[petsc-users] Element connectivity of a DMPlex
Matthew Knepley
knepley at gmail.com
Wed Jun 18 19:43:14 CDT 2025
On Wed, Jun 18, 2025 at 6:49 PM Noam T. <dontbugthedevs at proton.me> wrote:
> See image attached.
> Connectivity of the top mesh (first order triangle), can be obtained with
> the code shared before.
> Connectivity of the bottom mesh (second order triangle) is what I would
> be interested in obtaining.
>
> However, given your clarification on what the Plex and the PetscSection
> handle, it might not work; I am trying to get form the Plex what's only
> available from the PetscSection.
>
> The purpose of this extended connectivity is plotting; in particular,
> using VTU files, where the "connectivity" of cells is required, and the
> extra nodes would be needed when using higher-order elements (e.g.
> VTK_QUADRATIC_TRIANGLE, VTK_QUADRATIC_QUAD, etc).
>
Oh yes. VTK does this in a particularly ugly and backward way. Sigh. There
is nothing we can do about this now, but someone should replace VTK with a
proper interface at some point.
So I understand why you want it and it is a defensible case, so here is how
you get that (with some explanation). Those locations, I think, should not
be understood as topological things, but rather as the locations of point
evaluation functionals constituting a basis for the dual space (to your
approximation space). I would call DMPlexGetClosureIndices() (
https://urldefense.us/v3/__https://petsc.org/main/manualpages/DMPlex/DMPlexGetClosureIndices/__;!!G_uCfscf7eWS!YK9T8_rEaNbJIndfx3tWHNlZlZ5GTj_KRDshR-nc5atZltZCcw73PtSNcrtvjWXZY73l5jQsAUx6qbM0Fge5$ ) with a
Section having the layout of P2 or Q2. This is the easy way to make that
PetscSection gs;
PetscFE fe;
DMPolytopeType ct;
PetscInt dim, cStart;
PetscCall(DMGetDimension(dm, &dim));
PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, NULL));
PetscCall(DMPlexGetCellType(dm, cStart, &ct));
PetscCall(PetscFECreateLagrangeByCell(PETSC_COMM_SELF, dim, 1, ct, 2,
PETSC_DETERMINE, &fe));
PetscCall(DMSetField(dm, 0, NULL, (PetscObject)fe));
PetscCall(PetscFEDestroy(&fe));
PetscCall(DMCreateDS(dm));
PetscCall(DMGetGlobalSection(dm, &gs));
PetscInt *indices = NULL;
PetscInt Nidx;
PetscCall(DMPlexGetClosureIndices(dm, gs, gs, cell, PETSC_TRUE, &Nidx,
&indices, NULL, NULL));
Thanks,
MAtt
> Perhaps I am over complicating things, and all this information can be
> obtained in a different, simpler way.
>
> Thanks.
> Noam
> On Tuesday, June 17th, 2025 at 5:42 PM, Matthew Knepley <knepley at gmail.com>
> wrote:
>
> On Tue, Jun 17, 2025 at 12:43 PM Noam T. <dontbugthedevs at proton.me> wrote:
>
>> Thank you. For now, I am dealing with vertices only.
>>
>> Perhaps I did not explain myself properly, or I misunderstood your
>> response.
>> What I meant to say is, given an element of order higher than one, the
>> connectivity matrix I obtain this way only contains as many entries as the
>> first order element: 3 for a triangle, 4 for a tetrahedron, etc.
>>
>> Looking at the closure of any cell in the mesh, this is also the
>> case.However, the nodes are definitely present; e.g. from
>>
>> DMPlexGetCellCoordinates(dm, cell, NULL, nc, NULL, NULL)
>>
>> nc returns the expected value (12 for a 2nd order 6-node planar triangle,
>> 30 for a 2nd order 10-node tetrahedron, etc).
>>
>> The question is, are the indices of these extra nodes obtainable in a
>> similar way as with the code shared before? So that one can have e.g. [0,
>> 1, 2, 3, 4, 5] for a second order triangle, not just [0, 1, 2].
>>
>
> I am having a hard time understanding what you are after. I think this is
> because many FEM approaches confuse topology with analysis.
>
> The Plex stores topology, and you can retrieve adjacencies between any two
> mesh points.
>
> The PetscSection maps mesh points (cells, faces, edges , vertices) to sets
> of dofs. This is how higher order elements are implemented. Thus, we do not
> have to change topology to get different function spaces.
>
> The intended interface is for you to call DMPlexVecGetClosure() to get the
> closure of a cell (or face, or edge). You can also call
> DMPlexGetClosureIndices(), but index wrangling is what I intended to
> eliminate.
>
> What exactly are you looking for here?
>
> Thanks,
>
> Matt
>
>> Thank you.
>> Noam
>> On Friday, June 13th, 2025 at 3:05 PM, Matthew Knepley <knepley at gmail.com>
>> wrote:
>>
>> On Thu, Jun 12, 2025 at 4:26 PM Noam T. <dontbugthedevs at proton.me> wrote:
>>
>>>
>>> Thank you for the code; it provides exactly what I was looking for.
>>>
>>> Following up on this matter, does this method not work for higher order
>>> elements? For example, using an 8-node quadrilateral, exporting to a
>>> PETSC_VIEWER_HDF5_VIZ viewer provides the correct matrix of node
>>> coordinates in geometry/vertices
>>>
>>
>> If you wanted to include edges/faces, you could do it. First, you would
>> need to decide how you would number things For example, would you number
>> all points contiguously, or separately number cells, vertices, faces and
>> edges. Second, you would check for faces/edges in the closure loop. Right
>> now, we only check for vertices.
>>
>> I would say that this is what convinced me not to do FEM this way.
>>
>> Thanks,
>>
>> Matt
>>
>>> (here a quadrilateral in [0, 10])
>>> 5.0, 5.0
>>> 0.0, 0.0
>>> 10.0, 0.0
>>> 10.0, 10.0
>>> 0.0, 10.0
>>> 5.0, 0.0
>>> 10.0, 5.0
>>> 5.0, 10.0
>>> 0.0, 5.0
>>>
>>> but the connectivity in viz/topology is
>>>
>>> 0 1 2 3
>>>
>>> which are likely the corner nodes of the initial, first-order element,
>>> before adding extra nodes for the higher degree element.
>>>
>>> This connectivity values [0, 1, 2, 3, ...] are always the same,
>>> including for other elements, whereas the coordinates are correct
>>>
>>> E.g. for 3rd order triangle in [0, 1], coordinates are given left to
>>> right, bottom to top
>>> 0, 0
>>> 1/3, 0,
>>> 2/3, 0,
>>> 1, 0
>>> 0, 1/3
>>> 1/3, 1/3
>>> 2/3, 1/3
>>> 0, 2/3,
>>> 1/3, 2/3
>>> 0, 1
>>>
>>> but the connectivity (viz/topology/cells) is [0, 1, 2].
>>>
>>> Test meshes were created with gmsh from the python API, using
>>> gmsh.option.setNumber("Mesh.ElementOrder", n), for n = 1, 2, 3, ...
>>>
>>> Thank you.
>>> Noam
>>> On Friday, May 23rd, 2025 at 12:56 AM, Matthew Knepley <
>>> knepley at gmail.com> wrote:
>>>
>>> On Thu, May 22, 2025 at 12:25 PM Noam T. <dontbugthedevs at proton.me>
>>> wrote:
>>>
>>>> Hello,
>>>>
>>>> Thank you the various options.
>>>>
>>>> Use case here would be obtaining the exact output generated by option
>>>> 1), DMView() with PETSC_VIEWER_HDF5_VIZ; in particular, the matrix
>>>> generated under /viz/topology/cells.
>>>>
>>>> There are several ways you might do this. It helps to know what you are
>>>> aiming for.
>>>>
>>>> 1) If you just want this output, it might be easier to just DMView()
>>>> with the PETSC_VIEWER_HDF5_VIZ format, since that just outputs the
>>>> cell-vertex topology and coordinates
>>>>
>>>>
>>>> Is it possible to get this information in memory, onto a Mat, Vec or
>>>> some other Int array object directly? it would be handy to have it in order
>>>> to manipulate it and/or save it to a different format/file. Saving to an
>>>> HDF5 and loading it again seems redundant.
>>>>
>>>>
>>>> 2) You can call DMPlexUninterpolate() to produce a mesh with just cells
>>>> and vertices, and output it in any format.
>>>>
>>>> 3) If you want it in memory, but still with global indices (I don't
>>>> understand this use case), then you can use DMPlexCreatePointNumbering()
>>>> for an overall global numbering, or DMPlexCreateCellNumbering() and
>>>> DMPlexCreateVertexNumbering() for separate global numberings.
>>>>
>>>>
>>>> Perhaps I missed it, but getting the connectivity matrix in
>>>> /viz/topology/cells/ did not seem directly trivial to me from the list of
>>>> global indices returned by DMPlexGetCell/Point/VertexNumbering() (i.e. I
>>>> assume all the operations done when calling DMView()).
>>>>
>>>
>>> Something like
>>>
>>> DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);
>>> DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);
>>> DMPlexGetVertexNumbering(dm, &globalVertexNumbers);
>>> ISGetIndices(globalVertexNumbers, &gv);
>>> for (PetscInt c = cStart; c < cEnd; ++c) {
>>> PetscInt *closure = NULL;
>>>
>>> DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &Ncl, &closure);
>>> for (PetscInt cl = 0; c < Ncl * 2; cl += 2) {
>>> if (closure[cl] < vStart || closure[cl] >= vEnd) continue;
>>> const PetscInt v = gv[closure[cl]] < 0 ? -(gv[closure[cl]] + 1) :
>>> gv[closure[cl]];
>>>
>>> // Do something with v
>>> }
>>> DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &Ncl, &closure);
>>> }
>>> ISRestoreIndices(globalVertexNumbers, &gv);
>>> ISDestroy(&globalVertexNumbers);
>>>
>>> Thanks,
>>>
>>> Matt
>>>
>>> Thanks,
>>>> Noam.
>>>>
>>>
>>>
>>> --
>>> 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://urldefense.us/v3/__https://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!YK9T8_rEaNbJIndfx3tWHNlZlZ5GTj_KRDshR-nc5atZltZCcw73PtSNcrtvjWXZY73l5jQsAUx6qcjKXTR_$
>>> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!YK9T8_rEaNbJIndfx3tWHNlZlZ5GTj_KRDshR-nc5atZltZCcw73PtSNcrtvjWXZY73l5jQsAUx6qWpg0hOI$ >
>>>
>>>
>>>
>>
>> --
>> 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://urldefense.us/v3/__https://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!YK9T8_rEaNbJIndfx3tWHNlZlZ5GTj_KRDshR-nc5atZltZCcw73PtSNcrtvjWXZY73l5jQsAUx6qcjKXTR_$
>> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!YK9T8_rEaNbJIndfx3tWHNlZlZ5GTj_KRDshR-nc5atZltZCcw73PtSNcrtvjWXZY73l5jQsAUx6qWpg0hOI$ >
>>
>>
>>
>
> --
> 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://urldefense.us/v3/__https://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!YK9T8_rEaNbJIndfx3tWHNlZlZ5GTj_KRDshR-nc5atZltZCcw73PtSNcrtvjWXZY73l5jQsAUx6qcjKXTR_$
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!YK9T8_rEaNbJIndfx3tWHNlZlZ5GTj_KRDshR-nc5atZltZCcw73PtSNcrtvjWXZY73l5jQsAUx6qWpg0hOI$ >
>
>
>
--
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://urldefense.us/v3/__https://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!YK9T8_rEaNbJIndfx3tWHNlZlZ5GTj_KRDshR-nc5atZltZCcw73PtSNcrtvjWXZY73l5jQsAUx6qcjKXTR_$ <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!YK9T8_rEaNbJIndfx3tWHNlZlZ5GTj_KRDshR-nc5atZltZCcw73PtSNcrtvjWXZY73l5jQsAUx6qWpg0hOI$ >
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20250618/9212f8d5/attachment-0001.html>
More information about the petsc-users
mailing list