[petsc-users] coordinate degrees of freedom for 2nd-order gmsh mesh

Thu Jan 12 19:59:05 CST 2023

On Thu, Jan 12, 2023 at 3:57 PM Blaise Bourdin <bourdin at mcmaster.ca> wrote:

> 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?
>

So we can use meshes that other people design I think.

   Matt

> Regards,
> Blaise
>
>
> On Jan 12, 2023, at 7:13 PM, Matthew Knepley <knepley at gmail.com> wrote:
>
> On Thu, Jan 12, 2023 at 1:33 PM Jed Brown <jed at jedbrown.org> wrote:
>
>> 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" <shapero at uw.edu> 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 <knepley at gmail.com>
>> 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 <shapero at uw.edu>
>> 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
>
> https://www.cse.buffalo.edu/~knepley/
> <http://www.cse.buffalo.edu/~knepley/>
>
>
> —
> 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
>
>

-- 
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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