[petsc-users] DMPlexSetRefinementFunction

Matthew Knepley knepley at gmail.com
Sat Apr 13 06:25:08 CDT 2019 

On Sat, Apr 13, 2019 at 6:08 AM David Fuentes <fuentesdt at gmail.com> wrote:

> 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?
>

Okay, I finally understand what the background mesh does. It gives the mesh
sizing function.


> $ 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?
>

Sure, I can turn on that interface for you. I often have a few meshes in
the code.


> a coarse and fine mesh. and load a uniformly refined fine dmplex mesh as
> the background mesh?
>

This is the only thing I dod not understand. If the background mesh is
uniformly refined, can't you just
use a cell volume limit? Maybe I am missing something in the terminology.

   Matt



>
> 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/>
>>>
>>

-- 
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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