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Out of curiosity, what is the rationale for _reading_ high order gmsh meshes?
Is it so that one can write data back in native gmsh format?
Regards,
Blaise
It's confusing, but this line makes high order simplices always read as discontinuous coordinate spaces. I would love if someone would revisit that, perhaps also using DMPlexSetIsoperiodicFaceSF(),
Perhaps as a switch, but there is no way I am getting rid of the current periodicity. As we have discussed before, breaking the topological relation is a non-starter for me.
It does look like higher order Gmsh does read as DG. We can just project that to CG for non-periodic stuff.
Thanks,
Matt
which should simplify the code and avoid the confusing cell coordinates pattern. Sadly, I don't have time to dive in.
https://gitlab.com/petsc/petsc/-/commit/066ea43f7f75752f012be6cd06b6107ebe84cc6d#3616cad8148970af5b97293c49492ff893e25b59_1552_1724
"Daniel R. Shapero" <[email protected]> writes:
> Sorry either your mail system or mine prevented me from attaching the file,
> so I put it on pastebin:
> https://pastebin.com/awFpc1Js
>
> On Wed, Jan 11, 2023 at 4:54 PM Matthew Knepley <[email protected]> wrote:
>
>> Can you send the .msh file? I still have not installed Gmsh :)
>>
>> Thanks,
>>
>> Matt
>>
>> On Wed, Jan 11, 2023 at 2:43 PM Daniel R. Shapero <[email protected]> wrote:
>>
>>> Hi all -- I'm trying to read in 2nd-order / piecewise quadratic meshes
>>> that are generated by gmsh and I don't understand how the coordinates are
>>> stored in the plex. I've been discussing this with Matt Knepley here
>>> <https://urldefense.com/v3/__https://github.com/firedrakeproject/firedrake/issues/982__;!!K-Hz7m0Vt54!hL9WLR51ieyHFZx8N9AjhDwJCRpvmQto9CL1XOTkkAxFfUbtsabHuBDOATnWyP6lQszhA2gOStva7A$>
>>> as it pertains to Firedrake but I think this is more an issue at the PETSc
>>> level.
>>>
>>> This code
>>> <https://urldefense.com/v3/__https://gist.github.com/danshapero/a140daaf951ba58c48285ec29f5973cc__;!!K-Hz7m0Vt54!hL9WLR51ieyHFZx8N9AjhDwJCRpvmQto9CL1XOTkkAxFfUbtsabHuBDOATnWyP6lQszhA2hho2eD1g$>
>>> uses gmsh to generate a 2nd-order mesh of the unit disk, read it into a
>>> DMPlex, print out the number of cells in each depth stratum, and finally
>>> print a view of the coordinate DM's section. The resulting mesh has 64
>>> triangles, 104 edges, and 41 vertices. For 2nd-order meshes, I'd expected
>>> there to be 2 degrees of freedom at each node and 2 at each edge. The
>>> output is:
>>>
>>> ```
>>> Depth strata: [(64, 105), (105, 209), (0, 64)]
>>>
>>> PetscSection Object: 1 MPI process
>>> type not yet set
>>> 1 fields
>>> field 0 with 2 components
>>> Process 0:
>>> ( 0) dim 12 offset 0
>>> ( 1) dim 12 offset 12
>>> ( 2) dim 12 offset 24
>>> ...
>>> ( 62) dim 12 offset 744
>>> ( 63) dim 12 offset 756
>>> ( 64) dim 0 offset 768
>>> ( 65) dim 0 offset 768
>>> ...
>>> ( 207) dim 0 offset 768
>>> ( 208) dim 0 offset 768
>>> PetscSectionSym Object: 1 MPI process
>>> type: label
>>> Label 'depth'
>>> Symmetry for stratum value 0 (0 dofs per point): no symmetries
>>> Symmetry for stratum value 1 (0 dofs per point): no symmetries
>>> Symmetry for stratum value 2 (12 dofs per point):
>>> Orientation range: [-3, 3)
>>> Symmetry for stratum value -1 (0 dofs per point): no symmetries
>>> ```
>>>
>>> The output suggests that there are 12 degrees of freedom in each
>>> triangle. That would mean the coordinate field is discontinuous across cell
>>> boundaries. Can someone explain what's going on? I tried reading the .msh
>>> file but it's totally inscrutable to me. I'm happy to RTFSC if someone
>>> points me in the right direction. Matt tells me that the coordinate field
>>> should only be discontinuous if the mesh is periodic, but this mesh
>>> shouldn't be periodic.
>>>
>>
>>
>> --
>> 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/
>> <https://urldefense.com/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!K-Hz7m0Vt54!hL9WLR51ieyHFZx8N9AjhDwJCRpvmQto9CL1XOTkkAxFfUbtsabHuBDOATnWyP6lQszhA2go23tjRg$>
>>
--
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
—
Canada Research Chair in Mathematical and Computational Aspects of Solid Mechanics (Tier 1)
Professor, Department of Mathematics & Statistics
Hamilton Hall room 409A, McMaster University
1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
https://www.math.mcmaster.ca/bourdin | +1 (905) 525 9140 ext. 27243
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