[petsc-users] DMPlexSetRefinementFunction

Mon Jan 7 15:27:25 CST 2019

ha! thanks for you time on this Matt. I'm trying to generate a mesh from
image segmentation data.
I would like to use an image segmentation to guide the refinement. Figure
25 of this paper - https://www.ices.utexas.edu/media/reports/2017/1707.pdf

On Mon, Jan 7, 2019 at 2:53 PM Matthew Knepley <knepley at gmail.com> wrote:

> On Mon, Jan 7, 2019 at 11:41 AM David Fuentes <fuentesdt at gmail.com> wrote:
>
>> thanks Matt,
>>
>> I posted a slightly modified example
>>
>> https://github.com/fuentesdt/dmplexrefinement/blob/master/ex45.c
>>
>> and changes from the orginal
>>
>> https://github.com/fuentesdt/dmplexrefinement/blob/master/refinement.diff
>>
>>
>> This is what I'm seeing
>>
>> https://github.com/fuentesdt/dmplexrefinement/blob/master/paraview.png
>>
>>
>> I'm refining based on this element centroid:
>>
>> https://github.com/fuentesdt/dmplexrefinement/blob/master/testcentroid.stl
>>
>> unrefined -
>> https://github.com/fuentesdt/dmplexrefinement/blob/master/unrefined.vtu
>>
>> refined -
>> https://github.com/fuentesdt/dmplexrefinement/blob/master/refined.vtu
>>
>>
>> Maybe I don't understand the refinement algorithm, but the refinement is
>> a little offset from what I was expecting.
>>
>
> Okay, I have that working. I will make a branch and put this in it. For
> right now, I attach ex45.c (but it will not run since I put in stuff to
> take lower/upper from the command line). 3D refinement just sucks, but you
> can see it is refining cell 7, not 8. Its just that refinement
> propagates a long, long way.
>
> I have pretty much abandoned this type of refinement since it will not
> work in parallel, and the mesh generator
> interface is poor. I am transitioning everything to
>
>   - uniform refinement (ha!)
>   - cell marking (p4est likes this)
>   - metric tensor (Pragmatic likes this)
>
> I have some routines to convert marking <--> metric but they are not
> perfect I think. I can try and help do what you want with
> AMR if I have a better idea what it is.
>
>   Thanks,
>
>     Matt
>
>
>>
>> Also, can you pass an application context to the user refinement function
>> ?
>>
>> https://github.com/fuentesdt/dmplexrefinement/blob/master/ex45.c#L119
>>
>>
>>
>> On Thu, Jan 3, 2019 at 7:49 AM Matthew Knepley <knepley at gmail.com> wrote:
>>
>>> On Wed, Jan 2, 2019 at 7:28 PM David Fuentes via petsc-users <
>>> petsc-users at mcs.anl.gov> wrote:
>>>
>>>> Hi,
>>>>
>>>> Starting with TS example 45
>>>>
>>>> $ pwd
>>>> /opt/apps/PETSc/petsc-3.10.2
>>>> $ ls src/ts/examples/tutorials/ex45.c
>>>> src/ts/examples/tutorials/ex45.c
>>>>
>>>> petsc configured with: ./config/configure.py --with-shared-libraries
>>>> --with-clanguage=c++ --CFLAGS='-g -O0' --CXXFLAGS='-g -O0'  --with-c2html=0
>>>> --download-ctetgen  --download-triangle --with-debugging=yes
>>>> --download-netcdf  --download-zlib  --download-exodusii --download-hdf5
>>>> --download-pnetcdf
>>>>
>>>> I'm trying to refine the DMPlexCreateBoxMesh  with the
>>>> DMPlexSetRefinementFunction.
>>>> It generally seems to be working, except that the refined element is
>>>> slightly offset from what I was expecting.
>>>> Based on my application specific criteria, element id number 7 is
>>>> flagged to be refined by the DMPlexSetRefinementFunction but when I open in
>>>> paraview, it looks like element id number 8 is being refined. See attached
>>>> pic.
>>>>
>>>> [image: Screen Shot 2019-01-02 at 6.02.02 PM.png]
>>>> [image: Screen Shot 2019-01-02 at 6.02.11 PM.png]
>>>>
>>>> Is it possible that the maxVolumes array is 'off by one' when
>>>> transfering to tetgen data structures somehow ?
>>>>
>>>
>>> I looked through and cannot see it by eye. Could you send me your
>>> modified example and I will walk through it with the
>>> debugger?
>>>
>>>   Thanks,
>>>
>>>      Matt
>>>
>>>
>>>>
>>>> https://bitbucket.org/petsc/petsc/src/bd27d3f284687498e4c4678d234c0e308a5bc236/src/dm/impls/plex/plexadapt.c?at=master&fileviewer=file-view-default#plexadapt.c-252
>>>>
>>>>
>>>>
>>>> (gdb) bt
>>>> #0  DMPlexRefine_CTetgen (dm=0x932180, maxVolumes=0x919710,
>>>> dmRefined=0x7fffffffb938) at
>>>> /opt/apps/PETSc/petsc-3.10.2/src/dm/impls/plex/generators/ctetgen/ctetgenerate.c:182
>>>> #1  0x00007ffff6b76401 in DMPlexRefine_Internal (dm=0x932180,
>>>> adaptLabel=0x0, dmRefined=0x7fffffffb938) at
>>>> /opt/apps/PETSc/petsc-3.10.2/src/dm/impls/plex/plexadapt.c:252
>>>> #2  0x00007ffff6b72720 in DMRefine_Plex (dm=0x932180, comm=0x6b,
>>>> dmRefined=0x7fffffffb938) at
>>>> /opt/apps/PETSc/petsc-3.10.2/src/dm/impls/plex/plexrefine.c:10361
>>>> #3  0x00007ffff6dad8ff in DMRefine (dm=0x932180, comm=0x6b,
>>>> dmf=0x7fffffffb938) at
>>>> /opt/apps/PETSc/petsc-3.10.2/src/dm/interface/dm.c:1808
>>>> #4  0x0000000000405274 in CreateMesh (comm=0x7ffff5891680
>>>> <ompi_mpi_comm_world>, dm=0x7fffffffb9d0, ctx=0x7fffffffba00) at
>>>> /rsrch1/ip/dtfuentes/github/thermoembo/tutorials/exac.c:253
>>>> #5  0x00000000004063c4 in main (argc=32, argv=0x7fffffffdb68) at
>>>> /rsrch1/ip/dtfuentes/github/thermoembo/tutorials/exac.c:336
>>>>
>>>>
>>>
>>> --
>>> 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://www.cse.buffalo.edu/~knepley/
>>> <http://www.cse.buffalo.edu/~knepley/>
>>>
>>
>
> --
> 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://www.cse.buffalo.edu/~knepley/
> <http://www.cse.buffalo.edu/~knepley/>
>
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