[petsc-users] DMPlex and Boundary facets

[Karin&NiKo]

Dear Matthew,

You are (again) right. This Gmsh test file is "dirty" : some triangles do
not belong to tests. Sorry for that.
I have tried with another geo file (which is clean in that sense) and PETSc
reads with no error.

I take this opportunity to ask my initial question : are the labels of the
Physical Entities saved somewhere ?
A gmsh test file with several Physical entities is attached to this email.

Thank you again,
Nicolas

Le mer. 19 mai 2021 à 15:12, Matthew Knepley <knepley at gmail.com> a écrit :

> Okay, what Plex is saying is that Gmsh gave it a facet (a set of
> vertices), but those are not the vertices
> of any tetrahedral face in the mesh. It is hard to verify such a thing
> with 12K tets. I have definitely read in
> GMsh files before with facets, so I don't think the code is completely
> wrong.
>
> Would it be possible to make a smaller mesh (10-20 cells) that shows the
> same bug?
>
>   Thanks,
>
>      Matt
>
> On Tue, May 18, 2021 at 12:25 PM Karin&NiKo <niko.karin at gmail.com> wrote:
>
>> Sure! I send you both, one with the facets and one without.
>>
>> Thanks,
>> Nicolas
>>
>> Le mar. 18 mai 2021 à 17:49, Matthew Knepley <knepley at gmail.com> a
>> écrit :
>>
>>> On Tue, May 18, 2021 at 8:18 AM Karin&NiKo <niko.karin at gmail.com> wrote:
>>>
>>>> Dear PETSc team,
>>>>
>>>> I have tried to load a test mesh available in Gmsh' s demos directory
>>>>  (share/doc/gmsh/demos/simple_geo/filter.geo, attached to this email) as a
>>>> DMPlex.
>>>> So I produced a msh4 file by doing :
>>>>         gmsh -3 filter.geo -o /tmp/test.msh4
>>>> Then I used src/dm/impls/plex/tutorials/ex2.c to load the mesh by doing
>>>> :
>>>>         ./ex2 -filename /tmp/test.msh4
>>>>
>>>> Unfortunately I get the error :
>>>>
>>>> [0]PETSC ERROR: --------------------- Error Message
>>>> --------------------------------------------------------------
>>>> [0]PETSC ERROR: No support for this operation for this object type
>>>> [0]PETSC ERROR: Could not determine Plex facet for Gmsh element 1268
>>>> (Plex cell 12681)
>>>>
>>>> The error seems to come from the fact that the msh file contains
>>>> tets *and* facets *only on the Physical entities* (aka parts of the mesh
>>>> boundary where
>>>> the user will assign Dirichlet or Neuman conditions).
>>>> If I suppress these facets by commenting  the "Physical Surface" lines
>>>> in the geo file and regenerating the mesh, everything is fine.
>>>>
>>>> But the use of these "Physical" stuff is very common in lots of finite
>>>> element codes in order to assign boundary conditions.
>>>> How should I do to keep  these boundary groups of 2D elements (with
>>>> corresponding names) ?
>>>>
>>>
>>> Can you also send the *.msh file? I do not have Gmsh on this machine.
>>>
>>>   Thanks,
>>>
>>>      Matt
>>>
>>>
>>>> Thanks for your help,
>>>> Nicolas
>>>>
>>>>
>>>>
>>>
>>> --
>>> What most experimenters take for granted before they begin their
>>> experiments is infinitely more interesting than any results to which their
>>> experiments lead.
>>> -- Norbert Wiener
>>>
>>> https://www.cse.buffalo.edu/~knepley/
>>> <http://www.cse.buffalo.edu/~knepley/>
>>>
>>
>
> --
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> -- Norbert Wiener
>
> https://www.cse.buffalo.edu/~knepley/
> <http://www.cse.buffalo.edu/~knepley/>
>
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