[petsc-users] DMPlexSetRefinementFunction

Matthew Knepley knepley at gmail.com
Tue Jan 8 11:19:58 CST 2019 

On Mon, Jan 7, 2019 at 4:27 PM David Fuentes <fuentesdt at gmail.com> wrote:

> 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
>

Very cool. We can do that. Lets make an example and iterate. Want to make a
repo you control? I will
stick in a PETSc example that refines meshes (maybe Plex ex19), and we can
experiment with both p4est
and Pragmatic (installation of those is hardest part :) This sounds great.

   Matt


> 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/>
>>
>

-- 
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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