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checkMesh error after reconstructParMesh

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Old   April 10, 2024, 04:36
Default checkMesh error after reconstructParMesh
  #1
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Marius
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Hello,


I run into some errors when running checkMesh after using reconstructParMesh. I also ran checkMesh before reconstructParMesh and it finished fine without any errors.


I am not sure how to fix that now?




Here are the two checkMesh results.


Before reconstructParMesh:



Code:
/*---------------------------------------------------------------------------*\
| =========                 |                                                 |
| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
|  \\    /   O peration     | Version:  2312                                  |
|   \\  /    A nd           | Website:  www.openfoam.com                      |
|    \\/     M anipulation  |                                                 |
\*---------------------------------------------------------------------------*/
Build  : _c39a0f64-20231220 OPENFOAM=2312 version=2312
Arch   : "LSB;label=32;scalar=64"
Exec   : checkMesh -allGeometry -allTopology
Date   : Apr 10 2024
Time   : 01:36:00
Host   : f47623f43039
PID    : 1459
I/O    : uncollated
Case   : /home/openfoam/CFD-Openfoam/Clio2024-2
nProcs : 1
trapFpe: Floating point exception trapping enabled (FOAM_SIGFPE).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster (fileModificationSkew 5, maxFileModificationPolls 20)
allowSystemOperations : Allowing user-supplied system call operations

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time

Create mesh for time = 0

Check mesh...
    Enabling all (cell, face, edge, point) topology checks.
    Enabling all geometry checks.

Time = 0

Mesh stats
    points:           5526661
    faces:            16326000
    internal faces:   16074000
    cells:            5400000
    faces per cell:   6
    boundary patches: 5
    point zones:      0
    face zones:       0
    cell zones:       0

Overall number of cells of each type:
    hexahedra:     5400000
    prisms:        0
    wedges:        0
    pyramids:      0
    tet wedges:    0
    tetrahedra:    0
    polyhedra:     0

Checking topology...
    Boundary definition OK.
    Cell to face addressing OK.
    Point usage OK.
    Upper triangular ordering OK.
    Face vertices OK.
    Topological cell zip-up check OK.
    Face-face connectivity OK.
    Number of regions: 1 (OK).

Checking patch topology for multiply connected surfaces...
    Patch               Faces    Points     Surface topology  Bounding box
    frontAndBack        36000    36722    ok (non-closed singly connected)   (-15 -5 -1) (30 5 3)
    inlet               18000    18361    ok (non-closed singly connected)   (-15 -5 -1) (-15 5 3)
    outlet              18000    18361    ok (non-closed singly connected)   (30 -5 -1) (30 5 3)
    lowerWall           90000    90601    ok (non-closed singly connected)   (-15 -5 -1) (30 5 -1)
    upperWall           90000    90601    ok (non-closed singly connected)   (-15 -5 3) (30 5 3)
    ".*"                252000   252002   ok (closed singly connected)       (-15 -5 -1) (30 5 3)


Checking faceZone topology for multiply connected surfaces...
    No faceZones found.

Checking basic cellZone addressing...
    No cellZones found.

Checking basic pointZone addressing...
    No pointZones found.

Checking geometry...
    Overall domain bounding box (-15 -5 -1) (30 5 3)
    Mesh has 3 geometric (non-empty/wedge) directions (1 1 1)
    Mesh has 3 solution (non-empty) directions (1 1 1)
    Boundary openness (1.93603e-18 1.01851e-15 -2.88777e-16) OK.
    Max cell openness = 3.90313e-16 OK.
    Max aspect ratio = 4.5 OK.
    Minimum face area = 0.00222222. Maximum face area = 0.01.  Face area magnitudes OK.
    Min volume = 0.000333333. Max volume = 0.000333333.  Total volume = 1800.  Cell volumes OK.
    Mesh non-orthogonality Max: 0 average: 0
    Non-orthogonality check OK.
    Face pyramids OK.
    Max skewness = 5.47788e-13 OK.
    Coupled point location match (average 0) OK.
    Face tets OK.
    Min/max edge length = 0.0333333 0.15 OK.
    All angles in faces OK.
    Face flatness (1 = flat, 0 = butterfly) : min = 1  average = 1
    All face flatness OK.
    Cell determinant (wellposedness) : minimum: 0.0310652 average: 0.33736
    Cell determinant check OK.
    Concave cell check OK.
    Face interpolation weight : minimum: 0.5 average: 0.5
    Face interpolation weight check OK.
    Face volume ratio : minimum: 1 average: 1
    Face volume ratio check OK.

Mesh OK.

End





After running reconstructParMesh:


Code:
/*---------------------------------------------------------------------------*\
| =========                 |                                                 |
| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
|  \\    /   O peration     | Version:  2312                                  |
|   \\  /    A nd           | Website:  www.openfoam.com                      |
|    \\/     M anipulation  |                                                 |
\*---------------------------------------------------------------------------*/
Build  : _c39a0f64-20231220 OPENFOAM=2312 version=2312
Arch   : "LSB;label=32;scalar=64"
Exec   : checkMesh -allGeometry -allTopology
Date   : Apr 10 2024
Time   : 06:25:19
Host   : f47623f43039
PID    : 1469
I/O    : uncollated
Case   : /home/openfoam/CFD-Openfoam/Clio2024-2
nProcs : 1
trapFpe: Floating point exception trapping enabled (FOAM_SIGFPE).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster (fileModificationSkew 5, maxFileModificationPolls 20)
allowSystemOperations : Allowing user-supplied system call operations

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time

Create mesh for time = 0

Check mesh...
    Enabling all (cell, face, edge, point) topology checks.
    Enabling all geometry checks.

Time = 0

Mesh stats
    points:           20974724
    faces:            53927464
    internal faces:   50311460
    cells:            16639761
    faces per cell:   6.26445
    boundary patches: 6
    point zones:      1
    face zones:       0
    cell zones:       0

Overall number of cells of each type:
    hexahedra:     13399550
    prisms:        645551
    wedges:        1
    pyramids:      0
    tet wedges:    16833
    tetrahedra:    292
    polyhedra:     2577534
    Breakdown of polyhedra by number of faces:
        faces   number of cells
            4   112810
            5   157031
            6   529654
            7   472431
            8   127210
            9   834428
           10   11929
           11   10512
           12   259655
           13   1148
           14   2265
           15   50933
           16   133
           17   353
           18   6973
           19   2
           20   4
           21   63

Checking topology...
    Boundary definition OK.
    Cell to face addressing OK.
    Point usage OK.
    Upper triangular ordering OK.
    Face vertices OK.
    Topological cell zip-up check OK.
  <<Number of duplicate (not baffle) faces found: 40. This might indicate a problem.
  <<Number of faces with non-consecutive shared points: 77. This might indicate a problem.
  <<Writing 194 faces with non-standard edge connectivity to set edgeFaces
  <<Writing 1 cells with two non-boundary faces to set twoInternalFacesCells
    Number of regions: 1 (OK).

Checking patch topology for multiply connected surfaces...
                   Patch    Faces   Points  Surface topology  Bounding box
            frontAndBack    36000    36722  ok (non-closed singly connected) (-15 -5 -1) (30 5 3)
                   inlet    18000    18361  ok (non-closed singly connected) (-15 -5 -1) (-15 5 3)
                  outlet    18000    18361  ok (non-closed singly connected) (30 -5 -1) (30 5 3)
               lowerWall    90000    90601  ok (non-closed singly connected) (-15 -5 -1) (30 5 -1)
               upperWall    90000    90601  ok (non-closed singly connected) (-15 -5 3) (30 5 3)
                 clio3rs  3364004  3700790  multiply connected (shared edge) (-0.862136 -0.88747 -4.8231e-05) (3.31436 0.888929 1.47039)
                    ".*"  3616004  3952792  multiply connected (shared edge) (-15 -5 -1) (30 5 3)

Detected 1 bad edges (possibly relevant for finite-area)

Checking faceZone topology for multiply connected surfaces...
    No faceZones found.
  <<Writing 2 conflicting points to set nonManifoldPoints

Checking basic cellZone addressing...
    No cellZones found.

Checking basic pointZone addressing...
               PointZone  PointsBoundingBox
            frozenPoints       0(1e+150 1e+150 1e+150) (-1e+150 -1e+150 -1e+150)

Checking geometry...
    Overall domain bounding box (-15 -5 -1) (30 5 3)
    Mesh has 3 geometric (non-empty/wedge) directions (1 1 1)
    Mesh has 3 solution (non-empty) directions (1 1 1)
    Boundary openness (1.97747e-16 -1.47266e-15 -9.93147e-15) OK.
    Max cell openness = 1.609e-15 OK.
    Max aspect ratio = 189.935 OK.
    Minimum face area = 1.2264e-09. Maximum face area = 0.0105787.  Face area magnitudes OK.
    Min volume = 1.64322e-11. Max volume = 0.000359184.  Total volume = 1794.95.  Cell volumes OK.
    Mesh non-orthogonality Max: 82.0127 average: 16.2043
   *Number of severely non-orthogonal (> 70 degrees) faces: 88.
    Non-orthogonality check OK.
  <<Writing 88 non-orthogonal faces to set nonOrthoFaces
    Face pyramids OK.
 ***Max skewness = 16.9642, 3434 highly skew faces detected which may impair the quality of the results
  <<Writing 3434 skew faces to set skewFaces
    Coupled point location match (average 0) OK.
 ***Error in face tets: 11 faces with low quality or negative volume decomposition tets.
  <<Writing 11 faces with low quality or negative volume decomposition tets to set lowQualityTetFaces
   *Edges too small, min/max edge length = 3.01501e-07 0.155124, number too small: 2065
  <<Writing 2065 points on short edges to set shortEdges
   *There are 327518 faces with concave angles between consecutive edges. Max concave angle = 89.5995 degrees.
  <<Writing 327518 faces with concave angles to set concaveFaces
    Face flatness (1 = flat, 0 = butterfly) : min = 0.121865  average = 0.998712
   *There are 26447 faces with ratio between projected and actual area < 0.8
    Minimum ratio (minimum flatness, maximum warpage) = 0.121865
  <<Writing 26447 warped faces to set warpedFaces
    Cell determinant (wellposedness) : minimum: 2.68592e-18 average: 0.570997
 ***Cells with small determinant (< 0.001) found, number of cells: 21487
  <<Writing 21487 under-determined cells to set underdeterminedCells
 ***Concave cells (using face planes) found, number of cells: 1451494
  <<Writing 1451494 concave cells to set concaveCells
    Face interpolation weight : minimum: 0.00616374 average: 0.45225
 ***Faces with small interpolation weight (< 0.05) found, number of faces: 32023
  <<Writing 32023 faces with low interpolation weights to set lowWeightFaces
    Face volume ratio : minimum: 0.00284747 average: 0.798579
 ***Faces with small volume ratio (< 0.01) found, number of faces: 62
  <<Writing 62 faces with low volume ratio cells to set lowVolRatioFaces

Failed 6 mesh checks.

End



Should I run snappyHexMesh without decomposePar? But that would take forever... Any help or idea is really appreciated!


Thanks.


Marius
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Old   April 10, 2024, 04:46
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Yann
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Hello Marius,

Your first checkMesh (before reconstructing) should be run in parallel in order to check the parallelized mesh.

I guess you meshed your case with snappy. Since you didn't run the first checkMesh in parallel, you actually checked the mesh created by blockMesh, rather than your actual mesh.

The 2nd checkMesh (after reconstructing) is the actual check of the mesh you created.

Cheers,
Yann
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Old   April 10, 2024, 05:11
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Marius
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Hello Yann,


thanks for the explanation, that makes sense. Okay, then I need to check how to fix the errors in the mesh.
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Old   April 10, 2024, 06:02
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Yann
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I would advise to run checkMesh with the -writeSets vtk option. It will write vtk files containing the errors cells/faces. I can be handy to load it alongside your mesh in paraview to see what's wrong and where.
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