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CreatePatch crashes segmentation violation in createPatch for cyclic boundaries

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Old   September 29, 2008, 15:56
Default I was trying to make a cyclic
  #1
sek
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Sung-Eun Kim
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I was trying to make a cyclic boundary out of two patches on a mesh converted from FLUENT mesh. And createPatch crashed, giving segmentation error as shown below.


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

Reading createPatchDict.

Using relative tolerance 0.001 to match up faces and points

Create polyMesh for time = 0

Adding new patch periodic-wake of type cyclic as patch 20

Moving faces from patch periodic_wake to patch 20
Moving faces from patch periodic_wake_shadow to patch 20

Doing topology modification to order faces.

#0 Foam::error::printStack(Foam:stream&) in "/home/sek/OpenFOAM/OpenFOAM-1.5/lib/linux64GccDPOpt/libOpenFOAM.so"
#1 Foam::sigSegv::sigSegvHandler(int) in "/home/sek/OpenFOAM/OpenFOAM-1.5/lib/linux64GccDPOpt/libOpenFOAM.so"
#2 __restore_rt in "/lib64/tls/libc.so.6"
#3 Foam::face::normal(Foam::Field<foam::vector<double > > const&) const in "/home/sek/OpenFOAM/OpenFOAM-1.5/lib/linux64GccDPOpt/libOpenFOAM.so"
#4 Foam::cyclicPolyPatch::getCentresAndAnchors(Foam:: PrimitivePatch<foam::face,> > const&, Foam::Vector<double> > const&, Foam::List<foam::face> const&, Foam::List<foam::face> const&, Foam::Field<foam::vector<double> >&, Foam::Field<foam::vector<double> >&, Foam::Field<foam::vector<double> >&, Foam::Field<double>&) const in "/home/sek/OpenFOAM/OpenFOAM-1.5/lib/linux64GccDPOpt/libOpenFOAM.so"
#5 Foam::cyclicPolyPatch::order(Foam::PrimitivePatch< foam::face,> > const&, Foam::Vector<double> > const&, Foam::List<int>&, Foam::List<int>&) const in "/home/sek/OpenFOAM/OpenFOAM-1.5/lib/linux64GccDPOpt/libOpenFOAM.so"
#6 Foam::polyTopoChange::reorderCoupledFaces(bool, Foam::polyBoundaryMesh const&, Foam::List<int> const&, Foam::List<int> const&, Foam::Field<foam::vector<double> > const&) in "/home/sek/OpenFOAM/OpenFOAM-1.5/lib/linux64GccDPOpt/libdynamicMesh.so"
#7 Foam::polyTopoChange::compactAndReorder(Foam::poly Mesh const&, bool, bool, bool, int&, Foam::Field<foam::vector<double> >&, Foam::List<int>&, Foam::List<int>&, Foam::List<foam::objectmap>&, Foam::List<foam::objectmap>&, Foam::List<foam::objectmap>&, Foam::List<foam::objectmap>&, Foam::List<foam::objectmap>&, Foam::List<foam::objectmap>&, Foam::List<foam::objectmap>&, Foam::List<foam::objectmap>&, Foam::List<foam::map<int> >&, Foam::List<int>&, Foam::List<int>&, Foam::List<foam::map<int> >&) in "/home/sek/OpenFOAM/OpenFOAM-1.5/lib/linux64GccDPOpt/libdynamicMesh.so"
#8 Foam::polyTopoChange::changeMesh(Foam::polyMesh&, bool, bool, bool, bool) in "/home/sek/OpenFOAM/OpenFOAM-1.5/lib/linux64GccDPOpt/libdynamicMesh.so"
#9 main in "/home/sek/OpenFOAM/OpenFOAM-1.5/applications/bin/linux64GccDPOpt/createPatch"
#10 __libc_start_main in "/lib64/tls/libc.so.6"
#11 __gxx_personality_v0 in "/home/sek/OpenFOAM/OpenFOAM-1.5/applications/bin/linux64GccDPOpt/createPatch"
Segmentation fault
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Old   September 30, 2008, 03:42
Default Could you try the 1.5.x versio
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Could you try the 1.5.x version and let us know if it works? 1.5.x should have some fixes regarding matching. If still persists could you post the case or send it directly to me?
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Old   March 19, 2009, 12:14
Default createPatch does not work to make cyclic patch
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mohd mojab
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hello

I do not why making a cyclic patch with createPatch is impossible for me. I made a simple box in blockMeshDict just to test createPatch. I tried to patch front and back with both version 1.5 and 1.5-x but both gave me the same error:

Create time
Reading createPatchDict.
Using relative tolerance 0.001 to match up faces and points
Create polyMesh for time = 0
Adding new patch Z of type cyclic as patch 5
Moving faces from patch maxZ to patch 5
Moving faces from patch minZ to patch 5

Doing topology modification to order faces.

#0 Foam::error:rintStack(Foam::Ostream&) in "/home/mou/OpenFOAM/OpenFOAM-1.5/lib/linux64GccDPOpt/libOpenFOAM.so"
#1 Foam::sigSegv::sigSegvHandler(int) in "/home/mou/OpenFOAM/OpenFOAM-1.5/lib/linux64GccDPOpt/libOpenFOAM.so"
.
.
.
#10 __libc_start_main in "/lib/libc.so.6"
#11 _start in "/home/mou/OpenFOAM/OpenFOAM-1.5/applications/bin/linux64GccDPOpt/createPatch"
Segmentation fault


I attached the case directory.
I appreciate any comments.

Mou
Attached Files
File Type: gz createPatch_case.tar.gz (32.8 KB, 45 views)
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Old   March 19, 2009, 14:47
Default
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Markus Weinmann
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Hi

I had the same/similar problem a while ago.
I was able to solve it by removing all additional entries in the controlDict file, e.g. libs() or other probe/averaging functions.

Markus
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Old   March 19, 2009, 15:23
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Thank you Markus for your reply. I checked the controlDict file but there is not any of extra things that you mentioned. Would you post a sample case that createPatch can work for that?

Thank you
mou
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Old   March 19, 2009, 16:17
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Switch off pointSync in the createPatchDict and it works for me in 1.5.x.

(the point synchronisation doesn't handle points being on multiple cyclics)
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Old   March 19, 2009, 18:33
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As you said mattijs, I put "false" for pointSync in the createPatchDict, and checked it by 1.5-x. I faced the same error. I just copied the createPatch directory from 1.5-x in .../utilities/mesh/manipulation/ of OpenFOAM-1.5 and compile it. Do I need to compile whole 1.5-x package?

Regards
Mou
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Old   March 19, 2009, 19:16
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Yes, the changes are also to the libraries, not just to the createPatch application. You will need to compile the whole 1.5.x.
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Old   March 23, 2009, 06:02
Default Cyclic BC's
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Hi Foamers,

I am also struggling with the cyclic buondaries.

I created a mesh in gambit with inlet and outet face meshes linked. Now I imported the ascii mesh in OF-1.5 and tried to couple the inlet and outlet face boundaries into a single patch of type cyclic using createPatch utility.

However the utillity crashes giving the similar segmentation fault error as posted in the topic. I also removed the custom libraries libs( ...) and any function objects from controldict system file as suggested by Markus in this topic.

I also tried to switch off the pointsyn flag as suggested by mattijs, but its giving the same segmentation fault error.

I am posting the error messages I received :-

--------------------------------------------------------------------------------------------------------------------------------
sm.kumar@linux-3:~/OpenFOAM/sm.kumar-1.5/Sumeet/annulus/annulus_case> createPatch
/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.5 |
| \\ / A nd | Web: http://www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
Exec : createPatch
Date : Mar 23 2009
Time : 14:52:57
Host : linux-3
PID : 19511
Case : /home/sm.kumar/OpenFOAM/sm.kumar-1.5/Sumeet/annulus/annulus_case
nProcs : 1

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

Reading createPatchDict.

Using relative tolerance 0.001 to match up faces and points

Create polyMesh for time = 0

Adding new patch perd of type cyclic as patch 4

Moving faces from patch symmetry-3 to patch 4
Moving faces from patch periodic to patch 4

Sumeet Chechk1
Doing topology modification to order faces.

Sumeet Chechk2
#0 Foam::error:rintStack(Foam::Ostream&) in "/home/sm.kumar/OpenFOAM/OpenFOAM-1.5/lib/linux64GccDPOpt/libOpenFOAM.so"
#1 Foam::sigSegv::sigSegvHandler(int) in "/home/sm.kumar/OpenFOAM/OpenFOAM-1.5/lib/linux64GccDPOpt/libOpenFOAM.so"
#2 ?? in "/lib64/libc.so.6"
#3 Foam::face::normal(Foam::Field<Foam::Vector<double > > const&) const in "/home/sm.kumar/OpenFOAM/OpenFOAM-1.5/lib/linux64GccDPOpt/libOpenFOAM.so"
#4 Foam::cyclicPolyPatch::getCentresAndAnchors(Foam:: PrimitivePatch<Foam::face, Foam::SubList, Foam::Field<Foam::Vector<double> > const&, Foam::Vector<double> > const&, Foam::List<Foam::face> const&, Foam::List<Foam::face> const&, Foam::Field<Foam::Vector<double> >&, Foam::Field<Foam::Vector<double> >&, Foam::Field<Foam::Vector<double> >&, Foam::Field<double>&) const in "/home/sm.kumar/OpenFOAM/OpenFOAM-1.5/lib/linux64GccDPOpt/libOpenFOAM.so"
#5 Foam::cyclicPolyPatch:rder(Foam::PrimitivePatch< Foam::face, Foam::SubList, Foam::Field<Foam::Vector<double> > const&, Foam::Vector<double> > const&, Foam::List<int>&, Foam::List<int>&) const in "/home/sm.kumar/OpenFOAM/OpenFOAM-1.5/lib/linux64GccDPOpt/libOpenFOAM.so"
#6 Foam:olyTopoChange::reorderCoupledFaces(bool, Foam:olyBoundaryMesh const&, Foam::List<int> const&, Foam::List<int> const&, Foam::Field<Foam::Vector<double> > const&) in "/home/sm.kumar/OpenFOAM/OpenFOAM-1.5/lib/linux64GccDPOpt/libdynamicMesh.so"
#7 Foam:olyTopoChange::compactAndReorder(Foam:oly Mesh const&, bool, bool, bool, int&, Foam::Field<Foam::Vector<double> >&, Foam::List<int>&, Foam::List<int>&, Foam::List<Foam:bjectMap>&, Foam::List<Foam:bjectMap>&, Foam::List<Foam:bjectMap>&, Foam::List<Foam:bjectMap>&, Foam::List<Foam:bjectMap>&, Foam::List<Foam:bjectMap>&, Foam::List<Foam:bjectMap>&, Foam::List<Foam:bjectMap>&, Foam::List<Foam::Map<int> >&, Foam::List<int>&, Foam::List<int>&, Foam::List<Foam::Map<int> >&) in "/home/sm.kumar/OpenFOAM/OpenFOAM-1.5/lib/linux64GccDPOpt/libdynamicMesh.so"
#8 FoamlyTopoChange::changeMesh(FoamlyMesh&, bool, bool, bool, bool) in "/home/sm.kumar/OpenFOAM/OpenFOAM-1.5/lib/linux64GccDPOpt/libdynamicMesh.so"
#9 main in "/home/sm.kumar/OpenFOAM/OpenFOAM-1.5/applications/bin/linux64GccDPOpt/createPatch"
#10 __libc_start_main in "/lib64/libc.so.6"
#11 __gxx_personality_v0 in "/home/sm.kumar/OpenFOAM/OpenFOAM-1.5/applications/bin/linux64GccDPOpt/createPatch"
Segmentation fault
--------------------------------------------------------------------------------------------------------------------------------

I tried to go through the createPatch source to find out the step causing errors


Code snippet :-
Line numbers 545-555
--------------------------------------------------------------------------------------------------------------------------------

// Change mesh, use inflation to reforce calculation of transformation
// tensors.

Info<< " Sumeet Chechk1 " << endl; // Debug statements
Info<< "Doing topology modification to order faces." << nl << endl;
Info<< " Sumeet Chechk2 " << endl; // Debug statements

autoPtr<mapPolyMesh> map = meshMod.changeMesh(mesh, true);

Info<< " Sumeet Chechk3 " << endl; // Debug statements
Info<< "mapping done " << nl << endl;
-----------------------------------------------------------------------------------------------------------------------------

However I could not figure out the sources of error caused during the mapping process. Please someone help me to find out what could be the possible source of error. Also share your previous similar experiences and how you resolved it.

Thanks
SK
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Old   March 23, 2009, 06:11
Default
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You seem to be using 1.5. Have you tried 1.5.x? It contains fixes to do with cyclic patch matching.
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Old   March 23, 2009, 07:08
Default openFOAM 1.5.x installation
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Hi mattijs,

I am quite new to OF. I started with OF-1.5 and it works gr8 on my linux terminal.

I did a search to find out the topics on 1.5.x installation. On link "http://powerlab.fsb.hr/ped/kturbo/OpenFOAM/release/" I found two compressed archives
OpenFOAM-1.5-de.r1094.tgz (30Mb)
ThirdParty.General_2008-12-11.tgz (125Mb)Could you specify which link to continue with?

I am using openSUSE 10.3 (x86_64)

Thanks in adv
SK
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Old   March 23, 2009, 07:25
Default Found!
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Sumeet Kumar
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Hi mattijs,

I just found the installation webpage the git repository. for OF 1.5.x

http://www.opencfd.co.uk/openfoam/do....html#download

Ignore the previous msg.

Thanks!
SK
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Old   March 24, 2009, 04:17
Default Face Area Matching
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Hi mattijs,

The segmentation fault error is fixed in OF-1.5.x. it works fine. However it still posts errors:-

--------------------------------------------------------------------------------------------------------------------------------
Patcher_final : Cannot match vectors to faces on both sides of patch
Perhaps your faces do not match? The obj files written contain the current match.
Continuing with incorrect face ordering from now on!

face 6 area does not match neighbour 5006 by 0.108917% -- possible face ordering problem.
patcher_final my area:0.0102764 neighbour area:0.0102876 matching tolerance:0.001
Mesh face:55406 vertices:4((-9.82281 -1.87413 10) (-9.92119 -1.25298 10) (-9.93765 -1.25488 10) (-9.8386 -1.87729 10))
Neighbour face:60406 vertices:4((-9.92124 -1.25262 0) (-9.82275 -1.87446 0) (-9.83854 -1.87762 0) (-9.93769 -1.25453 0))
Rerun with cyclic debug flag set for more information.

From function cyclicPolyPatch::calcTransforms()
in file meshes/polyMesh/polyPatches/constraint/cyclic/cyclicPolyPatch.C at l ine 158.

FOAM exiting

--------------------------------------------------------------------------------------------------------------------------------
I have set the writeprecision to be 12 in ControlDict. I also used utilities to output the face centers of both the patches. Both the face centers differ by 9th dec place onwards. Any suggestions??

Incase I change the tol value to 0.01, it may end up in incorrect face matching. However, same tol levels would be different when running the simulations.
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Old   March 24, 2009, 04:55
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So what happens if you increase the matchTolerance and enable pointSync? It should still pick the closest match to couple to and the pointSync will snap the points such that there are no future errors.
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Old   March 24, 2009, 08:15
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Hi Again,

I started increasing the matchTol from 0.001 and finally ended up to 1 at which createPatch could finally order the faces and create a new merged cyclic patch. (pointsync set as false).

Then I tried with pointsync set as true. I got following messages :-

-----------------------------------------------------------------------------------------------------------------------
Create time
Reading createPatchDict.
Using relative tolerance 1 to match up faces and points
Create polyMesh for time = 0
Adding new patch per_final of type cyclic as patch 4

Moving faces from patch periodic to patch 4
Moving faces from patch symmetry-3 to patch 4

Doing topology modification to order faces.

cyclicPolyPatch:rder : Writing half0 faces to OBJ file "per_final_half0_faces.obj"
cyclicPolyPatch:rder : Writing half1 faces to OBJ file "per_final_half1_faces.obj"
cyclicPolyPatch:rder : Dumping currently found cyclic match as lines between corresponding face centres to file "/home/lcfd/OpenFOAM/lcfd-1.5.x/Sumeet/annulus_case/per_final_faceCentres.obj"
--> FOAM Serious Error :
From function cyclicPolyPatch:rder(const primitivePatch&, labelList&, labelList&) const
in file meshes/polyMesh/polyPatches/constraint/cyclic/cyclicPolyPatch.C at line 1257
Patcher_final : Cannot match vectors to faces on both sides of patch
Perhaps your faces do not match? The obj files written contain the current match.
Continuing with incorrect face ordering from now on!

Synchronising points.
--> FOAM Warning :
From function syncTools<class T, class CombineOp>::syncPointList(const polyMesh&, UList<T>&, const CombineOp&, const T&, const bool)
in file /home/lcfd/OpenFOAM/OpenFOAM-1.5.x/src/OpenFOAM/lnInclude/syncToolsTemplates.C at line 1047
There are decomposed cyclics in this mesh with transformations.
This is not supported. The result will be incorrect
Points changed by average:0.174201962375 max:10.020097921

face 0 area does not match neighbour 5000 by 199.314% -- possible face ordering problem.
patcher_final my area:0.0161796 neighbour area:9.41746 matching tolerance:1
Mesh face:55400 vertices:4((-9.98025 -0.628118 10) (-9.99742 0.628969 10) (-9.99741 -0.629182 10) (-9.92119 -1.25298 10))
Neighbour face:60400 vertices:4((-9.98025 -0.628118 -1.77636e-15) (-9.92119 -1.25298 10) (-9.99741 -0.629182 10) (-9.99742 0.628969 10))
Rerun with cyclic debug flag set for more information.

From function cyclicPolyPatch::calcTransforms()
in file meshes/polyMesh/polyPatches/constraint/cyclic/cyclicPolyPatch.C at line 158.

FOAM exiting
-------------------------------------------------------------------------------------------------------------------------------

This states that it is not able to sync points as again newpatch-face0 is not able to match with newpatch-face(n/2).(which it was able to when pointsync was switched off)

I have been rather successful with coarse grids with cyclic bc's in OF, but this is a fine mesh. Is this the cause of error and to check if there is a loss of significant digits while converting the meshes and writing new patches in OF etc etc.( leading to causing errors in calculating face areas by clipping significant digits of nodes and in face ordering) I tried setting the write precision IO in fluent3D.. mesh converter to 16.

However this did not resolve the problem. It continues with the same face matching errors.

Is something wrong with the calculation of transformation matrix. as far as i know it automatically calculates the rotation/translational translational matrix - is it correct. (mine is a translational cyclic)
Plz help
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Old   March 24, 2009, 15:49
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It has dumped the match so far to obj files : "per_final_half0_faces.obj" etc. Use objToVTK+paraview to visualise those. Are both halves correctly picked up? Do the faces exactly overlay?
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Old   December 16, 2009, 10:50
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Does anybody know what pointSync does exactly ?
It is said that: " Do a synchronisation of coupled points after creation of any patches".
Can anyone further explain ?
Thanks a lot.
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Old   January 25, 2010, 08:47
Default createPatch segmentation fault with OF 1.6-x
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Hi everyone,

I've tried to use the createPatch utility to create a cyclic patch along the same lines as the rest of the users have already posted here and as Sumeet has indicated above, I get the same segmentation fault.
I'm actually using OF 1.6-x , which I'm assuming has the bugs fixed which were there prior to 1.5-x.

So any advice on how to overcome this segmentation fault would be much appreciated.

Thanks in advance.

Best,
Vasu
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Old   January 26, 2010, 09:14
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If you have multiple cyclics make sure to have pointSync switched off - it will try to synchronise points on opposite sides but cannot yet handle points on multiple cyclics.

Just run checkMesh on the resulting mesh (dumped to a new time directory) to make sure the resulting mesh is ok.

If the problem persists please post a simple testcase here.
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Old   February 2, 2010, 05:13
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Hello again,

Sorry for the delay in following up, I've had some end of term exams

Ok I've attached a test case for createPatch. It's a wedge shaped cylinder using blockMeshDict. I've done the same case using wedge patch types for the "front" and "back" patches, and it works alright.

But I want to create a cylinder with a central core region that is empty, which is why I made the mesh externally with Gambit and am trying to use createPatch on the "front" and "back" patches to make them cyclic, for an axisymmetric case. I hope that makes sense.

Any ideas on how to do this without createPatch would also be very welcome.

Here is the error I'm getting when I run the attached test case:

Create time

Create polyMesh for time = 0

Reading createPatchDict.

Using relative tolerance 1 to match up faces and points

Adding new patch new_front_back as patch 6 from
{
type cyclic;
}


Moving faces from patch front to patch 6
#0 Foam::error:rintStack(Foam::
Ostream&) in "/local/gvasudha/OpenFOAM/gvasudha-1.6.x/lib/linux64GccDPOpt/libOpenFOAM.so"
#1 Foam::sigSegv::sigSegvHandler(
int) in "/local/gvasudha/OpenFOAM/gvasudha-1.6.x/lib/linux64GccDPOpt/libOpenFOAM.so"
#2 __restore_rt at sigaction.c:0
#3 changePatchID(Foam:olyMesh const&, int, int, Foam:olyTopoChange&) in "/opt/software/OpenFOAM/
OpenFOAM-1.6.x/applications/bin/linux64GccDPOpt/createPatch"
#4 main in "/opt/software/OpenFOAM/
OpenFOAM-1.6.x/applications/bin/linux64GccDPOpt/createPatch"
#5 __libc_start_main in "/lib64/libc.so.6"
#6 _start in "/opt/software/OpenFOAM/
OpenFOAM-1.6.x/applications/bin/linux64GccDPOpt/createPatch"
Segmentation fault


Thanks in advance for any help.

Best regards,
Vasu
Attached Files
File Type: zip create_patch_test_case.zip (90.5 KB, 27 views)
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