Message: 4
Date: Fri, 26 May 2017 22:40:40 -0500
From: Matthew Knepley <[email protected]>
To: "Fabian.Jakub" <[email protected]>
Cc: PETSc <[email protected]>
Subject: Re: [petsc-users] DMPlex export to hdf5/vtk for
triangle/prism mesh
Message-ID:
<CAMYG4GkVOTtFL_OBpUBPGEcBTikMbLOb5ruz=vu7tvto6jq...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
On Fri, May 26, 2017 at 12:27 PM, Fabian.Jakub <
[email protected]> wrote:
> Dear Petsc Team,
>
> I am playing around with DMPlex, using it to generate the Mesh for the
> ICON weather model(http://doi.org/10.1002/2015MS000431), which
employs a
> triangle mesh horizontally and columns, vertically.
>
> This results in a grid, looking like prisms, where top and bottom
faces
> are triangles and side faces are rectangles.
>
> I was delighted to see that I could export the triangle DMPlex (2d
Mesh)
> to hdf5 and use petsc_gen_xdmf.py to then visualize the mesh in
> visit/paraview.
> This is especially nice when exporting petscsections/vectors
directly to
> VTK.
>
Great.
> I then tried the same approach for the prism grid in 3D.
> I attached the code for one single cell, as well as the output in
hdf5.
>
> However, trying to convert the hdf5 output, it fails with:
>
> make prism.xmf
>
> $PETSC_DIR/bin/petsc_gen_xdmf.py prism.h5
> Traceback (most recent call last):
> File
> "/software/meteo/xenial/x86_64/petsc/master/debug_gcc/..//
> bin/petsc_gen_xdmf.py",
> line 241, in <module>
> generateXdmf(f)
> File
> "/software/meteo/xenial/x86_64/petsc/master/debug_gcc/..//
> bin/petsc_gen_xdmf.py",
> line 235, in generateXdmf
> Xdmf(xdmfFilename).write(hdfFilename, topoPath, numCells,
> numCorners, cellDim, geomPath, numVertices, spaceDim, time, vfields,
> cfields)
> File
> "/software/meteo/xenial/x86_64/petsc/master/debug_gcc/..//
> bin/petsc_gen_xdmf.py",
> line 193, in write
> self.writeSpaceGridHeader(fp, numCells, numCorners, cellDim,
spaceDim)
> File
> "/software/meteo/xenial/x86_64/petsc/master/debug_gcc/..//
> bin/petsc_gen_xdmf.py",
> line 75, in writeSpaceGridHeader
> ''' % (self.cellMap[cellDim][numCorners], numCells, "XYZ" if
> spaceDim > 2 else "XY"))
> KeyError: 6
>
>
> Also, if I try to export a vector directly to vtk, visit and paraview
> fail to open it.
>
> My question is:
> Is this a general limitation of these output formats, that I can
not mix
> faces with 3 and 4 vertices or is it a limitation of the
> petsc_gen_xdmf.py or the VTK Viewer.
>
petsc_gen_xdmf. Take a look here
https://bitbucket.org/petsc/petsc/src/1731673c3fe570066779d46b51a4aee7a45775ed/bin/petsc_gen_xdmf.py?at=master&fileviewer=file-view-default#petsc_gen_xdmf.py-9
This is what fails. You need to add something like
6: "Wedge"
in the dictionary. See
http://www.xdmf.org/index.php/XDMF_Model_and_Format
> I'd also welcome any thoughts on the prism mesh in general.
> Is it that uncommon to use and do you foresee other complications
with it?
>
You need an element that works with prisms, but it seems you already
have
one. I know
there is good work from here: https://arxiv.org/abs/1411.2940
> I fear I cannot change the discretization of the host model but
maybe it
> makes sense to use a different grid for my radiative transfer code?
>
I do not really do RT, but would be happy to try and think about it.
Thanks,
Matt
> Many thanks,
>
>
> Fabian
>
