[Error] While Using My Own Mesh #563

Mohsin-Bashir · 2024-01-13T05:23:39Z

Mohsin-Bashir
Jan 13, 2024

I have created tetrahedral mesh in gmsh. Then converted that to OpenFoam format using gmshToFoam command. I also checked the quality of mesh and it said ok. See the following output.

dafoamuser@eca3e5623a04:~/mount$ checkMesh
/*---------------------------------------------------------------------------*\
| =========                 |                                                 |
| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
|  \\    /   O peration     | Version:  v1812                                 |
|   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
|    \\/     M anipulation  |                                                 |
\*---------------------------------------------------------------------------*/
Build  : v1812 OPENFOAM=1812
Arch   : "LSB;label=32;scalar=64"
Exec   : checkMesh
Date   : Jan 12 2024
Time   : 23:17:56
Host   : eca3e5623a04
PID    : 636
I/O    : uncollated
Case   : /home/dafoamuser/mount
nProcs : 1
trapFpe: Floating point exception trapping enabled (FOAM_SIGFPE).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster (fileModificationSkew 10)
allowSystemOperations : Allowing user-supplied system call operations

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

Overriding DebugSwitches according to controlDict
    SolverPerformance 0;

Create mesh for time = 0

Time = 0

Mesh stats
    points:           73579
    faces:            702253
    internal faces:   624291
    cells:            331636
    faces per cell:   4
    boundary patches: 3
    point zones:      0
    face zones:       0
    cell zones:       1

Overall number of cells of each type:
    hexahedra:     0
    prisms:        0
    wedges:        0
    pyramids:      0
    tet wedges:    0
    tetrahedra:    331636
    polyhedra:     0

Checking topology...
    Boundary definition OK.
    Cell to face addressing 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
    WING                68342    34251    ok (non-closed singly connected)
    SYMMETRY            8656     4438     ok (non-closed singly connected)
    FARFIELD            964      514      ok (non-closed singly connected)

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

Checking basic cellZone addressing...
    CellZone            Cells        Points       Volume       BoundingBox
    VOLUME              331636       73579        5999966416051.452 (-10000 0 -10000) (20000 10000 10000.00000000001)

Checking geometry...
    Overall domain bounding box (-10000 0 -10000) (20000 10000 10000.00000000001)
    Mesh has 3 geometric (non-empty/wedge) directions (1 1 1)
    Mesh has 3 solution (non-empty) directions (1 1 1)
    Boundary openness (-6.398466158832806e-18 1.417180934353051e-16 2.538234509289047e-18) OK.
    Max cell openness = 3.044663788015041e-16 OK.
    Max aspect ratio = 11.41232264333115 OK.
    Minimum face area = 0.2998934551693578. Maximum face area = 5634409.459819945.  Face area magnitudes OK.
    Min volume = 0.3111556302058394. Max volume = 4391546362.691623.  Total volume = 5999966416051.452.  Cell volumes OK.
    Mesh non-orthogonality Max: 79.96933611303108 average: 22.80827323071654
   *Number of severely non-orthogonal (> 70 degrees) faces: 9.
    Non-orthogonality check OK.
  <<Writing 9 non-orthogonal faces to set nonOrthoFaces
    Face pyramids OK.
    Max skewness = 2.010749144858107 OK.
    Coupled point location match (average 0) OK.

Mesh OK.

End

After generating mesh, I created a new folder "0" and copied the contents of "0.orig" here. Then I edited all files according to my boundary names in both folders.
Then I edited boundary file in 'constant\polymesh' folder. I did not change fvSolutions & fvSchemes files. These are the same as tutorial files of OneraM6.
Finally I ran edited "runScript_v2.py" with task as "runPrimal", but it gave errors related to following lines (idk why). So, I just commented these lines to see if it runs ....

# volume constraint
DVCon.addVolumeConstraint(leList, teList, nSpan=10, nChord=10, lower=1.0, upper=3, scaled=True)
# thickness constraint
DVCon.addThicknessConstraints2D(leList, teList, nSpan=10, nChord=10, lower=0.8, upper=3.0, scaled=True)

Then i ran the script again using this command "mpirun -np 1 python runScript_v2.py 2>&1 | tee logOpt.txt" and got the following error (I have copied last few lines of error as follows, if you want to view full error then you can see logOpt.txt)

[      1066.5       1174.2      -8.6536] [     -1065.3      -1174.2       9.8836]
[      1020.9       896.95      -5.1125] [     -1019.7      -896.92       6.3425]
[      240.42       397.44       -13.84] [     -239.24      -397.41        15.07]
[      920.68        935.1       -16.61] [      -919.5      -935.07        17.84]
[      627.32       996.89      -18.825] [     -626.14      -996.86       20.055]
[       776.9       1167.5      -20.839] [     -775.72      -1167.4       22.069]
[      407.34        370.6      -32.917] [     -406.16      -370.57       34.147]
[      631.01       1007.2      -18.514] [     -629.83      -1007.1       19.744]
[      839.34       196.29       -3.115] [     -838.16      -196.26        4.345]
[      1023.4       1116.6      -11.451] [     -1022.2      -1116.6       12.681]
[      854.66       428.88      -9.2152] [     -853.48      -428.85       10.445]
[      276.76       371.56      -24.734] [     -275.58      -371.53       25.964]
[      602.13       347.45      -30.084] [     -600.95      -347.42       31.314]
[      568.88       975.63      -8.9534] [      -567.7       -975.6       10.183]
[      998.14       711.24      -1.2733] [     -996.96      -711.21       2.5033]
[      442.29       272.15      -35.389] [     -441.11      -272.12       36.619]
[      682.05        319.3        -23.5] [     -680.87      -319.27        24.73]
[      349.56       597.91      -9.0681] [     -348.38      -597.88       10.298]
[      765.69       7.2315      -5.7595] [     -764.51      -7.2015       6.9895]
[      1028.2       819.24      -1.3312] [     -1027.1      -819.21       2.5612]
[      259.44       137.96      -34.951] [     -258.26      -137.93       36.181]
[      1088.6       1184.9      -6.5823] [     -1087.4      -1184.8       7.8123]
[      184.36       311.81      -9.7236] [     -183.18      -311.78       10.954]
DVGeo PointSet UpToDate: False
Updating DVGeo PointSet....
DVGeo PointSet UpToDate: True
Warping the volume mesh....
Setting up primal boundary conditions based on pyOptions:
Setting primal boundary conditions...
Setting U = (284.6094174050535 14.91574752923899 0) at FARFIELD
Setting primal boundary conditions...
Setting p = 101325 at FARFIELD
Setting primal boundary conditions...
Setting T = 300 at FARFIELD
Setting primal boundary conditions...
Setting nuTilda = 4.5e-05 at FARFIELD
Setting nut wall BC for WING. BCType=nutUSpaldingWallFunction
Running Primal Solver 001
Previous solution time -1e+10 not found and nothing deleted.

Starting time loop

Checking mesh quality for time = 0
    Overall domain bounding box (-10635.3764334847 -577.0856120245685 -10000.00000034471) (19358.27068055307 9447.348825952673 10000.00000034471)
    Mesh has 3 geometric (non-empty/wedge) directions 3{1}
    Mesh has 3 solution (non-empty) directions 3{1}
    Boundary openness (4.926090407662356e-18 5.796909303256859e-16 -6.778623734534983e-18) OK.
 ***Open cells found, max cell openness: 1, number of open cells 2084
  <<Writing 2084 non closed cells to set nonClosedCells
  <<Writing 145004 cells with high aspect ratio to set highAspectRatioCells
 ***Zero or negative face area detected.  Minimum area: 0
  <<Writing 72029 zero area faces to set zeroAreaFaces
 ***Zero or negative cell volume detected.  Minimum negative volume: -1111.996503386515, Number of negative volume cells: 114786
  <<Writing 114786 zero volume cells to set zeroVolumeCells
    Mesh non-orthogonality Max: 179.9460059730046 average: 80.16041767227593
   *Number of severely non-orthogonal (> 70 degrees) faces: 316586.
 ***Number of non-orthogonality errors: 185355.
  <<Writing 501941 non-orthogonal faces to set nonOrthoFaces
 ***Error in face pyramids: 203289 faces are incorrectly oriented.
  <<Writing 171350 faces with incorrect orientation to set wrongOrientedFaces
 ***Max skewness = 1.063792776428286e+151, 62853 highly skew faces detected which may impair the quality of the results
  <<Writing 62853 skew faces to set skewFaces
    Coupled point location match (average 0) OK.

Failed 6 mesh checks.


+------------------------------------------------------------------------------+
| pyDAFoam Error: Primal solution failed for the baseline design!            |
+------------------------------------------------------------------------------+

runScript_v2.py:162: ComplexWarning: Casting complex values to real discards the imaginary part
  inletU = [float(U0 * np.cos(aoa)), float(U0 * np.sin(aoa)), 0]
Traceback (most recent call last):
  File "runScript_v2.py", line 253, in <module>
    optFuncs.runPrimal()
  File "/home/dafoamuser/dafoam/packages/miniconda3/lib/python3.8/site-packages/dafoam/optFuncs.py", line 402, in runPrimal
    funcs, fail = objFun(xDV)
  File "/home/dafoamuser/dafoam/packages/miniconda3/lib/python3.8/site-packages/dafoam/optFuncs.py", line 55, in calcObjFuncValues
    DASolver.evalFunctions(funcs, evalFuncs=evalFuncs)
  File "/home/dafoamuser/dafoam/packages/miniconda3/lib/python3.8/site-packages/dafoam/pyDAFoam.py", line 1424, in evalFunctions
    raise Error("Primal solution failed for the baseline design!")
dafoam.pyDAFoam.Error
--------------------------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causingthe job to be terminated. The first process to do so was:

  Process name: [[8838,1],0]
  Exit code:    1
--------------------------------------------------------------------------

I have read this FAQ https://dafoam.github.io/mydoc_get_started_faq.html#can-i-use-my-own-mesh, but I don't know which openFoam solver should i use for OneraM6. I tried simpleFoam but it gives error that there is no transportproperties file. If I place this file to the required directory then it gives this error

--> FOAM FATAL ERROR:
Unknown patchDistMethod type meshWaveFrozen

So, which OpenFoam solver should I used for this test case?

Mohsin-Bashir · 2024-01-15T08:08:02Z

Mohsin-Bashir
Jan 15, 2024
Author

***Number of non-orthogonality errors: 185355.
<<Writing 501941 non-orthogonal faces to set nonOrthoFaces
***Error in face pyramids: 203289 faces are incorrectly oriented.
<<Writing 171350 faces with incorrect orientation to set wrongOrientedFaces
***Max skewness = 1.063792776428286e+151, 62853 highly skew faces detected which may impair the quality of the results
<<Writing 62853 skew faces to set skewFaces
Coupled point location match (average 0) OK.
Failed 6 mesh checks.

This error was probably related to FFD because my FFD did not enclose design surface fully. After enclosing it, I am not getting this error anymore.

nuTilda Initial residual: 4.056148549546982e-07
          Final residual: 3.493079818863799e-08
Bounding nuTilda>1e-16
yPlus min: 8.668698506755666 max: 4514.97589245185 mean: 1658.249495615881
CD-part1-force: 0.01018692430890464
CL-part1-force: -0.1438004824229512
ExecutionTime = 891.78 s  ClockTime = 893 s

Printing Primal Residual Statistics.
U Residual Norm2: (38538.88133382874 17334.56078577002 15998.35138120318)
U Residual Mean: (23.30037434671122 8.207513811504143 10.02510702316563)
U Residual Max: (15210.21705447137 10802.60804739594 3908.727005123161)
p Residual Norm2: 407.3415462494842
p Residual Mean: 0.03866870038672474
p Residual Max: 290.4256470717314
T Residual Norm2: 55251040.03818401
T Residual Mean: 30811.84867909031
T Residual Max: 13459283.02777311
nuTilda Residual Norm2: 5.748009366816618
nuTilda Residual Mean: 0.0005857514833985381
nuTilda Residual Max: 5.614808193993489
phi Residual Norm2: 64.26053886511822
phi Residual Mean: 0.0005745472410140475
phi Residual Max: 20.63803855599597
End

runScript_v2.py:162: ComplexWarning: Casting complex values to real discards the imaginary part
  inletU = [float(U0 * np.cos(aoa)), float(U0 * np.sin(aoa)), 0]
Objective Functions: 
{'CD': 0.010186924308904636, 'CL': -0.14380048242295124, 'fail': False}
Flow Runtime: 889.733

But I am still unsure why I am getting negative value of "CL". Also, I had to increase primalMinResTol to 1e-5 otherwise i was getting error discussed here https://dafoam.github.io/mydoc_get_started_faq.html#how-to-fix-the-primal-solution-failed-for-the-baseline-design-error. I ran primal solution in SU2 with same mesh and I obtained CD=0.011906 & CL=0.27989 with same boundary conditions (without any constraints). I have commented most of the lines of DVCon in my runScript_v2.py because I don't want to apply constraints on the model. (Actually for my project, I don't want to use FFD at all. I just need volume deformation, primal and adjoint solutions. IDK why we need correctly defined FFD box for running primal, its not the case in SU2.)

All of the files are here in a zip file.
OneraM6 Testing.zip

1 reply

Mohsin-Bashir Jan 18, 2024
Author

My bad!! The values of Cd and Cl mentioned here for SU2 are for inviscid case.

friedenhe · 2024-01-15T22:25:01Z

friedenhe
Jan 15, 2024
Maintainer

The problem is in your coordinate system. Your mesh has z as the vertical and y as the spanwise directions, but your script says otherwise...

2 replies

Mohsin-Bashir Jan 16, 2024
Author

Hi, thank you for response. Could you please help me edit my script according to my mesh's coordinate system. I made some changes to the script but still I am not able to get the desired coefficients of lift and drag.
Here is my script file:
runScript_v2.py.txt

Mohsin-Bashir Jan 18, 2024
Author

I think my script is ok now. Please have a look and let me know if I made some mistake. runScript_v2.py.txt
I can get following results for my mesh.

{'CD': 0.027677427538050907, 'CL': 0.28558233245798775, 'fail': False}

I ran primal solution for OneraM6 tutorial and got these results:
'CD': 0.029768870326765756, 'CL': 0.2704712039600742, 'fail': False}
Though on website https://dafoam.github.io/mydoc_tutorials_aero_m6.html its mentioned that the initial drag is 0.016597241 Why is this the case?

Mohsin-Bashir · 2024-01-16T09:53:05Z

Mohsin-Bashir
Jan 16, 2024
Author

For my mesh, when I run "runAdjoint", I get the following error. What could be the issue?

+--------------------------------------------------------------------------+
[logOpt.txt](https://github.com/mdolab/dafoam/files/13948177/logOpt.txt)
|                       Running Coloring Solver                            |
+--------------------------------------------------------------------------+
I/O    : uncollated
Case   : /home/dafoamuser/mount
nProcs : 1
Create time

Overriding DebugSwitches according to controlDict
    SolverPerformance 0;

Create mesh for time = 0
Selecting thermodynamics package
{
    mixture         pureMixture;
    specie          specie;
    equationOfState perfectGas;
    energy          sensibleInternalEnergy;
    thermo          hConst;
    type            hePsiThermo;
    transport       const;
}

Selecting turbulence model type RAS
Selecting RAS turbulence model SpalartAllmaras
Selecting patchDistMethod meshWaveFrozen
Checking if Coloring file exists..
--------------------------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 0 on node 872c5e07ad49 exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------

1 reply

Mohsin-Bashir Jan 18, 2024
Author

Fixed!. This was a memory related issue. Just ran the simulation on an another Pc with more ram and could run it easily.

Mohsin-Bashir · 2024-01-20T04:31:28Z

Mohsin-Bashir
Jan 20, 2024
Author

Hi @friedenhe! Could you please check this one too? I ran OneraM6 tutorial but objective function values are significantly different than the ones mentioned on website. Thank you for your assistance.
Objective function did not decrease at all..opt_IPOPT.txt
logOpt.txt

I think my script is ok now. Please have a look and let me know if I made some mistake. runScript_v2.py.txt I can get following results for my mesh.
{'CD': 0.027677427538050907, 'CL': 0.28558233245798775, 'fail': False}
I ran primal solution for OneraM6 tutorial and got these results: 'CD': 0.029768870326765756, 'CL': 0.2704712039600742, 'fail': False} Though on website https://dafoam.github.io/mydoc_tutorials_aero_m6.html its mentioned that the initial drag is 0.016597241 Why is this the case?

0 replies

friedenhe · 2024-01-24T01:40:21Z

friedenhe
Jan 24, 2024
Maintainer

This is because the Onera tutorial mesh is coarse while the tutorial used much finer mesh. We have updated the tutorial website to mention this.

0 replies

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[Error] While Using My Own Mesh #563

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[Error] While Using My Own Mesh #563

Mohsin-Bashir Jan 13, 2024

Replies: 5 comments · 4 replies

Mohsin-Bashir Jan 15, 2024 Author

Mohsin-Bashir Jan 18, 2024 Author

friedenhe Jan 15, 2024 Maintainer

Mohsin-Bashir Jan 16, 2024 Author

Mohsin-Bashir Jan 18, 2024 Author

Mohsin-Bashir Jan 16, 2024 Author

Mohsin-Bashir Jan 18, 2024 Author

Mohsin-Bashir Jan 20, 2024 Author

friedenhe Jan 24, 2024 Maintainer

Mohsin-Bashir
Jan 13, 2024

Replies: 5 comments 4 replies

Mohsin-Bashir
Jan 15, 2024
Author

Mohsin-Bashir Jan 18, 2024
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friedenhe
Jan 15, 2024
Maintainer

Mohsin-Bashir Jan 16, 2024
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Mohsin-Bashir Jan 18, 2024
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Mohsin-Bashir
Jan 16, 2024
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Mohsin-Bashir Jan 18, 2024
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Mohsin-Bashir
Jan 20, 2024
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friedenhe
Jan 24, 2024
Maintainer