[petsc-users] DMPlexSetRefinementFunction

David Fuentes fuentesdt at gmail.com
Sat Apr 13 05:07:49 CDT 2019 

this refinement seems to work pretty well for what I was looking for.
still testing... but tetgen seems to load these  background mesh files at
the higher resolution to guide the refinement?

$ tetgen -Vrmqk coarse.1.node
Opening coarse.1.node.
Opening coarse.1.ele.
Opening coarse.1.face.
Opening coarse.1.b.node.
Opening coarse.1.b.ele.
Opening coarse.1.b.mtr.
.
.

do you think a reasonable approach would be for me work with two meshes in
petsc? a coarse and fine mesh. and load a uniformly refined fine dmplex
mesh as the background mesh?

https://bitbucket.org/petsc/ctetgen/src/8ca66eb7de95b82f7969984bab6aacada6626b1d/ctetgen.c?at=master&fileviewer=file-view-default#ctetgen.c-22245

[image: Screen Shot 2019-04-13 at 4.50.06 AM.png]

On Tue, Jan 8, 2019 at 11:29 AM David Fuentes <fuentesdt at gmail.com> wrote:

> 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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