[petsc-users] How to find the map between the high order coordinates of DMPlex and vertex numbering?

[Matthew Knepley]

On Thu, Jun 16, 2022 at 12:06 PM Zongze Yang <yangzongze at gmail.com> wrote:

>
>
> 在 2022年6月16日，23:22，Matthew Knepley <knepley at gmail.com> 写道：
>
> 
> On Thu, Jun 16, 2022 at 11:11 AM Zongze Yang <yangzongze at gmail.com> wrote:
>
>> Hi, if I load a `gmsh` file with second-order elements, the coordinates
>> will be stored in a DG-P2 space. After obtaining the coordinates of a cell,
>> how can I map the coordinates to vertex and edge?
>>
>
> By default, they are stored as P2, not DG.
>
>
> I checked the coordinates vector, and found the dogs only defined on cell
> other than vertex and edge, so I said they are stored as DG.
> Then the function DMPlexVecGetClosure
> <https://petsc.org/main/docs/manualpages/DMPLEX/DMPlexVecGetClosure/> seems return
> the coordinates in lex order.
>
> Some code in reading gmsh file reads that
>
>
> 1756:     if (isSimplex) continuity = PETSC_FALSE
> <https://petsc.org/main/docs/manualpages/Sys/PETSC_FALSE/>; /* XXX FIXME
> Requires DMPlexSetClosurePermutationLexicographic() */
>
>
> 1758:     GmshCreateFE(comm, NULL, isSimplex, continuity, nodeType, dim,
> coordDim, order, &fe)
>
>
> The continuity is set to false for simplex.
>

Oh, yes. That needs to be fixed. For now, you can just project it to P2 if
you want using

  https://petsc.org/main/docs/manualpages/DM/DMProjectCoordinates/

  Thanks,

     Matt


> Thanks,
> Zongze
>
> You can ask for the coordinates of a vertex or an edge directly using
>
>   https://petsc.org/main/docs/manualpages/DMPLEX/DMPlexPointLocalRead/
>
> by giving the vertex or edge point. You can get all the coordinates on a
> cell, in the closure order, using
>
>   https://petsc.org/main/docs/manualpages/DMPLEX/DMPlexVecGetClosure/
>
>   Thanks,
>
>      Matt
>
>
>> Below is some code load the gmsh file, I want to know the relation
>> between `cl` and `cell_coords`.
>>
>> ```
>> import firedrake as fd
>> import numpy as np
>>
>> # Load gmsh file (2rd)
>> plex = fd.mesh._from_gmsh('test-fd-load-p2-rect.msh')
>>
>> cs, ce = plex.getHeightStratum(0)
>>
>> cdm = plex.getCoordinateDM()
>> csec = dm.getCoordinateSection()
>> coords_gvec = dm.getCoordinates()
>>
>> for i in range(cs, ce):
>>     cell_coords = cdm.getVecClosure(csec, coords_gvec, i)
>>     print(f'coordinates for cell {i} :\n{cell_coords.reshape([-1, 3])}')
>>     cl = dm.getTransitiveClosure(i)
>>     print('closure:', cl)
>>     break
>> ```
>>
>> Best wishes,
>> Zongze
>>
>
>
> --
> 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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