[petsc-users] Visualizing higher order finite element output in ParaView

[Sanjay Govindjee]

We do exactly this by using the same prefix for each file and bump the 
number with each load step, then paraview does the stacking 
automagically for us.  However we write out VTU files for our FEA 
computations.

Perhaps you could examine some of the other formats that paraview can 
read and see if they do the trick.

-sanjay

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On 1/30/25 11:59 PM, Anna Dalklint via petsc-users wrote:
>
> I want to save e.g. the discretized displacement field obtained from a 
> quasi-static non-linear finite element simulation using 10 node 
> tetrahedral elements (i.e. which has edge dofs). As mentioned, I use 
> PetscSection to add the additional dofs on edges. I have also written 
> my own Newton solver, i.e. I do not use SNES. In conclusion, what I 
> want is to be able to save the discretized displacement field in each 
> outer iteration of the Newton loop (where I increase the pseudo-time, 
> i.e. scaling of the load). I would then preferably be able to load a 
> stack of these files (call them u001, u002, u003… for each 
> “load-step”) and step in “time” in ParaView.
>
> Thanks,
>
> Anna
>
> *From: *Matthew Knepley <knepley at gmail.com>
> *Date: *Thursday, 30 January 2025 at 16:19
> *To: *Anna Dalklint <anna.dalklint at solid.lth.se>
> *Cc: *Jed Brown <jed at jedbrown.org>, petsc-users at mcs.anl.gov 
> <petsc-users at mcs.anl.gov>
> *Subject: *Re: [petsc-users] Visualizing higher order finite element 
> output in ParaView
>
> On Thu, Jan 30, 2025 at 9:43 AM Anna Dalklint 
> <anna.dalklint at solid.lth.se> wrote:
>
>     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?
>
> We write two different outputs (by default). One has all the data, 
> and one has only cell and vertex data because Paraview does not 
> understand anything else. This can be customized with options. What do 
> you want to save?
>
>     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.
>
> Jed can explain how this works.
>
>     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!a4sytQFaGerzzN_lTE_veovAiiD5PEbkkSsBQtmJVRaCNlwnj_8aLFmgbxiIUYOHqbF1vxAkTv9vYSz9cFks3w$ 
>     <https://urldefense.us/v3/__https://petsc.org/release/manual/dmplex/__;!!G_uCfscf7eWS!frd8lJGukGrnZYqiJQyrOszbkCacSP2EftDVAAiYClDx1Ll0dEd7q8th5yDSI1bJgVmvCAGtgrNVnkfcw0i47jUVzWH0vcxIcg$>)
>     it looks like cell dofs -> vertex dofs-> face dofs-> edge dofs. Is
>     this correct?
>
> When you call DMPlexVecGetClosure(), the closure follows the point 
> numbering, in that for each point, we lookup the dofs in the local 
> Section, and push them into the array in order. So then you need the 
> point ordering. For the closure, it goes by dimension, so cell dofs, 
> face dofs, edge dofs, vertex dofs. You can see the definition of faces 
> (and edges) here:
>
> https://urldefense.us/v3/__https://gitlab.com/petsc/petsc/-/blob/main/src/dm/impls/plex/plexinterpolate.c?ref_type=heads*L196__;Iw!!G_uCfscf7eWS!a4sytQFaGerzzN_lTE_veovAiiD5PEbkkSsBQtmJVRaCNlwnj_8aLFmgbxiIUYOHqbF1vxAkTv9vYSwPYMmhlg$  
> <https://urldefense.us/v3/__https://gitlab.com/petsc/petsc/-/blob/main/src/dm/impls/plex/plexinterpolate.c?ref_type=heads*L196__;Iw!!G_uCfscf7eWS!frd8lJGukGrnZYqiJQyrOszbkCacSP2EftDVAAiYClDx1Ll0dEd7q8th5yDSI1bJgVmvCAGtgrNVnkfcw0i47jUVzWFlsiC2ww$>
>
> and triangles are ordered here
>
> https://urldefense.us/v3/__https://gitlab.com/petsc/petsc/-/blob/main/src/dm/impls/plex/plexinterpolate.c?ref_type=heads*L115__;Iw!!G_uCfscf7eWS!a4sytQFaGerzzN_lTE_veovAiiD5PEbkkSsBQtmJVRaCNlwnj_8aLFmgbxiIUYOHqbF1vxAkTv9vYSwzO7AdZg$  
> <https://urldefense.us/v3/__https://gitlab.com/petsc/petsc/-/blob/main/src/dm/impls/plex/plexinterpolate.c?ref_type=heads*L115__;Iw!!G_uCfscf7eWS!frd8lJGukGrnZYqiJQyrOszbkCacSP2EftDVAAiYClDx1Ll0dEd7q8th5yDSI1bJgVmvCAGtgrNVnkfcw0i47jUVzWFvuUov2w$>
>
> The idea is that DMPlexVecGetClosure() delivers the dofs in a standard 
> order on the element, so that you can write
>
> your residual function once. Also, for multiple fields, they are 
> stacked contiguously, so the numbering is [field, point, dof on point].
>
> Let me know if that does not make sense.
>
>   Thanks,
>
>      Matt
>
>     Thanks,
>
>     Anna
>
>     *From: *Matthew Knepley <knepley at gmail.com>
>     *Date: *Thursday, 30 January 2025 at 00:39
>     *To: *Jed Brown <jed at jedbrown.org>
>     *Cc: *Anna Dalklint <anna.dalklint at solid.lth.se>,
>     petsc-users at mcs.anl.gov<petsc-users at 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 <jed at 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 at 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!a4sytQFaGerzzN_lTE_veovAiiD5PEbkkSsBQtmJVRaCNlwnj_8aLFmgbxiIUYOHqbF1vxAkTv9vYSx-ftOXcA$ 
>     <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!frd8lJGukGrnZYqiJQyrOszbkCacSP2EftDVAAiYClDx1Ll0dEd7q8th5yDSI1bJgVmvCAGtgrNVnkfcw0i47jUVzWH7uFxLgw$>
>
>
> -- 
>
> What most experimenters take for granted before they begin their 
> experiments is infinitely more interesting than any results to which 
> their experiments lead.
> -- Norbert Wiener
>
> https://urldefense.us/v3/__https://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!a4sytQFaGerzzN_lTE_veovAiiD5PEbkkSsBQtmJVRaCNlwnj_8aLFmgbxiIUYOHqbF1vxAkTv9vYSx-ftOXcA$  
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!frd8lJGukGrnZYqiJQyrOszbkCacSP2EftDVAAiYClDx1Ll0dEd7q8th5yDSI1bJgVmvCAGtgrNVnkfcw0i47jUVzWH7uFxLgw$>
>
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