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

[Matthew Knepley]

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/>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20230112/b6dee2c2/attachment.html>