Thank you once again, the code provides exactly what needed. An alternative for the VTK use was subdividing cells using corner nodes and integration points, such that all cells were first order. Any "better" alternative format/visualization software for this purpose?
Possibly the last question in relation to this matter. We use first order meshes only, as you suggest, and let PETSc handle everything high-order through the approximation space. Hence, when retrieving node coordinates with DMGetCoordinates(Local) or DMPlexGetCellCoordinates, one gets the corner nodes only. Is the list of additional, high-order nodes coordinates readily available (stored) somewhere to be retrieved? They can be computed (e.g. using DMPlexReferenceToCoordinates knowing their position in the reference cell; or using corner nodes coordinates), but this will result in shared nodes being computed possibly several times; the large the mesh, the worse. E.g. in the example of the image attached before, DMPlexGetClosureIndices returns [4, 5, 6, 0, 1, 3] for the first cell [7, 8, 5, 1, 2, 3] for the second cell so that 3 nodes (5, 1, 3) will be computed twice if done naively, cell by cell. Thank you, Noam On Thursday, June 19th, 2025 at 12:43 AM, Matthew Knepley <knep...@gmail.com> wrote: > On Wed, Jun 18, 2025 at 6:49 PM Noam T. <dontbugthed...@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!YswUx8vrAy00gLbhVHtR6nHAcUoAPFp5cyc5dEZ_bGmq7P3nb2BmpMlM28YywJBsvA4etxZNR_ARL3vqfTK42Cu61h7-Anfk$ > ) 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 <knep...@gmail.com> >> wrote: >> >>> On Tue, Jun 17, 2025 at 12:43 PM Noam T. <dontbugthed...@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 <knep...@gmail.com> >>>> wrote: >>>> >>>>> On Thu, Jun 12, 2025 at 4:26 PM Noam T. <dontbugthed...@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 >>>>>> <knep...@gmail.com> wrote: >>>>>> >>>>>>> On Thu, May 22, 2025 at 12:25 PM Noam T. <dontbugthed...@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/*(http:/*www.cse.buffalo.edu/*knepley/)__;fl0vfg!!G_uCfscf7eWS!YswUx8vrAy00gLbhVHtR6nHAcUoAPFp5cyc5dEZ_bGmq7P3nb2BmpMlM28YywJBsvA4etxZNR_ARL3vqfTK42Cu61uefq04u$ >>>>>>> >>>>> >>>>> -- >>>>> >>>>> 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/*(http:/*www.cse.buffalo.edu/*knepley/)__;fl0vfg!!G_uCfscf7eWS!YswUx8vrAy00gLbhVHtR6nHAcUoAPFp5cyc5dEZ_bGmq7P3nb2BmpMlM28YywJBsvA4etxZNR_ARL3vqfTK42Cu61uefq04u$ >>>>> >>> >>> -- >>> >>> 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/*(http:/*www.cse.buffalo.edu/*knepley/)__;fl0vfg!!G_uCfscf7eWS!YswUx8vrAy00gLbhVHtR6nHAcUoAPFp5cyc5dEZ_bGmq7P3nb2BmpMlM28YywJBsvA4etxZNR_ARL3vqfTK42Cu61uefq04u$ >>> > > -- > > 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/*(http:/*www.cse.buffalo.edu/*knepley/)__;fl0vfg!!G_uCfscf7eWS!YswUx8vrAy00gLbhVHtR6nHAcUoAPFp5cyc5dEZ_bGmq7P3nb2BmpMlM28YywJBsvA4etxZNR_ARL3vqfTK42Cu61uefq04u$ >
