SnappyHexMesh breaks nonCouple connections when using layers, by generating different numbers of points in the nonCouple patches #10
Description
Hi, I post this in CFD forum link here but I think that this can be an issue of the code so I duplicate it here
I don´t know if this is a bug, or if I'm doing something wrong, I'm sharing my test case for those who want to test. and the STL file can 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 Non-Conformal Coupling (NCC) for rotatory machines like wind turbines
This is my snappyHexMeshDict from now on, I will just activate or deactivate the addLayers feature, which I detect is causing the simulation to explode, with simpleFoam and also with pimpleFoam.
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;
After the meshing process with addLayers I get this checkMesh result:
...
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
As you can notice the NonCopule patch has a slightly different number of points, which didn't occur if I mesh is generated without the layers, as you can notice here in the other checkMesh result after meshing without layer addition:
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 I use SHM with layers and nonCouple patches with a different numbers of points.
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).
--------------------------------------------------------------------------