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Polytopochanger broken in 15x due to mesh format change

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Old   September 16, 2008, 04:45
Default Hi, I think that the polyt
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Andrew King
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Hi,

I think that the polytopochanger library is broken, mostly due to the new mesh format (no neighbours).
I have fixed a couple of these

http://www.cfd-online.com/OpenFOAM_D.../126/8450.html

http://www.cfd-online.com/OpenFOAM_D.../126/8631.html

however I have stumbled across some more (I think)
this time trying to use mixerFvMesh.

currently it segfaults with

#0 Foam::error::printStack(Foam:stream&) in "/home/anders/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libOpenFOAM.so"
#1 Foam::sigSegv::sigSegvHandler(int) in "/home/anders/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libOpenFOAM.so"
#2 Uninterpreted: [0xb7f50420]
#3 Foam::primitiveMesh::calcCells(Foam::List<foam::ce ll>&, Foam::UList<int> const&, Foam::UList<int> const&, int) in "/home/anders/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libOpenFOAM.so"
#4 Foam::primitiveMesh::calcCells() const in "/home/anders/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libOpenFOAM.so"
#5 Foam::primitiveMesh::cells() const in "/home/anders/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libOpenFOAM.so"
#6 Foam::mixerFvMesh::calcMovingMasks() const in "/home/anders/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libtopoChangerFvMesh.so"
#7 Foam::mixerFvMesh::movingPointsMask() const in "/home/anders/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libtopoChangerFvMesh.so"
#8 Foam::mixerFvMesh::update() in "/home/anders/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libtopoChangerFvMesh.so"
#9 main in "/home/anders/OpenFOAM/OpenFOAM-1.5.x/applications/bin/linuxGccDPOpt/icoDyMFoam"
#10 __libc_start_main in "/lib/tls/i686/cmov/libc.so.6"
#11 Foam::regIOobject::writeObject(Foam::IOstream::str eamFormat, Foam::IOstream::versionNumber, Foam::IOstream::compressionType) const in "/home/anders/OpenFOAM/OpenFOAM-1.5.x/applications/bin/linuxGccDPOpt/icoDyMFoam"
Segmentation fault


which I think I have traced to an access past the end of the neighbour label list.

I have been posting patches as I make them, however I'm not that familiar with the code and its a rather piecemeal approach.
It would help me greatly if anyone who knows the code better could go through and find a list of the problem areas (and patch them? - ;-) )

Note that this I am running from the latest git repo version.

Regards,
Andrew
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Old   September 19, 2008, 22:09
Default I'm glad someone is looking in
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I'm glad someone is looking into this. I'm having similar problems trying to run the mixer2D case in OF-1.5. icoDyMFoam quits after calling polyModifyFace() from line 1693 of coupleSlidingInterface.C.

After uncommenting all of the debug messages from coupleSlidingInterface.C, I get this output:

old rich slave face: 4(551 560 561 552) old face: 4(551 560 561 552)
found edge: 88
Modifying slave stick-out face 1728 old face: 4(551 560 561 552) new face: 4(955 560 561 956)


Patch face has got a neighbour This is not allowed.
Face: 4(955 560 561 956) faceID:1728 owner:224 neighbour:135391008 patchID:4#0 Foam::error::printStack(Foam:stream&) in "/home/mwilkins/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libOpenFOAM.so"
#1 Foam::error::abort() in "/home/mwilkins/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libOpenFOAM.so"
#2 Foam::polyModifyFace::polyModifyFace(Foam::face const&, int, int, int, bool, int, bool, int, bool) in "/home/mwilkins/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libdynamicMesh.so"
#3 Foam::slidingInterface::coupleInterface(Foam::poly TopoChange&) const in "/home/mwilkins/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libdynamicMesh.so"
#4 Foam::slidingInterface::setRefinement(Foam::polyTo poChange&) const in "/home/mwilkins/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libdynamicMesh.so"
#5 Foam::polyTopoChanger::topoChangeRequest() const in "/home/mwilkins/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libdynamicMesh.so"
#6 Foam::polyTopoChanger::changeMesh(bool, bool, bool, bool) in "/home/mwilkins/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libdynamicMesh.so"
#7 Foam::mixerFvMesh::update() in "/home/mwilkins/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libtopoChangerFvMesh.s o"


Matt
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Old   November 28, 2008, 08:26
Default I am trying to run the example
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I am trying to run the examples mixer2D and mixer 3D using icoDyMFoam, both examples fail with the following output. Any thoughts on how to correct this?


icoDyMFoam
/*---------------------------------------------------------------------------*\
| ========= | |
| \ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \ / O peration | Version: 1.5 |
| \ / A nd | Web: http://www.OpenFOAM.org |
| \/ M anipulation | |
\*---------------------------------------------------------------------------*/
Exec : icoDyMFoam
Date : Nov 28 2008
Time : 12:23:06
Host : abpc-109.bath.ac.uk
PID : 18577
Case : /home/mp340/temp/OpenFOAM-1.5.x/tutorials/icoDyMFoam/mixer3D
nProcs : 1

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

Create mesh for time = 0

Selecting dynamicFvMesh mixerFvMesh
void mixerFvMesh::addZonesAndModifiers() : Zones and modifiers already present. Skipping.
Mixer mesh:
origin: (0 0 0)
axis: (0 0 1)
rpm: 10
Reading transportProperties

Reading field p

Reading field U

Reading/calculating face flux field phi

Reading field rAU if present


Starting time loop

Courant Number mean: 0 max: 0
deltaT = 0.000595238
Time = 0.000595238



Patch face has got a neighbour This is not allowed.
Face: 4(3768 2166 2167 3769) faceID:18112 owner:1440 neighbour:8598544 patchID:4#0 Foam::error::printStack(Foam:stream&) in "/home/mp340/OpenFOAM/OpenFOAM-1.5/lib/linux64GccDPOpt/libOpenFOAM.so"
#1 Foam::error::abort() in "/home/mp340/OpenFOAM/OpenFOAM-1.5/lib/linux64GccDPOpt/libOpenFOAM.so"
#2 Foam::polyModifyFace::polyModifyFace(Foam::face const&, int, int, int, bool, int, bool, int, bool) in "/home/mp340/OpenFOAM/OpenFOAM-1.5/lib/linux64GccDPOpt/libdynamicMesh.so"
#3 Foam::slidingInterface::coupleInterface(Foam::poly TopoChange&) const in "/home/mp340/OpenFOAM/OpenFOAM-1.5/lib/linux64GccDPOpt/libdynamicMesh.so"
#4 Foam::slidingInterface::setRefinement(Foam::polyTo poChange&) const in "/home/mp340/OpenFOAM/OpenFOAM-1.5/lib/linux64GccDPOpt/libdynamicMesh.so"
#5 Foam::polyTopoChanger::topoChangeRequest() const in "/home/mp340/OpenFOAM/OpenFOAM-1.5/lib/linux64GccDPOpt/libdynamicMesh.so"
#6 Foam::polyTopoChanger::changeMesh(bool, bool, bool, bool) in "/home/mp340/OpenFOAM/OpenFOAM-1.5/lib/linux64GccDPOpt/libdynamicMesh.so"
#7 Foam::mixerFvMesh::update() in "/home/mp340/OpenFOAM/OpenFOAM-1.5/lib/linux64GccDPOpt/libtopoChangerFvMesh.so"
#8 main in "/home/mp340/OpenFOAM/OpenFOAM-1.5/applications/bin/linux64GccDPOpt/icoDyMFoam"
#9 __libc_start_main in "/lib64/libc.so.6"
#10 Foam::regIOobject::writeObject(Foam::IOstream::str eamFormat, Foam::IOstream::versionNumber, Foam::IOstream::compressionType) const in "/home/mp340/OpenFOAM/OpenFOAM-1.5/applications/bin/linux64GccDPOpt/icoDyMFoam"


From function polyModifyFace::polyModifyFace
(
const face& f,
const label faceID,
const label owner,
const label neighbour,
const bool flipFaceFlux,
const label patchID,
const bool removeFromZone,
const label zoneID,
const bool zoneFlip
)
in file lnInclude/polyModifyFace.H at line 221.

FOAM aborting

Aborted
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Old   January 6, 2009, 18:29
Default Hi, Having imported a spl
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Hi,


Having imported a split gmsh mesh merged using mergeMeshes, I was able to fix the "Patch face has got a neighbour This is not allowed." error by renaming patches that had the same name on both parts of the mesh (prior to patching) to different ones; however an error still remains (I get a segmentation fault error from, I think, calcMovingMasks).

Im looking into it at the moment,

regards,
-Louis
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Old   January 7, 2009, 16:24
Default Simply, I am the one who wrote
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Hrvoje Jasak
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Simply, I am the one who wrote this code and all the bug fixes are in 1.5-dev. I think you would be well advised to use this if you with to run any topo changer simulations. 1.5 and 1.5.x are broken beyond repair - they is at least 150 fixes behind.

Hrv
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Old   January 8, 2009, 21:20
Default Hi prof. Jasak, Exactly wha
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Hi prof. Jasak,

Exactly what I did and I am very satisfied with the results so far!

Thank you very much,

-Louis
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Old   January 19, 2009, 05:34
Default hi Gagnon sir i am new
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hi Gagnon sir

i am new to openfoam....i am facing difficult to install liftDrag tool in openfoam 1.4.1 on 64 bit machine..can u please send me compilation procedure of that..
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