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IDProjectCategoryView StatusLast Update
0003426OpenFOAMBugpublic2020-01-17 18:05
ReporterJeroenJanssenAssigned Tohenry 
PrioritynormalSeverityminorReproducibilityalways
Status resolvedResolutionfixed 
PlatformAWSOSLinux UbuntuOS Version18
Product Version7 
Fixed in Versiondev 
Summary0003426: no triangulated vtk files with cuttingPlane post processing
DescriptionAfter upgrading from OF6 to OF7, it seems that the 'triangulate' flag doesn't work anymore for the cuttingPlane postprocessor. The vtk files in the results all have meshes with faces with >=4 vertices, while the triangulate flag is set to true. All else works well (I do get triangulated vtk files for the 'patchInternalField', just not for the 'cuttingPlane').

Any help would be greatly appreciated.

Many thanks,
Jeroen
Steps To ReproduceAfter finishing the simpleFoam simulations I run the command:
mpirun -np 36 simpleFoam -parallel -postProcess -funcs "(surfaces)" -latestTime > log

An extract of the surfaces dictionary file:

...
surfaces
(
extractSurface_Ground_U13
    {
        type patchInternalField;
        patches (Ground Ground_Explicit Ground_Water);
        offsetMode uniform;
        offset (0 0 1.5);
        interpolate true;
        triangulate true;
    }

cuttingPlane14_X_000
    {
        type cuttingPlane;
        planeType pointAndNormal;
        pointAndNormalDict
        {
        basePoint (-798.600203421432 52.1308814897659 0);
        normalVector (0 1 -1.192093E-07);
        }
        interpolate true;
        triangulate true;
    }
)
...
TagsNo tags attached.

Activities

henry

2020-01-10 16:36

manager   ~0011051

We don't have access to the case you are running, can you reproduce the issue on one of the tutorial cases?

JeroenJanssen

2020-01-13 12:28

reporter   ~0011053

Hi Henry,

Thank you for your quick response.
No problem, please find attached the motorBike example (I only modified the 'cuttingPlane' dictionary, where I included the triangulate true - flag as I was used to in OF6 and before, and then the decomposeDict as I ran it on 36 cores). I've also included the resulting postProcessing file for U for timestep 500. As you can see there are a few tri's in there, but most of the faces have 4 or more vertices.
Hope that helps.

Thanks,
Jeroen

motorBike.zip (16,942 bytes)
U_yNormal.vtk (989,026 bytes)

henry

2020-01-13 14:36

manager   ~0011054

If you set
            triangulate rubbish;

you will find that there as no error message; there is no triangulate option in the latest cuttingPlane. However you can control the surface filtering which by default simplifies the triangulation into quads where possible but if you switch it off:

            filtering none;

then the original triangulated surface is written.

henry

2020-01-13 14:41

manager   ~0011055

Alternatively you can use the original cutting plane implementation by selecting

            type plane;
            .
            .
            .
            triangulate false;

but this has all the limitations and quirks of that version and I would recommend that you use the new one.

JeroenJanssen

2020-01-14 11:16

reporter   ~0011058

Thanks Henry,
I've tried the filtering none option you suggested, but where should I place that line? I put it within the cuttingPlane dict, both in the main body as well as within the individual plane, but there is no difference in the resulting vtk file. Still faces with 4 or more vertices. I've also tried to change the flag to rubbish and don't get any errors.

Am I putting it in the correct place, or not?

Thank you for your help

henry

2020-01-14 11:30

manager   ~0011059

With cuttingPlane in OpenFOAM-dev use

    filtering none;

instead and in place of

     triangulate true;

JeroenJanssen

2020-01-14 15:44

reporter   ~0011063

Thanks. I was using the OF7 distribution.
I just installed the dev and tried and it does create a triangulated vtk, however, running the motorBike example straight out the box causes snappyHexMesh to crash...
I've attached the log file for snappyHexMesh.

log.snappyHexMesh (12,032 bytes)

henry

2020-01-14 16:35

manager   ~0011066

I've attached the log file for snappyHexMesh that I get with OpenFOAM-dev

log.snappyHexMesh.gz (15,935 bytes)

JeroenJanssen

2020-01-17 13:00

reporter   ~0011072

Hi Henry,

Thanks. I've tried it again just now. Unfortunately it still crashes at the same point...
I've gone through these steps this morning:

- launch a fresh AWS instance with Linux Ubuntu Server 18.04 LTS (ami-0be057a22c63962cb)
- install OpenFOAM-dev (downloaded this morning) through the command line according the instructions (https://openfoam.org/download/dev-ubuntu/)
- copy the motorBike tutorial to the run folder
- run ./Allrun

snappyHexMesh crashes at the same location with an IOStream error:
[5] --> FOAM FATAL IO ERROR:
[5] incorrect first token, expected '(', found on line 0 the punctuation token '['
[5]
[5] file: IOstream at line 0.
[5]
[5] From function Foam::Istream& Foam::operator>>(Foam::Istream&, Foam::List<T>&) [with T = Foam::Vector<double>]
[5] in file /home/ubuntu/OpenFOAM/OpenFOAM-dev/src/OpenFOAM/lnInclude/ListIO.C at line 131.
[5]
FOAM parallel run exiting

I've gone through all the case files and compared the OF7 and OF-dev versions, they are both identical. The only small difference I can see between your and my log file is the OF Build (dev-7fdfe4224aad for mine and dev-2771c1f85c26 for yours) and I noticed that your log file has an additional line printed in line 33:
SetNaN : Initialising allocated memory to NaN (FOAM_SETNAN).

I've also run another tutorial windAroundBuildings. It succeeds on a single core, but crashes too in parallel with the same error. (Let me know if you'd prefer for me to raise a separate issue, as it seems this is probably not related to my original question anymore).

In addition, I put a cuttingPlane in this case and can confirm that it produces triangulated vtk files (see the images attached). The meshes are not very pretty, as it introduces triangles with a very high aspect ratio between each cell. I use these triangulated .vtk files to visualise results back in Rhino (3d CAD package), which only allows for tri or quad meshes. As these vtk files are quite large usually, I expect these additional triangles will make these meshes quite heavy, it would be great to have this original triangulate flag back in the dictionaries.

I hope that helps getting to the bottom of this...

Thanks,
Jeroen


PS: Also... The interface of this site is not that great. I had to type this twice as it timed out while I was typing and finding some stuff out (the suggested back button is bringing you back to the main page and therefore all the typed input and files disappear ...)

cuttingPlane_windAroundBuildings.PNG (342,414 bytes)
cuttingPlane_windAroundBuildings02.PNG (599,940 bytes)
log-2.snappyHexMesh (12,035 bytes)

henry

2020-01-17 13:49

manager   ~0011073

You will need

commit 2771c1f85c267e9925c2796b52b3ae010fae6179
Author: Henry Weller <http://openfoam.org>
Date: Mon Jan 13 19:55:18 2020 +0000

    coupledPolyPatch: Added initialisation of ordering_ data member
    
    Resolves bug-report https://bugs.openfoam.org/view.php?id=3428

which is more recent than commit-7fdfe4224aad.

Try compiling the latest OpenFOAM-dev sources.

henry

2020-01-17 13:51

manager   ~0011074

> PS: Also... The interface of this site is not that great. I had to type this twice as it timed out while I was typing and finding some stuff out (the suggested back button is bringing you back to the main page and therefore all the typed input and files disappear ...)

Agreed, I have also had this problem in the past. Have you reported it to the maintainers of the Mantis software?

JeroenJanssen

2020-01-17 17:48

reporter   ~0011076

yes that worked!
It's fully running and exporting the triangulated .vtk files.
Thanks!

ok, no, I didn't report it yet, but I will push my comment through to Mantis.

henry

2020-01-17 18:05

manager   ~0011077

Resolved by commit 2771c1f85c267e9925c2796b52b3ae010fae6179

Issue History

Date Modified Username Field Change
2020-01-10 12:04 JeroenJanssen New Issue
2020-01-10 16:36 henry Note Added: 0011051
2020-01-13 12:28 JeroenJanssen File Added: motorBike.zip
2020-01-13 12:28 JeroenJanssen File Added: U_yNormal.vtk
2020-01-13 12:28 JeroenJanssen Note Added: 0011053
2020-01-13 14:36 henry Note Added: 0011054
2020-01-13 14:41 henry Note Added: 0011055
2020-01-14 11:16 JeroenJanssen Note Added: 0011058
2020-01-14 11:30 henry Note Added: 0011059
2020-01-14 15:44 JeroenJanssen File Added: log.snappyHexMesh
2020-01-14 15:44 JeroenJanssen Note Added: 0011063
2020-01-14 16:35 henry File Added: log.snappyHexMesh.gz
2020-01-14 16:35 henry Note Added: 0011066
2020-01-17 13:00 JeroenJanssen File Added: cuttingPlane_windAroundBuildings.PNG
2020-01-17 13:00 JeroenJanssen File Added: cuttingPlane_windAroundBuildings02.PNG
2020-01-17 13:00 JeroenJanssen File Added: log-2.snappyHexMesh
2020-01-17 13:00 JeroenJanssen Note Added: 0011072
2020-01-17 13:49 henry Note Added: 0011073
2020-01-17 13:51 henry Note Added: 0011074
2020-01-17 17:48 JeroenJanssen Note Added: 0011076
2020-01-17 18:05 henry Assigned To => henry
2020-01-17 18:05 henry Status new => resolved
2020-01-17 18:05 henry Resolution open => fixed
2020-01-17 18:05 henry Fixed in Version => dev
2020-01-17 18:05 henry Note Added: 0011077