[petsc-users] DMPlex export to hdf5/vtk for triangle/prism mesh

[Fabian Jakub]

Hi,

I did just as Matt suggested which works nicely... thanks by the way!

Inserted in the petsc_gen_xdmf.py the "6: 'Wedge' " entry .

Calling the example with:

<example_program> -show_plex hdf5:output.h5 -show_vector 
hdf5:output.h5::append

exports the mesh and a vector to hdf5.

Then calling

$PETSC_DIR/bin/petsc_gen_xdmf.py output.h5

correctly creates the descriptor file and just loads to visit.


Many thanks again to you, Matt :)


Fab


On 30.05.2017 00:13, Adrian Croucher wrote:
> hi,
>
> I was asking about support for exactly these 6-node wedge elements in 
> DMPlex back in January.
>
> At the time, there was no support for them. Has there been some 
> progress since then?
>
> We are going to need them before we can release our software, which 
> we're aiming to do by the end of the year.
>
> Cheers, Adrian
>
>> Message: 4
>> Date: Fri, 26 May 2017 22:40:40 -0500
>> From: Matthew Knepley <knepley at gmail.com>
>> To: "Fabian.Jakub" <Fabian.Jakub at physik.uni-muenchen.de>
>> Cc: PETSc <petsc-users at mcs.anl.gov>
>> Subject: Re: [petsc-users] DMPlex export to hdf5/vtk for
>>     triangle/prism mesh
>> Message-ID:
>>     <CAMYG4GkVOTtFL_OBpUBPGEcBTikMbLOb5ruz=VU7tVTO6JQHTQ at mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> On Fri, May 26, 2017 at 12:27 PM, Fabian.Jakub <
>> Fabian.Jakub at physik.uni-muenchen.de> 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
>> >
>>
>