I looked deeper into the petsc codebase regarding HDF5. From what I understood (which of course can be wrong), the current version of petsc does not save edge degrees-of-freedom to HDF5? Is this something you plan to allow?
Otherwise I’m fine with using CGNS. But could you please explain how I could save timeseries that paraview recognizes using this format? Right now I’m saving files e.g. file0001.cgns, file0002.cgns, … where each .cgns file is written using VecView (i.e. it stores a discretized field). But paraview cannot load this as a timeseries. Also, do you have any documentation regarding node (vertex, edge, face, cell) numbering? E.g. how would a 10 node tetrahedral be numbered? From the documentation on your webpage (https://urldefense.us/v3/__https://petsc.org/release/manual/dmplex/__;!!G_uCfscf7eWS!YN1YSNd9hXq_llC7ZDmL9mgPHk9MSj5qzY_48p_GdnmxA7t1x_WN35JB-m5nhb7JF8vE9pBC4VWkpIwr2fYbQdjJUVd3h3-Pag$ ) it looks like cell dofs -> vertex dofs-> face dofs-> edge dofs. Is this correct? Thanks, Anna From: Matthew Knepley <knep...@gmail.com> Date: Thursday, 30 January 2025 at 00:39 To: Jed Brown <j...@jedbrown.org> Cc: Anna Dalklint <anna.dalkl...@solid.lth.se>, petsc-users@mcs.anl.gov <petsc-users@mcs.anl.gov> Subject: Re: [petsc-users] Visualizing higher order finite element output in ParaView That is all true. If you want lower level pieces to make it yourself, I have -dm_plex_high_order_view, which activates DMPlexCreateHighOrderSurrogate_Internal(). This is a simple function that refines the mesh lg(p) times to try and resolve the high order behavior. Thanks, Matt On Wed, Jan 29, 2025 at 4:55 PM Jed Brown <j...@jedbrown.org<mailto:j...@jedbrown.org>> wrote: I like the CGNS workflow for this, at least with quadratic and cubic elements. You can use options like -snes_view_solution cgns:solution.cgns (configure with --download-cgns). It can also monitor transient solves with flexible batch sizes (geometry and connectivity are stored only once within a batch of output frames). Anna Dalklint via petsc-users <petsc-users@mcs.anl.gov<mailto:petsc-users@mcs.anl.gov>> writes: > Hello, > > We have created a finite element code in PETSc for unstructured meshes using > DMPlex. The first order meshes are created in gmsh and loaded into PETSc. To > introduce higher order elements, e.g. 10 node tetrahedral elements, we start > from scratch using PetscSection and loop over the relevant points it the DM > to introduce additional degrees-of-freedom (example; for 10 node tets we have > 4 vertices “nodes” and 6 edge “nodes”). The coordinates of the new “nodes” > are obtained by interpolation using the finite element basis functions. > > The simulations seem to run well, but we face issues when trying to visualize > the results in ParaView. We have tried to use both CGNS and HDF5+XDMF file > formats for e.g. VecView. CGNS works, but the edge degrees-of-freedom appear > to not be interpolated correctly (we observe oscillations in the fields, > don’t know if this is a PETSc och ParaView issue). Also, we would prefer to > use another file format than CGNS since it does not appear to directly allow > timeseries (at least ParaView doesn’t recognize it). We haven’t got the > HDF5+XDMF file format to work at all when running on more than one core (the > mesh is highly distorted when saving using VecView and DMView + running the > “petsc_gen_xdmf.py” script on the .h5 output file). > > VTU format works but then only the vertices’ degrees-of-freedom are > visualized. As far as we have understood it, this is because VTU/VTK only > supports degrees-of-freedom on vertices/cell level. > > Does anyone have any idea of how to visualize fields generated from higher > order elements in ParaView? Or understand what we might be doing wrong? > > Best regards, > Anna -- 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!YN1YSNd9hXq_llC7ZDmL9mgPHk9MSj5qzY_48p_GdnmxA7t1x_WN35JB-m5nhb7JF8vE9pBC4VWkpIwr2fYbQdjJUVdLtH1U2A$ <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!YN1YSNd9hXq_llC7ZDmL9mgPHk9MSj5qzY_48p_GdnmxA7t1x_WN35JB-m5nhb7JF8vE9pBC4VWkpIwr2fYbQdjJUVdMGQragQ$ >
