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
-------------------------------------------------------------------
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 <knep...@gmail.com>
*Date: *Thursday, 30 January 2025 at 16:19
*To: *Anna Dalklint <anna.dalkl...@solid.lth.se>
*Cc: *Jed Brown <j...@jedbrown.org>, petsc-users@mcs.anl.gov
<petsc-users@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.dalkl...@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 <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> 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> 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$>
