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Old   November 26, 2013, 07:42
Default Error during reconstructing lagarangian fields
  #1
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Yogesh Bapat
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Hi,
I am using icoUncoupledKinematicParcelDyMFoam to track particles in parallel. Case involves sliding mesh with AMI BCs in 2.2.2 version

I get following error message when I try to reconstruct lagrangian fields.

econstructing lagrangian fields for cloud kinematicCloud

AMI: Creating addressing and weights between 0 source faces and 0 target faces
AMI: Creating addressing and weights between 80 source faces and 80 target faces
AMI: Patch source weights min/max/average = 1.00035, 1.00036, 1.00036
AMI: Patch target weights min/max/average = 1.00035, 1.00036, 1.00036


--> FOAM FATAL ERROR:
cell, tetFace and tetPt search failure at position (-3.19372 0.689824 0)
for requested cell 456

From function void Foam:article::initCellFacePt()
in file particle/particleI.H at line 758.

FOAM aborting

Let me know if any one knows how to resolve this issue.
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Old   November 27, 2013, 12:54
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Martin Novák
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Hi,

I am experiencing simmilar issue with dynamicTopoFvMesh motion solver together with sprayEngineFoam solver.

Code:
Reconstructing lagrangian fields for cloud sprayCloud



--> FOAM FATAL ERROR: 
cell, tetFace and tetPt search failure at position (-0.0392443485 -0.0051150567 -0.0769150187)
for requested cell 158

    From function void Foam::particle::initCellFacePt()
    in file particle/particleI.H at line 758.

FOAM aborting

#0  Foam::error::printStack(Foam::Ostream&) in "/usr/users/novakm/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
#1  Foam::error::abort() in "/usr/users/novakm/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
#2  Foam::particle::initCellFacePt() in "/usr/users/novakm/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/liblagrangian.so"
#3  Foam::Cloud<Foam::passiveParticle>::initCloud(bool) in "/usr/users/novakm/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/liblagrangian.so"
#4  Foam::reconstructLagrangianPositions(Foam::polyMesh const&, Foam::word const&, Foam::PtrList<Foam::fvMesh> const&, Foam::PtrList<Foam::IOList<int> > const&, Foam::PtrList<Foam::IOList<int> > const&) in "/usr/users/novakm/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libreconstruct.so"
#5  
 in "/usr/users/novakm/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/bin/reconstructPar"
#6  __libc_start_main in "/lib/x86_64-linux-gnu/libc.so.6"
#7  
 in "/usr/users/novakm/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/bin/reconstructPar"
Aborted (core dumped)

Any clue what possibly can cause it?

I ve found bug trace:
HTML Code:
http://www.openfoam.org/mantisbt/view.php?id=464
that could be related to it.


With the extended version the reconstruction complained, however, at least finished wih log:
Code:
Reconstructing lagrangian fields for cloud sprayCloud

--> FOAM Warning : 
    From function Cloud<ParticleType>::initCloud(const bool checkClass)
    in file /usr/users/novakm/OpenFOAM/OpenFOAM-1.6-ext/src/lagrangian/basic/lnInclude/CloudIO.C at line 125
    Cannot read particle positions file 
    "/srv/groot/novakm/OpenFOAM/novakm-2.2.x/myCases/pE_final/pE_2_530/processor0/558/lagrangian/sprayCloud"
    assuming the initial cloud contains 0 particles.
--> FOAM Warning : 
    From function Cloud<ParticleType>::initCloud(const bool checkClass)
    in file /usr/users/novakm/OpenFOAM/OpenFOAM-1.6-ext/src/lagrangian/basic/lnInclude/CloudIO.C at line 125
    Cannot read particle positions file 
    "/srv/groot/novakm/OpenFOAM/novakm-2.2.x/myCases/pE_final/pE_2_530/processor2/558/lagrangian/sprayCloud"
    assuming the initial cloud contains 0 particles.
--> FOAM Warning : 
    From function Cloud<ParticleType>::initCloud(const bool checkClass)
    in file /usr/users/novakm/OpenFOAM/OpenFOAM-1.6-ext/src/lagrangian/basic/lnInclude/CloudIO.C at line 125
    Cannot read particle positions file 
    "/srv/groot/novakm/OpenFOAM/novakm-2.2.x/myCases/pE_final/pE_2_530/processor3/558/lagrangian/sprayCloud"
    assuming the initial cloud contains 0 particles.
--> FOAM Warning : 
    From function Cloud<ParticleType>::initCloud(const bool checkClass)
    in file /usr/users/novakm/OpenFOAM/OpenFOAM-1.6-ext/src/lagrangian/basic/lnInclude/CloudIO.C at line 125
    Cannot read particle positions file 
    "/srv/groot/novakm/OpenFOAM/novakm-2.2.x/myCases/pE_final/pE_2_530/processor4/558/lagrangian/sprayCloud"
    assuming the initial cloud contains 0 particles.
--> FOAM Warning : 
    From function Cloud<ParticleType>::initCloud(const bool checkClass)
    in file /usr/users/novakm/OpenFOAM/OpenFOAM-1.6-ext/src/lagrangian/basic/lnInclude/CloudIO.C at line 125
    Cannot read particle positions file 
    "/srv/groot/novakm/OpenFOAM/novakm-2.2.x/myCases/pE_final/pE_2_530/processor5/558/lagrangian/sprayCloud"
    assuming the initial cloud contains 0 particles.
--> FOAM Warning : 
    From function Cloud<ParticleType>::initCloud(const bool checkClass)
    in file /usr/users/novakm/OpenFOAM/OpenFOAM-1.6-ext/src/lagrangian/basic/lnInclude/CloudIO.C at line 125
    Cannot read particle positions file 
    "/srv/groot/novakm/OpenFOAM/novakm-2.2.x/myCases/pE_final/pE_2_530/processor6/558/lagrangian/sprayCloud"
    assuming the initial cloud contains 0 particles.
--> FOAM Warning : 
    From function Cloud<ParticleType>::initCloud(const bool checkClass)
    in file /usr/users/novakm/OpenFOAM/OpenFOAM-1.6-ext/src/lagrangian/basic/lnInclude/CloudIO.C at line 125
    Cannot read particle positions file 
    "/srv/groot/novakm/OpenFOAM/novakm-2.2.x/myCases/pE_final/pE_2_530/processor7/558/lagrangian/sprayCloud"
    assuming the initial cloud contains 0 particles.
--> FOAM Warning : 
    From function Cloud<ParticleType>::initCloud(const bool checkClass)
    in file /usr/users/novakm/OpenFOAM/OpenFOAM-1.6-ext/src/lagrangian/basic/lnInclude/CloudIO.C at line 125
    Cannot read particle positions file 
    "/srv/groot/novakm/OpenFOAM/novakm-2.2.x/myCases/pE_final/pE_2_530/processor11/558/lagrangian/sprayCloud"
    assuming the initial cloud contains 0 particles.
--> FOAM Warning : 
    From function Cloud<ParticleType>::initCloud(const bool checkClass)
    in file /usr/users/novakm/OpenFOAM/OpenFOAM-1.6-ext/src/lagrangian/basic/lnInclude/CloudIO.C at line 125
    Cannot read particle positions file 
    "/srv/groot/novakm/OpenFOAM/novakm-2.2.x/myCases/pE_final/pE_2_530/processor13/558/lagrangian/sprayCloud"
    assuming the initial cloud contains 0 particles.
--> FOAM Warning : 
    From function Cloud<ParticleType>::initCloud(const bool checkClass)
    in file /usr/users/novakm/OpenFOAM/OpenFOAM-1.6-ext/src/lagrangian/basic/lnInclude/CloudIO.C at line 125
    Cannot read particle positions file 
    "/srv/groot/novakm/OpenFOAM/novakm-2.2.x/myCases/pE_final/pE_2_530/processor14/558/lagrangian/sprayCloud"
    assuming the initial cloud contains 0 particles.
--> FOAM Warning : 
    From function Cloud<ParticleType>::initCloud(const bool checkClass)
    in file /usr/users/novakm/OpenFOAM/OpenFOAM-1.6-ext/src/lagrangian/basic/lnInclude/CloudIO.C at line 125
    Cannot read particle positions file 
    "/srv/groot/novakm/OpenFOAM/novakm-2.2.x/myCases/pE_final/pE_2_530/processor15/558/lagrangian/sprayCloud"
    assuming the initial cloud contains 0 particles.
--> FOAM Warning : 
    From function Cloud<ParticleType>::initCloud(const bool checkClass)
    in file /usr/users/novakm/OpenFOAM/OpenFOAM-1.6-ext/src/lagrangian/basic/lnInclude/CloudIO.C at line 125
    Cannot read particle positions file 
    "/srv/groot/novakm/OpenFOAM/novakm-2.2.x/myCases/pE_final/pE_2_530/processor16/558/lagrangian/sprayCloud"
    assuming the initial cloud contains 0 particles.
--> FOAM Warning : 
    From function Cloud<ParticleType>::initCloud(const bool checkClass)
    in file /usr/users/novakm/OpenFOAM/OpenFOAM-1.6-ext/src/lagrangian/basic/lnInclude/CloudIO.C at line 125
    Cannot read particle positions file 
    "/srv/groot/novakm/OpenFOAM/novakm-2.2.x/myCases/pE_final/pE_2_530/processor17/558/lagrangian/sprayCloud"
    assuming the initial cloud contains 0 particles.
--> FOAM Warning : 
    From function Cloud<ParticleType>::initCloud(const bool checkClass)
    in file /usr/users/novakm/OpenFOAM/OpenFOAM-1.6-ext/src/lagrangian/basic/lnInclude/CloudIO.C at line 125
    Cannot read particle positions file 
    "/srv/groot/novakm/OpenFOAM/novakm-2.2.x/myCases/pE_final/pE_2_530/processor18/558/lagrangian/sprayCloud"
    assuming the initial cloud contains 0 particles.
--> FOAM Warning : 
    From function Cloud<ParticleType>::initCloud(const bool checkClass)
    in file /usr/users/novakm/OpenFOAM/OpenFOAM-1.6-ext/src/lagrangian/basic/lnInclude/CloudIO.C at line 125
    Cannot read particle positions file 
    "/srv/groot/novakm/OpenFOAM/novakm-2.2.x/myCases/pE_final/pE_2_530/processor20/558/lagrangian/sprayCloud"
    assuming the initial cloud contains 0 particles.
--> FOAM Warning : 
    From function Cloud<ParticleType>::initCloud(const bool checkClass)
    in file /usr/users/novakm/OpenFOAM/OpenFOAM-1.6-ext/src/lagrangian/basic/lnInclude/CloudIO.C at line 125
    Cannot read particle positions file 
    "/srv/groot/novakm/OpenFOAM/novakm-2.2.x/myCases/pE_final/pE_2_530/processor21/558/lagrangian/sprayCloud"
    assuming the initial cloud contains 0 particles.
--> FOAM Warning : 
    From function Cloud<ParticleType>::initCloud(const bool checkClass)
    in file /usr/users/novakm/OpenFOAM/OpenFOAM-1.6-ext/src/lagrangian/basic/lnInclude/CloudIO.C at line 125
    Cannot read particle positions file 
    "/srv/groot/novakm/OpenFOAM/novakm-2.2.x/myCases/pE_final/pE_2_530/processor22/558/lagrangian/sprayCloud"
    assuming the initial cloud contains 0 particles.
    Reconstructing lagrangian labelFields

        origProcId
        origId
        typeId
        active

    Reconstructing lagrangian scalarFields

        tMom
        tc
        d
        dTarget
        KHindex
        nParticle
        rho
        d0
        age
        tTurb
        yDot
        injector
        Cp
        mass0
        YIC8H18(l)
        ms
        T
        user
        liquidCore
        y

    Reconstructing lagrangian vectorFields

        UTurb
        angularMomentum
        U
        position0
        f
        torque
It seems that there is a problem with functionality inheritance between versions...


Martin
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Old   November 29, 2013, 07:44
Default bug report
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Martin Novák
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reported as bug #0001097 on the http://www.openfoam.org/bugs/
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Old   November 29, 2013, 17:29
Default
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Bruno Santos
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Hi Martin,

Can you try the latest OpenFOAM 2.2.x?
Namely:
Code:
foam
git pull
./Allwmake
Because from your bug report, it looks very similar to this report: http://www.openfoam.org/mantisbt/view.php?id=1059 - which was fixed on the 26th of this month.

Best regards.
Bruno
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Old   November 29, 2013, 17:43
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Martin Novák
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Quote:
Originally Posted by wyldckat View Post
Hi Martin,

Can you try the latest OpenFOAM 2.2.x?
Namely:
Code:
foam
git pull
./Allwmake
Because from your bug report, it looks very similar to this report: http://www.openfoam.org/mantisbt/view.php?id=1059 - which was fixed on the 26th of this month.

Best regards.
Bruno
Hi Bruno.

My version is from 27th of this month. I ve noticed the bug 1059 and recompiled the openfoam.

Code:
r0:~/OpenFOAM/OpenFOAM-2.2.x>git diff --name-status master
M       etc/bashrc
M       etc/caseDicts/setConstraintTypes
M       etc/cellModels
M       etc/config/aliases.sh
M       etc/config/settings.sh
M       etc/controlDict
M       etc/cshrc
M       src/finiteVolume/cfdTools/general/solutionControl/pimpleControl/pimpleControl.C
M       src/lagrangian/basic/particle/particleI.H
M       src/lagrangian/intermediate/submodels/Kinematic/InjectionModel/ConeInjection/ConeInjection.H
M       src/lagrangian/intermediate/submodels/Kinematic/InjectionModel/ConeNozzleInjection/ConeNozzleInjection.C
M       src/lagrangian/intermediate/submodels/Kinematic/InjectionModel/ConeNozzleInjection/ConeNozzleInjection.H
M       src/lagrangian/intermediate/submodels/Kinematic/InjectionModel/InjectionModel/InjectionModel.C
M       src/lagrangian/intermediate/submodels/Kinematic/InjectionModel/InjectionModel/InjectionModel.H
M       src/thermophysicalModels/basic/basicThermo/basicThermo.H
M       src/thermophysicalModels/basic/heThermo/heThermo.H
M       src/thermophysicalModels/basic/psiThermo/psiThermos.C
M       src/thermophysicalModels/chemistryModel/chemistryModel/chemistryModel/chemistryModel.C
M       src/thermophysicalModels/laminarFlameSpeed/Gulders/Gulders.C
M       src/thermophysicalModels/reactionThermo/chemistryReaders/chemkinReader/chemkinLexer.L
M       src/thermophysicalModels/reactionThermo/mixtures/reactingMixture/reactingMixture.H
M       src/thermophysicalModels/reactionThermo/psiReactionThermo/psiReactionThermos.C
M       src/thermophysicalModels/specie/reaction/reactionRate/powerSeries/powerSeriesReactionRateI.H
The italic changes are done by me, the bold are new.
As a temporary solution, I have modified the particleI.H file. I ve changed foam error to warning in order to continue (thesis deadline is coming).


Martin
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Old   December 2, 2013, 08:17
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Yogesh Bapat
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Hello Martin,

Thanks for your reply.

You said you have converted Error to warning. Do you observe any impact of this on reconstructed lagrangian fields?

Regards,
-Yogesh
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Old   April 29, 2014, 03:45
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Hey,


are there any updates on that bug?

I got the same problem, but no idea anymore.

I tried reconstruction with 1.6.x, but I failed.

novakm..did you just convert the words error to warning?

greetings

Axel
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Old   May 1, 2014, 10:38
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Bruno Santos
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Greetings to all!

@Axel: Unfortunately I forgot back then to ask for an example case. Which without it also makes it considerably harder for the bug to be fixed...

If anyone can provide an example case, preferably based on a tutorial case from OpenFOAM, it would help to ascertain what the problem is and what might possible to do to fix it.

As for the change that Martin did, it was this:
Code:
diff --git a/src/lagrangian/basic/particle/particleI.H b/src/lagrangian/basic/particle/particleI.H
index e3c9a6e..52b629b 100644
--- a/src/lagrangian/basic/particle/particleI.H
+++ b/src/lagrangian/basic/particle/particleI.H
@@ -800,7 +800,7 @@ inline void Foam::particle::initCellFacePt()
 
                 if (tetFaceI_ == -1)
                 {
-                    FatalErrorIn("void Foam::particle::initCellFacePt()")
+                    WarningIn("void Foam::particle::initCellFacePt()")
                         << "cell, tetFace and tetPt search failure at position "
                         << position_ << abort(FatalError);
                 }
Best regards,
Bruno
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Old   July 8, 2014, 10:36
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Ananda Kannan
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Hi Bruno!!

Has there been a fix to this bug??? I am facing the same errors mentioned above while running the icoUncoupledKinematicParcelDyMFoam solver.. This error is encountered during the post-processing stage (while running foamToVTK) when the fields are reconstructed... Could you please advice on how this can be resolved.. You had asked for a case... I have attached my rather simple case set-up (not tutorial).. of an inclined box ( in which particles are released ) which is moved using the solidBodyMotionFunction --> oscillatingLinearMotion.. I would like to study the effect of mesh motion on particle distribution.. Here is the link to the files.. and some pictures of the set-up so that you can understand the case study ( works flawlessly with icoUncoupledKinematicParcelFoam solver ) -

https://www.dropbox.com/s/ihtrjifo0k...dynamic.tar.gz

Could you please help me??

BR

ansubru

PS - The change martin used did not work in my case
Attached Images
File Type: jpg suzuki_case3ai_t1.jpg (81.3 KB, 15 views)
File Type: jpg suzuki_case3ai_t5000.jpg (79.9 KB, 10 views)
File Type: jpg fine_mesh_case3a.jpg (58.3 KB, 9 views)
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Old   November 17, 2014, 08:52
Default same problem when running dsmcFoam
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Lianhua Zhu
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Hi! All,
I found the same error when running dsmcFoam to simulate a hypersonic rarefied gas flow past a circular cylinder.

Code:
/*---------------------------------------------------------------------------*\
| =========                 |                                                 |
| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
|  \\    /   O peration     | Version:  2.3.0                                 |
|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
|    \\/     M anipulation  |                                                 |
\*---------------------------------------------------------------------------*/
Build  : 2.3.0-f5222ca19ce6
Exec   : dsmcInitialise
Date   : Nov 17 2014
Time   : 20:35:05
Host   : "ws3"
PID    : 20028
Case   : /home/lhzhu/OpenFOAM/lhzhu-2.3.0/run/myCases/cylinder/dsmcKn0d1
nProcs : 1
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster
allowSystemOperations : Disallowing user-supplied system call operations

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

Create mesh for time = 0


Constructing dsmcCloud


--> FOAM FATAL ERROR:
cell, tetFace and tetPt search failure at position (0.05607113291 0.09463351433 0.0002451030235)
for requested cell 12832

    From function void Foam::particle::initCellFacePt()
    in file /home/lhzhu/OpenFOAM/OpenFOAM-2.3.0/src/lagrangian/basic/lnInclude/particleI.H at line 758.

FOAM aborting

#0  Foam::error::printStack(Foam::Ostream&) at ??:?
#1  Foam::error::abort() at ??:?
#2
 at ??:?
#3
 at ??:?
#4
 at ??:?
#5  __libc_start_main in "/lib64/libc.so.6"
#6
 at ??:?
Aborted (core dumped)
The computing domain is a concentric annular.

It is magic that if i change the mesh intervals to 50 or 100 along the radial direction, the error above disappears. But with other values such 60 or 80 or 51 it doesn't work.

The case dir can be found at https://www.dropbox.com/s/wydpkjt4mwzoc2y/dsmcKn0d1.tar.gz?dl=0


Best regards,

Lianhua
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