[petsc-users] DMPlexSetRefinementFunction

David Fuentes fuentesdt at gmail.com
Tue Jan 8 11:29:34 CST 2019 

sounds great! i've been working out of this guy -
https://github.com/fuentesdt/thermoembo

and loading vtk data for the segmentation:
https://github.com/fuentesdt/thermoembo/blob/master/tutorials/exac.c#L50

I can clean this up and separate into relevant directories ? or start an
new repo? which ever you prefer.



On Tue, Jan 8, 2019 at 11:20 AM Matthew Knepley <knepley at gmail.com> wrote:

> 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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