foamToVTK error for post-processing in Paraview. Error: cell, tetFace and tetPt search failure at position (0.0139743

Submitted by limone on Tue, 09/05/2017 - 15:17

Dear All,

I am performing a simulation similar to the ErgunTestMPI test, but with a different geometry than the cylinder showed in the tutorial. My geometry comes from three STL files. created with a CAD. From the STL files (inlet.stl, outlet.stl, wall.stl) I generated a volumetric mesh, employing the "snappyHexMesh", and I run successfully a CFDEM coupling, where an inlet gas (CFD) is moving the DEM particles.

My question is about the post-processing with Paraview.

I can visualise the "file.foam" file, with all the "mesh regions", as the "internal mesh", "inlet", "outlet", "wall", "lagrangian/paticle cloud", but when I try to convert the foam file to VTK (from the terminal, typing the command "foamToVTK") I get the following error message:

***************************************************************
[limone@limone processor1]$ foamToVTK
/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 3.0.x |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
Build : 3.0.x-ac3f6c67e02f
Exec : foamToVTK
Date : Sep 05 2017
Time : 14:45:49
Host :
PID :
Case : /data/ErgunTestMPI2c/CFD/processor1
nProcs : 1
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster
allowSystemOperations : Allowing user-supplied system call operations

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

Create mesh for time = 0

Deleting old VTK files in "/data/ErgunTestMPI2c/CFD/processor1/VTK"

At time: 0.005 detected cloud directory : "particleCloud"
Time: 0
volScalarFields : p Ksl nut voidfraction epsilon rho
volVectorFields : Us U

Internal : "/data/ErgunTestMPI2c/CFD/processor1/VTK/processor1_0.vtk"
Original cells:1618763 points:1680053 Additional cells:225012 additional points:23258

Patch : "/data/ErgunTestMPI2c/CFD/processor1/VTK/maxY/maxY_0.vtk"
Patch : "/data/ErgunTestMPI2c/CFD/processor1/VTK/minX/minX_0.vtk"
Patch : "/data/ErgunTestMPI2c/CFD/processor1/VTK/maxX/maxX_0.vtk"
Patch : "/data/ErgunTestMPI2c/CFD/processor1/VTK/minY/minY_0.vtk"
Patch : "/data/ErgunTestMPI2c/CFD/processor1/VTK/minZ/minZ_0.vtk"
Patch : "/data/ErgunTestMPI2c/CFD/processor1/VTK/maxZ/maxZ_0.vtk"
Patch : "/data/ErgunTestMPI2c/CFD/processor1/VTK/wall/wall_0.vtk"
Patch : "/data/ErgunTestMPI2c/CFD/processor1/VTK/inlet/inlet_0.vtk"
Patch : "/data/ErgunTestMPI2c/CFD/processor1/VTK/outlet/outlet_0.vtk"
Patch : "/data/ErgunTestMPI2c/CFD/processor1/VTK/procBoundary1to0/procBoundary1to0_0.vtk"
Patch : "/data/ErgunTestMPI2c/CFD/processor1/VTK/procBoundary1to3/procBoundary1to3_0.vtk"
Lagrangian: "/data/ErgunTestMPI2c/CFD/processor1/VTK/lagrangian/particleCloud/particleCloud_0.vtk"
Time: 0.005
volScalarFields : p Ksl voidfraction rho
volVectorFields : stored_U Us U

Internal : "/data/ErgunTestMPI2c/CFD/processor1/VTK/processor1_10.vtk"
Patch : "/data/ErgunTestMPI2c/CFD/processor1/VTK/maxY/maxY_10.vtk"
Patch : "/data/ErgunTestMPI2c/CFD/processor1/VTK/minX/minX_10.vtk"
Patch : "/data/ErgunTestMPI2c/CFD/processor1/VTK/maxX/maxX_10.vtk"
Patch : "/data/ErgunTestMPI2c/CFD/processor1/VTK/minY/minY_10.vtk"
Patch : "/data/ErgunTestMPI2c/CFD/processor1/VTK/minZ/minZ_10.vtk"
Patch : "/data/ErgunTestMPI2c/CFD/processor1/VTK/maxZ/maxZ_10.vtk"
Patch : "/data/ErgunTestMPI2c/CFD/processor1/VTK/wall/wall_10.vtk"
Patch : "/data/ErgunTestMPI2c/CFD/processor1/VTK/inlet/inlet_10.vtk"
Patch : "/data/ErgunTestMPI2c/CFD/processor1/VTK/outlet/outlet_10.vtk"
Patch : "/data/ErgunTestMPI2c/CFD/processor1/VTK/procBoundary1to0/procBoundary1to0_10.vtk"
Patch : "/data/ErgunTestMPI2c/CFD/processor1/VTK/procBoundary1to3/procBoundary1to3_10.vtk"
surfScalarFields : phi
Lagrangian: "/data/ErgunTestMPI2c/CFD/processor1/VTK/lagrangian/particleCloud/particleCloud_10.vtk"
labels :
scalars : r
vectors : v
spherical tensors :
symm tensors :
tensors :

--> FOAM FATAL ERROR:
cell, tetFace and tetPt search failure at position (0.0139743895097 -0.0389545171037 0.000510398559073)
for requested cell 0
If this is a restart or reconstruction/decomposition etc. it is likely that the write precision is not sufficient.
Either increase 'writePrecision' or set 'writeFormat' to 'binary'

From function void Foam::particle::initCellFacePt()
in file /home/appuser/OpenFOAM/OpenFOAM-3.0.x/src/lagrangian/basic/lnInclude/particleI.H at line 735.

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)
[limone@limone processor1]$ foamToVTK
***************************************************************

In the "controlDict" file I have already increased 'writePrecision' from 6 to 12 (but without any improvement) and the 'writeFormat' was already 'binary':

***************************************************************
/*--------------------------------*- C++ -*----------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.6 |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
FoamFile
{
version 2.0;
format ascii;
class dictionary;
location "system";
object controlDict;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

application cfdemSolverPiso;
startFrom startTime;
startTime 0;
stopAt endTime;
endTime 10;
deltaT 0.0005;
writeControl adjustableRunTime;
writeInterval 0.005;
purgeWrite 0;
// writeFormat ascii;
writeFormat binary;
writePrecision 12;
writeCompression uncompressed;
timeFormat general;
timePrecision 12;
runTimeModifiable yes;
adjustTimeStep no;
maxCo 0.1;
***************************************************************

Do you have any suggestion on how to get successfully the VTK files with "foamToVTK" ?
In the original ErgunTestMPI test I obtained the VTK files without problems.

Best regards,
Limone

paul | Tue, 09/12/2017 - 13:32

Hi,

The problem lies with the IOModel of CFDEMcoupling, which writes invalid Lagrangian data that is attempted to be parsed by OpenFOAM, causing the crash. As such, I would recommend switching it off in the couplingProperties.
Relevant particle data is preferably written by LIGGGHTS using the dump custom/vtk command or regular dumps + lpp.
The lagrangian data can be removed by deleting the processor*/lagrangian folders.

Hope this helps,
- Paul

limone | Wed, 09/20/2017 - 12:24

Thank you very much Paul!

It is working with "dump custom/vtk command or regular dumps + lpp". I generated dump files and converted to VTK, by using LPP.
Then the visualization of the particles (moved by the gas) is possible with Paraview.

Thank you again for your suggestions!

Cheers,
Limo