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[snappyHexMesh] SnappyHexMesh breaks nonCouple connections when using layers |
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May 7, 2023, 13:00
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SnappyHexMesh breaks nonCouple connections when using layers
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#1 |
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Member
Eduardo Firvida
Join Date: Dec 2010
Posts: 53
Rep Power: 15  |
Dear Foamers
I donīt know if this is a bug, or if I'm doing something wrong I will attach my test case for those who want to test. the STL file an be found here This is not a perfect SHM configuration or case setup, (I still working on it) but it will clarify my point. I'm using OpenFOAM 10 to work with the new mesh coupling method Non-Conformal Coupling (NCC) this is my snappyHexMeshDict from now on, I will just activate or deactivate the addLayers feature, which I detect is causing the simulation to explore, with simpleFoam and also with pimpleFoam. Code:
castellatedMesh true;
snap true;
addLayers true;
geometry
{
innerCylinder
{
type searchableCylinder;
point1 (-0.8 0 0);
point2 ( 0.2 0 0);
radius 2;
}
rotor
{
type triSurfaceMesh;
file "rotor.stl";
}
};
castellatedMeshControls
{
maxLocalCells 100000;
maxGlobalCells 20000000;
minRefinementCells 0;
maxLoadUnbalance 0.05;
nCellsBetweenLevels 1;
features
(
{
file "rotor.eMesh";
level 5;
}
);
refinementSurfaces
{
innerCylinder
{
level (4 4);
cellZone innerCylinder;
faceZone innerCylinder;
cellZoneInside inside;
}
rotor
{
level (6 6);
}
}
refinementRegions
{
innerCylinder
{
mode inside;
levels ((1E15 4));
}
rotor
{
mode distance;
levels (
(0.015 7)
(0.045 5)
);
}
}
resolveFeatureAngle 45;
locationInMesh (4 0 0);
allowFreeStandingZoneFaces false;
}
snapControls
{
nSmoothPatch 3;
tolerance 2.0;
nSolveIter 30;
nRelaxIter 5;
nFeatureSnapIter 30;
implicitFeatureSnap false;
explicitFeatureSnap true;
multiRegionFeatureSnap true;
}
addLayersControls
{
relativeSizes no;
layers
{
rotor
{
nSurfaceLayers 8;
}
}
expansionRatio 1.15;
thickness 0.0026;
//firstLayerThickness 0.00027;
minThickness 0.00027;
nGrow 0;
nLayerIter 200;
nRelaxIter 3;
nSmoothSurfaceNormals 1;
nSmoothThickness 10;
nSmoothNormals 10;
featureAngle 150;
mergePatchFacesAngle 90;
maxFaceThicknessRatio 0.5;
maxThicknessToMedialRatio 0.3;
nMedialAxisIter 10;
nSmoothDisplacement 45;
detectExtrusionIsland true;
minMedianAxisAngle 90;
nBufferCellsNoExtrude 0;
}
meshQualityControls
{
maxNonOrtho 50;
maxBoundarySkewness 4;
maxInternalSkewness 2;
maxConcave 80;
minVol -1E30;
minTetQuality 1E-30;
minArea -1;
minTwist 0.01;
minDeterminant 0.01;
minFaceWeight 0.05;
minVolRatio 0.01;
minTriangleTwist -1;
nSmoothScale 4;
errorReduction 0.75;
relaxed
{
maxNonOrtho 50;
}
}
mergeTolerance 1e-6;
Code:
...
Checking basic patch addressing...
Patch Faces Points
externalDomain 7560 7895
floor 2520 2671
inlet 1764 1849
outlet 1764 1849
rotor 136794 148215
nonCouple1 94800 97993
nonCouple2 94800 97991
nonConformalCyclic_on_nonCouple1 0 0
nonConformalCyclic_on_nonCouple2 0 0
nonConformalError_on_nonCouple1 0 0
nonConformalError_on_nonCouple2 0 0
Checking geometry...
Overall domain bounding box (-10 -7 -7) (10 7 7)
Mesh has 3 geometric (non-empty/wedge) directions (1 1 1)
Mesh has 3 solution (non-empty) directions (1 1 1)
Boundary openness (8.37944e-17 -9.93776e-18 2.88248e-17) OK.
Max cell openness = 4.54606e-16 OK.
Max aspect ratio = 17.7266 OK.
Minimum face area = 2.28786e-07. Maximum face area = 0.111982. Face area magnitudes OK.
Min volume = 4.283e-10. Max volume = 0.0373099. Total volume = 3919.99. Cell volumes OK.
Mesh non-orthogonality Max: 49.5951 average: 6.6127
Non-orthogonality check OK.
Face pyramids OK.
Max skewness = 3.8277 OK.
Coupled point location match (average 0) OK.
Mesh OK.
End
Code:
...
Checking topology...
Boundary definition OK.
Cell to face addressing OK.
Point usage OK.
Upper triangular ordering OK.
Face vertices OK.
*Number of regions: 2
The mesh has multiple regions which are not connected by any face.
<<Writing region information to "constant/cellToRegion"
<<Writing region 0 with 2473395 cells to cellSet region0
<<Writing region 1 with 326748 cells to cellSet region1
Checking basic patch addressing...
Patch Faces Points
externalDomain 7560 7747
floor 2520 2623
inlet 1764 1849
outlet 1764 1849
rotor 138310 149323
nonCouple1 94800 97922
nonCouple2 94800 97922
nonConformalCyclic_on_nonCouple1 0 0
nonConformalCyclic_on_nonCouple2 0 0
nonConformalError_on_nonCouple1 0 0
nonConformalError_on_nonCouple2 0 0
Checking geometry...
Overall domain bounding box (-10 -7 -7) (10 7 7)
Mesh has 3 geometric (non-empty/wedge) directions (1 1 1)
Mesh has 3 solution (non-empty) directions (1 1 1)
Boundary openness (4.04474e-18 1.16983e-17 -6.35165e-17) OK.
Max cell openness = 3.13835e-16 OK.
Max aspect ratio = 6.43264 OK.
Minimum face area = 3.73057e-07. Maximum face area = 0.11197. Face area magnitudes OK.
Min volume = 2.04163e-09. Max volume = 0.0373087. Total volume = 3919.99. Cell volumes OK.
Mesh non-orthogonality Max: 48.1571 average: 6.48066
Non-orthogonality check OK.
Face pyramids OK.
Max skewness = 3.72748 OK.
Coupled point location match (average 0) OK.
Mesh OK.
End
So if Run the pimpleFoam I get, the following errors every time that I use SHM with layers and nonCouple patches with different numbers of points. Code:
Create time
Create mesh for time = 0
patchToPatch: Calculating couplings between 94800 source faces and 94800 target faces
Source min/average/max coverage = 1/1/1
Target min/average/max coverage = 1/1/1
Source average openness/error/depth/angle = 7.3383e-17/4.88935e-15/1.8353e-15/1.2387e-07
Source max openness/error/depth/angle = 5.09752e-16/5.38361e-14/2.3632e-14/1.70755e-06
196512 couplings calculated in 4.79937s
fvMeshStitcher: Connecting
9/5 small couplings removed/added to nonConformalCyclic_on_nonCouple1
Cell min/avg/max openness = 0/5.04361e-17/3.15049e-15
Selecting fvMeshMover motionSolver
Selecting motion solver: solidBody
Selecting solid-body motion function rotatingMotion
Applying solid body motion to cellZone innerCylinder
PIMPLE: No convergence criteria found
PIMPLE: Corrector convergence criteria found
"(U|p)": tolerance 1e-05, relTol 0
Calculations will do 2 corrections if the convergence criteria are not met
PIMPLE: Operating solver in transient mode with 2 outer correctors
Reading field p
Reading field U
Reading/calculating face flux field phi
Selecting viscosity model constant
Selecting turbulence model type RAS
Selecting RAS turbulence model kOmegaSST
Selecting patchDistMethod meshWave
RAS
{
model kOmegaSST;
turbulence on;
printCoeffs on;
alphaK1 0.85;
alphaK2 1;
alphaOmega1 0.5;
alphaOmega2 0.856;
gamma1 0.555556;
gamma2 0.44;
beta1 0.075;
beta2 0.0828;
betaStar 0.09;
a1 0.31;
b1 1;
c1 10;
F3 false;
}
No MRF models present
No fvModels present
No fvConstraints present
Constructing face velocity Uf
Courant Number mean: 0.000160286 max: 0.571237
Starting time loop
forces forces:
Not including porosity effects
forces forces write:
sum of forces:
pressure : (0 0 0)
viscous : (0.00344544 0.00140939 0.00354055)
porous : (0 0 0)
sum of moments:
pressure : (0 0 0)
viscous : (-0.00122158 0.000314107 -0.000430482)
porous : (0 0 0)
Courant Number mean: 0.000160286 max: 0.571237
fvMeshStitcher: Disconnecting
Cell min/avg/max openness = 0/4.86921e-17/2.84231e-16
Time = 5e-06s
PIMPLE: Iteration 1
patchToPatch: Calculating couplings between 94800 source faces and 94800 target faces
Source min/average/max coverage = 0.992612/0.999979/1
Target min/average/max coverage = 0.992987/0.999979/1
Source average openness/error/depth/angle = 1.16439e-16/1.87615e-06/0.000106821/0.0127039
Source max openness/error/depth/angle = 8.26571e-16/0.00267606/0.00265116/0.322249
805944 couplings calculated in 1.61243s
fvMeshStitcher: Connecting
munmap_chunk(): invalid pointer
[Naboo:21796] *** Process received signal ***
[Naboo:21796] Signal: Aborted (6)
[Naboo:21796] Signal code: (-6)
[Naboo:21796] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x42520)[0x7fc7f8242520]
[Naboo:21796] [ 1] /lib/x86_64-linux-gnu/libc.so.6(pthread_kill+0x12c)[0x7fc7f8296a7c]
[Naboo:21796] [ 2] /lib/x86_64-linux-gnu/libc.so.6(raise+0x16)[0x7fc7f8242476]
[Naboo:21796] [ 3] /lib/x86_64-linux-gnu/libc.so.6(abort+0xd3)[0x7fc7f82287f3]
[Naboo:21796] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x896f6)[0x7fc7f82896f6]
[Naboo:21796] [ 5] /lib/x86_64-linux-gnu/libc.so.6(+0xa0d7c)[0x7fc7f82a0d7c]
[Naboo:21796] [ 6] /lib/x86_64-linux-gnu/libc.so.6(+0xa105c)[0x7fc7f82a105c]
[Naboo:21796] [ 7] /lib/x86_64-linux-gnu/libc.so.6(free+0xba)[0x7fc7f82a551a]
[Naboo:21796] [ 8] /home/efirvida/.local/easybuild/software/OpenFOAM/10-foss-2022a/OpenFOAM-10/platforms/linux64GccDPInt32Opt/lib/libfvMeshStitchers.so(+0x2e88b)[0x7fc7ef86a88b]
[Naboo:21796] [ 9] /home/efirvida/.local/easybuild/software/OpenFOAM/10-foss-2022a/OpenFOAM-10/platforms/linux64GccDPInt32Opt/lib/libfvMeshStitchers.so(+0x2e988)[0x7fc7ef86a988]
[Naboo:21796] [10] /home/efirvida/.local/easybuild/software/OpenFOAM/10-foss-2022a/OpenFOAM-10/platforms/linux64GccDPInt32Opt/lib/libfvMeshStitchers.so(_ZN4Foam15fvMeshStitchers6moving26internalFaceCorrectMeshPhiERNS_14GeometricFieldIdNS_13fvsPatchFieldENS_11surfaceMeshEEE+0x880)[0x7fc7ef872520]
[Naboo:21796] [11] /home/efirvida/.local/easybuild/software/OpenFOAM/10-foss-2022a/OpenFOAM-10/platforms/linux64GccDPInt32Opt/lib/libfvMeshStitchers.so(_ZN4Foam15fvMeshStitchers6moving14correctMeshPhiERKNS_22GeometricBoundaryFieldIiNS_13fvsPatchFieldENS_11surfaceMeshEEERNS_14GeometricFieldINS_6VectorIdEES3_S4_EESC_+0x2d8)[0x7fc7ef875698]
[Naboo:21796] [12] [6] #0 Foam::error::printStack(Foam::Ostream&)/home/efirvida/.local/easybuild/software/OpenFOAM/10-foss-2022a/OpenFOAM-10/platforms/linux64GccDPInt32Opt/lib/libfiniteVolume.so(_ZN4Foam14fvMeshStitcher7connectEbbb+0x2a5)[0x7fc7fa888095]
[Naboo:21796] [13] /home/efirvida/.local/easybuild/software/OpenFOAM/10-foss-2022a/OpenFOAM-10/platforms/linux64GccDPInt32Opt/lib/libfiniteVolume.so(_ZN4Foam6fvMesh4moveEv+0x5a)[0x7fc7fa75512a]
[Naboo:21796] [14] pimpleFoam[0x42c6a2]
[Naboo:21796] [15] /lib/x86_64-linux-gnu/libc.so.6(+0x29d90)[0x7fc7f8229d90]
[Naboo:21796] [16] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80)[0x7fc7f8229e40]
[Naboo:21796] [17] pimpleFoam[0x430a15]
[Naboo:21796] *** End of error message ***
at ??:?
[6] #1 Foam::sigSegv::sigHandler(int) at ??:?
[6] #2 ? in "/lib/x86_64-linux-gnu/libc.so.6"
[6] #3 free in "/lib/x86_64-linux-gnu/libc.so.6"
[6] #4 ? at fvMeshStitchersMoving.C:?
[6] #5 ? at fvMeshStitchersMoving.C:?
[6] #6 Foam::fvMeshStitchers::moving::internalFaceCorrectMeshPhi(Foam::GeometricField<double, Foam::fvsPatchField, Foam::surfaceMesh>&) at ??:?
[6] #7 Foam::fvMeshStitchers::moving::correctMeshPhi(Foam::GeometricBoundaryField<int, Foam::fvsPatchField, Foam::surfaceMesh> const&, Foam::GeometricField<Foam::Vector<double>, Foam::fvsPatchField, Foam::surfaceMesh>&, Foam::GeometricField<Foam::Vector<double>, Foam::fvsPatchField, Foam::surfaceMesh>&) at ??:?
[6] #8 Foam::fvMeshStitcher::connect(bool, bool, bool) at ??:?
[6] #9 Foam::fvMesh::move() at ??:?
[6] #10 --------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
? at ??:?
[6] #11 ? in "/lib/x86_64-linux-gnu/libc.so.6"
[6] #12 __libc_start_main in "/lib/x86_64-linux-gnu/libc.so.6"
[6] #13 ? at ??:?
[Naboo:21794:0:21794] Caught signal 11 (Segmentation fault: tkill(2) or tgkill(2) at address 0x3e800005522)
==== backtrace (tid: 21794) ====
0 0x0000000000042520 __GI___sigaction() :0
1 0x0000000000096a7c __pthread_kill_implementation() ./nptl/pthread_kill.c:43
2 0x0000000000096a7c __pthread_kill_internal() ./nptl/pthread_kill.c:78
3 0x0000000000096a7c __GI___pthread_kill() ./nptl/pthread_kill.c:89
4 0x0000000000042476 __GI_raise() ./signal/../sysdeps/posix/raise.c:26
5 0x0000000000042520 __GI___sigaction() :0
6 0x00000000000a54c9 arena_for_chunk() ./malloc/arena.c:162
7 0x00000000000a54c9 arena_for_chunk() ./malloc/arena.c:160
8 0x00000000000a54c9 __GI___libc_free() ./malloc/malloc.c:3390
9 0x000000000002e88b Foam::Pstream::gather<Foam::List<double>, Foam::ListOp<Foam::sumOp<double> > >() fvMeshStitchersMoving.C:0
10 0x000000000002e988 Foam::reduce<Foam::List<double>, Foam::ListOp<Foam::sumOp<double> > >() fvMeshStitchersMoving.C:0
11 0x0000000000036520 Foam::fvMeshStitchers::moving::internalFaceCorrectMeshPhi() ???:0
12 0x0000000000039698 Foam::fvMeshStitchers::moving::correctMeshPhi() ???:0
13 0x0000000000888095 Foam::fvMeshStitcher::connect() ???:0
14 0x000000000075512a Foam::fvMesh::move() ???:0
15 0x000000000042c6a2 main() ???:0
16 0x0000000000029d90 __libc_start_call_main() ./csu/../sysdeps/nptl/libc_start_call_main.h:58
17 0x0000000000029e40 __libc_start_main_impl() ./csu/../csu/libc-start.c:392
18 0x0000000000029e40 __libc_start_main_impl() ./csu/../csu/libc-start.c:379
19 0x0000000000430a15 _start() ???:0
=================================
[Naboo:21794] *** Process received signal ***
[Naboo:21794] Signal: Segmentation fault (11)
[Naboo:21794] Signal code: (-6)
[Naboo:21794] Failing at address: 0x3e800005522
[Naboo:21794] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x42520)[0x7f2fae842520]
[Naboo:21794] [ 1] /lib/x86_64-linux-gnu/libc.so.6(pthread_kill+0x12c)[0x7f2fae896a7c]
[Naboo:21794] [ 2] /lib/x86_64-linux-gnu/libc.so.6(raise+0x16)[0x7f2fae842476]
[Naboo:21794] [ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x42520)[0x7f2fae842520]
[Naboo:21794] [ 4] /lib/x86_64-linux-gnu/libc.so.6(free+0x69)[0x7f2fae8a54c9]
[Naboo:21794] [ 5] /home/efirvida/.local/easybuild/software/OpenFOAM/10-foss-2022a/OpenFOAM-10/platforms/linux64GccDPInt32Opt/lib/libfvMeshStitchers.so(+0x2e88b)[0x7f2fa806588b]
[Naboo:21794] [ 6] /home/efirvida/.local/easybuild/software/OpenFOAM/10-foss-2022a/OpenFOAM-10/platforms/linux64GccDPInt32Opt/lib/libfvMeshStitchers.so(+0x2e988)[0x7f2fa8065988]
[Naboo:21794] [ 7] /home/efirvida/.local/easybuild/software/OpenFOAM/10-foss-2022a/OpenFOAM-10/platforms/linux64GccDPInt32Opt/lib/libfvMeshStitchers.so(_ZN4Foam15fvMeshStitchers6moving26internalFaceCorrectMeshPhiERNS_14GeometricFieldIdNS_13fvsPatchFieldENS_11surfaceMeshEEE+0x880)[0x7f2fa806d520]
[Naboo:21794] [ 8] /home/efirvida/.local/easybuild/software/OpenFOAM/10-foss-2022a/OpenFOAM-10/platforms/linux64GccDPInt32Opt/lib/libfvMeshStitchers.so(_ZN4Foam15fvMeshStitchers6moving14correctMeshPhiERKNS_22GeometricBoundaryFieldIiNS_13fvsPatchFieldENS_11surfaceMeshEEERNS_14GeometricFieldINS_6VectorIdEES3_S4_EESC_+0x2d8)[0x7f2fa8070698]
[Naboo:21794] [ 9] /home/efirvida/.local/easybuild/software/OpenFOAM/10-foss-2022a/OpenFOAM-10/platforms/linux64GccDPInt32Opt/lib/libfiniteVolume.so(_ZN4Foam14fvMeshStitcher7connectEbbb+0x2a5)[0x7f2fb0e88095]
[Naboo:21794] [10] /home/efirvida/.local/easybuild/software/OpenFOAM/10-foss-2022a/OpenFOAM-10/platforms/linux64GccDPInt32Opt/lib/libfiniteVolume.so(_ZN4Foam6fvMesh4moveEv+0x5a)[0x7f2fb0d5512a]
[Naboo:21794] [11] pimpleFoam[0x42c6a2]
[Naboo:21794] [12] /lib/x86_64-linux-gnu/libc.so.6(+0x29d90)[0x7f2fae829d90]
[Naboo:21794] [13] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80)[0x7f2fae829e40]
[Naboo:21794] [14] pimpleFoam[0x430a15]
[Naboo:21794] *** End of error message ***
--------------------------------------------------------------------------
mpirun noticed that process rank 8 with PID 0 on node Naboo exited on signal 6 (Aborted).
--------------------------------------------------------------------------
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| Tags |
| layer addition, problem mesh, shm |
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