On Thu, Jan 12, 2023 at 4:10 PM Dave May <[email protected]> wrote:
> On Thu 12. Jan 2023 at 17:58, Blaise Bourdin <[email protected]> wrote: > >> Out of curiosity, what is the rationale for _reading_ high order gmsh >> meshes? >> > > GMSH can use a CAD engine like OpenCascade. This provides geometric > representations via things like BSplines. Such geometric representation are > not exposed to the users application code, nor are they embedded in any > mesh format GMSH emits. The next best thing is to use a high order > representation of the mesh geometry and project the CAD geometry (say a > BSpline) into this higher order function space. The projection of the > geometry is a quantity that can be described with the .msh format. > Note that PETSc can directly read CAD files now and mesh over them. > Is it so that one can write data back in native gmsh format? >> > > No. > > Cheers, > Dave > >> > > > >> Regards, >> Blaise >> >> >> On Jan 12, 2023, at 7:13 PM, Matthew Knepley <[email protected]> wrote: >> >> On Thu, Jan 12, 2023 at 1:33 PM Jed Brown <[email protected]> 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" <[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 >> >> 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, >> <https://www.google.com/maps/search/1280+Main+Street+West,+Hamilton,+Ontario+L8S+4K1,+Canada?entry=gmail&source=g> >> Ontario L8S 4K1, Canada >> <https://www.google.com/maps/search/1280+Main+Street+West,+Hamilton,+Ontario+L8S+4K1,+Canada?entry=gmail&source=g> >> >> 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/>
