[petsc-users] DMPlexSetRefinementFunction
David Fuentes
fuentesdt at gmail.com
Sat Apr 13 10:11:03 CDT 2019
that seems to be what's happening. I wrote a script to load a sizing
function from an image and two meshes into tetgen. then output an exodus
file to load into dmplex.
https://github.com/fuentesdt/thermoembo/blob/master/tutorials/phasemesh.py#L105
On Sat, Apr 13, 2019 at 9:27 AM Matthew Knepley <knepley at gmail.com> wrote:
> On Sat, Apr 13, 2019 at 9:29 AM David Fuentes <fuentesdt at gmail.com> wrote:
>
>> using this mesh sizing function defined on nodes of the background mesh
>> was the only way I could get it to work.
>>
>
> Okay, let me understand this. So you could specify a sizing function on
> the current mesh. However, TetGen only
> does 1 pass, so that gradiation might not be smooth enough. Thus you
> specify the sizing function on a refined
> background mesh, and get smoother gradiation.
>
> Okay, I can make that work. I have to turn on a bunch of things in CTetGen
> that were inactive.
>
> There is an alternative to this. Since you know the sizing function, you
> could use Pragmatic instead. The install is
> much much harder, but it does work, and works in parallel, and can do
> anisotropic refinement as well.
>
> Thanks,
>
> Matt
>
>
>
> http://wias-berlin.de/software/tetgen/1.5/doc/manual/manual006.html#ff_mtr
>>
>> On Sat, Apr 13, 2019 at 6:25 AM Matthew Knepley <knepley at gmail.com>
>> wrote:
>>
>>> 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/>
>>>
>>
>
> --
> 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/>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20190413/5a9b7269/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screen Shot 2019-04-13 at 4.50.06 AM.png
Type: image/png
Size: 84446 bytes
Desc: not available
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20190413/5a9b7269/attachment-0001.png>
More information about the petsc-users
mailing list