Initial residual = 2.58226e-05, Final residual = 1.77719e-06, No Iterations 6
GAMG: Solving for p, Initial residual = 1.7678e-06, Final residual = 1.27912e-07, No Iterations 6
time step continuity errors : sum local = 0.000100083, global = 1.29687e-06, cumulative = 7.35013e-07
DILUPBiCG: Solving for omega, Initial residual = 0.000384138, Final residual = 3.59847e-05, No Iterations 1
DILUPBiCG: Solving for k, Initial residual = 0.0116713, Final residual = 0.00105877, No Iterations 1
ExecutionTime = 175.52 s ClockTime = 175 s

Time = 5

DILUPBiCG: Solving for Ux, Initial residual = 0.0567542, Final residual = 0.00230703, No Iterations 1
DILUPBiCG: Solving for Uy, Initial residual = 0.0345311, Final residual = 0.00163081, No Iterations 1
DILUPBiCG: Solving for Uz, Initial residual = 0.0136472, Final residual = 0.000531466, No Iterations 1
GAMG: Solving for p, Initial residual = 0.015898, Final residual = 0.00142227, No Iterations 4
GAMG: Solving for p, Initial residual = 0.000205296, Final residual = 1.99854e-05, No Iterations 5
GAMG: Solving for p, Initial residual = 1.86487e-05, Final residual = 1.28029e-06, No Iterations 6
GAMG: Solving for p, Initial residual = 1.27547e-06, Final residual = 9.04708e-08, No Iterations 6
time step continuity errors : sum local = 8.73983e-05, global = 1.17262e-06, cumulative = 1.90763e-06
DILUPBiCG: Solving for omega, Initial residual = 0.000272353, Final residual = 2.48687e-05, No Iterations 1
DILUPBiCG: Solving for k, Initial residual = 0.00704169, Final residual = 0.000685767, No Iterations 1
ExecutionTime = 211.96 s ClockTime = 212 s

Time = 6

DILUPBiCG: Solving for Ux, Initial residual = 0.0505934, Final residual = 0.00345681, No Iterations 1
DILUPBiCG: Solving for Uy, Initial residual = 0.0418622, Final residual = 0.00363079, No Iterations 1
DILUPBiCG: Solving for Uz, Initial residual = 0.0108325, Final residual = 0.000825592, No Iterations 1
GAMG: Solving for p, Initial residual = 0.00819174, Final residual = 0.000724051, No Iterations 3
GAMG: Solving for p, Initial residual = 0.000227248, Final residual = 2.16144e-05, No Iterations 5
GAMG: Solving for p, Initial residual = 1.99455e-05, Final residual = 1.36262e-06, No Iterations 6
GAMG: Solving for p, Initial residual = 1.35665e-06, Final residual = 9.11873e-08, No Iterations 6
time step continuity errors : sum local = 6.61502e-05, global = 1.37282e-07, cumulative = 2.04491e-06
DILUPBiCG: Solving for omega, Initial residual = 0.000209738, Final residual = 1.9301e-05, No Iterations 1
DILUPBiCG: Solving for k, Initial residual = 0.00470266, Final residual = 0.000436278, No Iterations 1
ExecutionTime = 245.04 s ClockTime = 245 s

Time = 7

DILUPBiCG: Solving for Ux, Initial residual = 0.0991008, Final residual = 0.00667086, No Iterations 1
DILUPBiCG: Solving for Uy, Initial residual = 0.0711584, Final residual = 0.00591094, No Iterations 1
DILUPBiCG: Solving for Uz, Initial residual = 0.0278779, Final residual = 0.00193497, No Iterations 1
GAMG: Solving for p, Initial residual = 0.00632294, Final residual = 0.000219981, No Iterations 2
GAMG: Solving for p, Initial residual = 0.000284016, Final residual = 1.93529e-05, No Iterations 4
GAMG: Solving for p, Initial residual = 2.19301e-05, Final residual = 1.57307e-06, No Iterations 5
GAMG: Solving for p, Initial residual = 1.58729e-06, Final residual = 1.40923e-07, No Iterations 5
time step continuity errors : sum local = 3.20926e-05, global = 6.85727e-08, cumulative = 2.11349e-06
DILUPBiCG: Solving for omega, Initial residual = 0.000179259, Final residual = 1.5832e-05, No Iterations 1
DILUPBiCG: Solving for k, Initial residual = 0.00366453, Final residual = 0.000314028, No Iterations 1
ExecutionTime = 275.36 s ClockTime = 275 s

Time = 8

DILUPBiCG: Solving for Ux, Initial residual = 0.0998382, Final residual = 0.00637505, No Iterations 1
DILUPBiCG: Solving for Uy, Initial residual = 0.0676365, Final residual = 0.00532405, No Iterations 1
DILUPBiCG: Solving for Uz, Initial residual = 0.0387657, Final residual = 0.00257048, No Iterations 1
GAMG: Solving for p, Initial residual = 0.00684188, Final residual = 0.000443793, No Iterations 3
GAMG: Solving for p, Initial residual = 0.00117625, Final residual = 0.000106433, No Iterations 5
GAMG: Solving for p, Initial residual = 7.42813e-05, Final residual = 4.99522e-06, No Iterations 6
GAMG: Solving for p, Initial residual = 4.91373e-06, Final residual = 3.37231e-07, No Iterations 6
time step continuity errors : sum local = 5.60022e-05, global = -3.23231e-08, cumulative = 2.08116e-06
DILUPBiCG: Solving for omega, Initial residual = 0.000156607, Final residual = 1.42548e-05, No Iterations 1
DILUPBiCG: Solving for k, Initial residual = 0.00290969, Final residual = 0.000245979, No Iterations 1
ExecutionTime = 309.96 s ClockTime = 310 s

Time = 9

[10] #0 Foam::error::printStack(Foam::Ostream&) in "/opt1/OpenFOAM/SUSE11.1/OpenFOAM-1.6.x/lib/linux64GccDPOpt/libOpenFOAM.so"
[10] #1 Foam::sigFpe::sigFpeHandler(int) in "/opt1/OpenFOAM/SUSE11.1/OpenFOAM-1.6.x/lib/linux64GccDPOpt/libOpenFOAM.so"
[10] #2 ?? in "/lib64/libc.so.6"
[10] #3 Foam::LimitedScheme<Foam::Vector<double>, Foam::GammaLimiter<Foam::NVDVTVDV>, Foam::limitFuncs::null>::limiter(Foam::GeometricFi eld<F
oam::Vector<double>, Foam::fvPatchField, Foam::volMesh> const&) const in "/opt1/OpenFOAM/SUSE11.1/OpenFOAM-1.6.x/lib/linux64GccDPOpt/libfiniteVolume.so"
[10] #4 Foam::limitedSurfaceInterpolationScheme<Foam::Vect or<double> >::weights(Foam::GeometricField<Foam::Vector<doubl e>, Foam::fvPatchField, Foam::volMesh> const&) const in "/opt1/OpenFOAM/SUSE11.1/OpenFOAM-1.6.x/lib/linux64GccDPOpt/libfiniteVolume.so"
[10] #5 Foam::fv::gaussConvectionScheme<Foam::Vector<doubl e> >::fvmDiv(Foam::GeometricField<double, Foam::fvsPatchField, Foam::surfaceMesh> c
onst&, Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh>&) const in "/opt1/OpenFOAM/SUSE11.1/OpenFOAM-1.6.x/lib/linux64GccDPOpt/libfiniteVolume.so"
[10] #6 Foam::tmp<Foam::fvMatrix<Foam::Vector<double> > > Foam::fvm::div<Foam::Vector<double> >(Foam::GeometricField<double, Foam::fvsPatchFi
eld, Foam::surfaceMesh> const&, Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh>&, Foam::word const&) in "/opt1/OpenFOAM/SUSE11.1/OpenFOAM-1.6.x/applications/bin/linux64GccDPOpt/simpleFoam"
[10] #7 Foam::tmp<Foam::fvMatrix<Foam::Vector<double> > > Foam::fvm::div<Foam::Vector<double> >(Foam::GeometricField<double, Foam::fvsPatchFi
eld, Foam::surfaceMesh> const&, Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh>&) in "/opt1/OpenFOAM/SUSE11.1/OpenFOAM-1.6.x/applications/bin/linux64GccDPOpt/simpleFoam"
[10] #8 main in "/opt1/OpenFOAM/SUSE11.1/OpenFOAM-1.6.x/applications/bin/linux64GccDPOpt/simpleFoam"
[10] #9 __libc_start_main in "/lib64/libc.so.6"
[10] #10 _start at /usr/src/packages/BUILD/glibc-2.9/csu/../sysdeps/x86_64/elf/start.S:116
[ivk190:22464] *** Process received signal ***
[ivk190:22464] Signal: Floating point exception (8)
[ivk190:22464] Signal code: (-6)
[ivk190:22464] Failing at address: 0x7e3000057c0
[ivk190:22464] [ 0] /lib64/libc.so.6 [0x7f96109db6e0]
[ivk190:22464] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x7f96109db645]
[ivk190:22464] [ 2] /lib64/libc.so.6 [0x7f96109db6e0]
[ivk190:22464] [ 3] /opt1/OpenFOAM/SUSE11.1/OpenFOAM-1.6.x/lib/linux64GccDPOpt/libfiniteVolume.so(_ZNK4Foam13LimitedSchemeINS_6Ve ctorIdEENS_12GammaLimiterINS_8NVDVTVDVEEENS_10limi tFuncs4nullEE7limiterERKNS_14GeometricFieldIS2_NS_ 12fvPatchFieldENS_7volMeshEEE+0x446) [0x7f9612377eb6]
[ivk190:22464] [ 4] /opt1/OpenFOAM/SUSE11.1/OpenFOAM-1.6.x/lib/linux64GccDPOpt/libfiniteVolume.so(_ZNK4Foam33limitedSurfaceInterp olationSchemeINS_6VectorIdEEE7weightsERKNS_14Geome tricFieldIS2_NS_12fvPatchFieldENS_7volMeshEEE+0x2a ) [0x7f961235ad7a]
[ivk190:22464] [ 5] /opt1/OpenFOAM/SUSE11.1/OpenFOAM-1.6.x/lib/linux64GccDPOpt/libfiniteVolume.so(_ZNK4Foam2fv21gaussConvectionSc hemeINS_6VectorIdEEE6fvmDivERKNS_14GeometricFieldI dNS_13fvsPatchFieldENS_11surfaceMeshEEERNS5_IS3_NS _12fvPatchFieldENS_7volMeshEEE+0x59) [0x7f96126382c9]
[ivk190:22464] [ 6] simpleFoam [0x440b51]
[ivk190:22464] [ 7] simpleFoam [0x440d7c]
[ivk190:22464] [ 8] simpleFoam [0x41546f]
[ivk190:22464] [ 9] /lib64/libc.so.6(__libc_start_main+0xe6) [0x7f96109c7586]
[ivk190:22464] [10] simpleFoam [0x414899]
[ivk190:22464] *** End of error message ***
[ivk189][[63242,1],6][btl_tcp_frag.c:216:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104)
[ivk191][[63242,1],14][btl_tcp_frag.c:216:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104)
--------------------------------------------------------------------------
mpirun noticed that process rank 10 with PID 22464 on node 129.69.127.90 exited on signal 8 (Floating point exception).
--------------------------------------------------------------------------

HelloWorld May 13, 2010 07:48
No idea anyone?

santoo_cfd May 14, 2010 04:39
Have you tried kEpsilon model ?

josp May 14, 2010 04:47
Quote:
Originally Posted by HelloWorld (Post 258625)
No idea anyone?
<<Writing 6 conflicting points to set nonManifoldPoints

I'm not really sure but I think I had problems related to this before. See if you can remove that error.

HelloWorld May 14, 2010 06:41
Quote:
Originally Posted by santoo_cfd (Post 258742)
Have you tried kEpsilon model ?
I've tried it with an other model but it diverged after 150 iterations for some reason I couldn't understand so I continued with kOmegaSST. But I'll give this one a try, too.


Quote:
Originally Posted by josp (Post 258746)
<<Writing 6 conflicting points to set nonManifoldPoints
I'm not really sure but I think I had problems related to this before. See if you can remove that error.
I'm trying to reduce skewed faces by increasing the number of smoothing iterations... Will this fix the nonManifoldPoints-conflict, too? What else can I set up in snappyHexMeshDict to get rid of that error?

Thanks a lot so far.
Regards.
Yasar

josp May 14, 2010 07:35
Quote:
Originally Posted by HelloWorld (Post 258764)
I'm trying to reduce skewed faces by increasing the number of smoothing iterations... Will this fix the nonManifoldPoints-conflict, too? What else can I set up in snappyHexMeshDict to get rid of that error?
I'm not sure, but for starters you can convert the nonManifoldPoints set to VTK and take a look at the problem in Paraview.

josp May 14, 2010 07:38
Quote:
Originally Posted by HelloWorld (Post 258764)
actually took loads of time to mesh (about 9.5 hours only for meshing, is that normal?
How much memory do you have on you machine? SnappyHexMesh has a quite large memory footprint during meshing and you mesh is not exactly small.

HelloWorld May 14, 2010 11:28
Quote:
Originally Posted by josp (Post 258772)
How much memory do you have on you machine?
I'm running snappyHexMesh in parallel in a network of 5 PCs where each of them has the following specification:
processors : 4
model name : Intel(R) Core(TM)2 Quad CPU Q9400 @ 2.66GHz
cpu MHz : 1998.000
cache size : 3072 KB
total memory : 8047684 kB

Converting the nonManifoldPoint set to VTK and taking a look at it in Paraview is really not a bad idea. I'll try that when the meshing process is finished. I started a new meshing process with sHM in which I increased the number of smoothing iterations. It's running since 8 hours by now an hasn't even reached the addLayers process... I guess it will run the whole weekend...

Thanks again.
Regards.
Yasar


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