[petsc-users] Get the vertices composing the cells of a DMPlex Submesh

Mon Feb 22 06:23:08 CST 2021

>From your output, it seems a triangle cell.

Reading  the documentation of DMPlexGetTransitiveClosure I have already
pointed you to: the output is interleaved between points (cell, edges and
vertices in this case) and their relative orientation wrt the point of
higher dimension.

Reading your output

0 0 -> cell number 0 (relative orientation is 0)

then the edges (all edges are points locally numbered from eStart to eEnd,
where DMPlexGetDepthStratum(dm,1,&eStart,&eEnd))

370 -2 369 -2 368 -2 -> cell 0 is made up by points 370, 369 and 368
(traversed in this specific order), and each edge must be traversed -2
(from second endpoint to first)

then the vertices (start and end of local per process numbering via
DMPlexGetDepthStratum(dm,0,&vStart,&vEnd))

309 0 306 0 312 0  -> vertices have no orientation.

Il giorno lun 22 feb 2021 alle ore 15:09 Fabien Vergnet <
fabien.vergnet at sorbonne-universite.fr> ha scritto:

> Hi Stefano,
>
> Thank you for your response.
>
> Could you explain more what the output of DMPlexGetTransitiveClosure is ?
> For example for cell 0 I get the following array of size 14 for the closure:
>
> 0 0 370 -2 369 -2 368 -2 309 0 306 0 312 0
>
> but I do not understand the order of the points (center of the cell,
> middle of the edges, vertices ?). Also what the orientation means for each
> point ?
>
> Regards,
> Fabien
>
> Le 22 févr. 2021 à 12:48, Stefano Zampini <stefano.zampini at gmail.com> a
> écrit :
>
> The plex way is to use the transitive closure
> https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/DMPLEX/DMPlexGetTransitiveClosure.html
>  and filter out points you are not interested in.
> See for example
> https://gitlab.com/petsc/petsc/-/blob/master/src/dm/impls/plex/plex.c#L828
>  and
> https://gitlab.com/petsc/petsc/-/blob/master/src/dm/impls/plex/plex.c#L833
>
> Il giorno lun 22 feb 2021 alle ore 14:28 Fabien Vergnet <
> fabien.vergnet at sorbonne-universite.fr> ha scritto:
>
>> Dear PETSc community,
>>
>> Thank you for your amazing work. I discovered PETSc recently and I need
>> your help for a project.
>>
>> As a training, I would like to assemble the Finite Element Matrix for the
>> Poisson problem on a part of my mesh. So, I create a DMPlex from a .msh
>> file and I create a Submesh with
>>
>> DMPlexCreateSubmesh(dm, label, 1, PETSC_TRUE, &subdm);
>>
>> In order to assemble my Finite Element Matrix, I need to iterate over the
>> cells of the mesh (which are triangles) and identify the vertices
>> composing each cell.
>>
>> My question is the following : how can I get, for each cell, the vertices
>> composing the cell ?
>>
>> I have tried to uninterpolate the subdm with DMPlexUninterpolate (with
>> the objective to get the vertices from DMPlexGetCone) but it does not
>> seem to work for a Submesh since I get the following error:
>>
>> ----------
>>
>> [0]PETSC ERROR: --------------------- Error Message
>> --------------------------------------------------------------
>> [0]PETSC ERROR: Invalid argument
>> [0]PETSC ERROR: Not for partially interpolated meshes
>> [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html for
>> trouble shooting.
>> [0]PETSC ERROR: Petsc Release Version 3.14.4, Feb 03, 2021
>> [0]PETSC ERROR: Configure options
>> --prefix=/users/home/vergnet/apps/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9.3.0/petsc-3.14.4-xtae5tcwlzkb4oiifbayj77bqlz5nngk
>> --with-ssl=0 --download-c2html=0 --download-sowing=0 --download-hwloc=0
>> CFLAGS= FFLAGS= CXXFLAGS=
>> --with-cc=/users/home/vergnet/apps/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9.3.0/openmpi-4.0.5-ygn7zymoy7crl7b4xsdkc4zmfojugmdy/bin/mpicc
>> --with-cxx=/users/home/vergnet/apps/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9.3.0/openmpi-4.0.5-ygn7zymoy7crl7b4xsdkc4zmfojugmdy/bin/mpic++
>> --with-fc=/users/home/vergnet/apps/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9.3.0/openmpi-4.0.5-ygn7zymoy7crl7b4xsdkc4zmfojugmdy/bin/mpif90
>> --with-precision=double --with-scalar-type=real --with-shared-libraries=1
>> --with-debugging=0 --with-64-bit-indices=0 COPTFLAGS= FOPTFLAGS=
>> CXXOPTFLAGS=
>> --with-blaslapack-lib=/users/home/vergnet/apps/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9.3.0/openblas-0.3.13-6b3u6zc5j4hvauqh3ldcwnf7lm2o4vyl/lib/libopenblas.so
>> --with-x=0 --with-clanguage=C --with-scalapack=0 --with-cuda=0
>> --with-metis=1
>> --with-metis-dir=/users/home/vergnet/apps/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9.3.0/metis-5.1.0-lm3k7dh2vslghqtqc6dvcpnc54bfpqq2
>> --with-hypre=1
>> --with-hypre-dir=/users/home/vergnet/apps/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9.3.0/hypre-2.20.0-4pyxhku65wb5lmh2fpflhmjmow2pbjg7
>> --with-parmetis=1
>> --with-parmetis-dir=/users/home/vergnet/apps/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9.3.0/parmetis-4.0.3-pfiam4ccxkyqpapejcdjtlyr6cyz7irc
>> --with-mumps=0 --with-trilinos=0 --with-fftw=0 --with-valgrind=0
>> --with-gmp=0 --with-libpng=0 --with-giflib=0 --with-mpfr=0 --with-netcdf=0
>> --with-pnetcdf=0 --with-moab=0 --with-random123=0 --with-exodusii=0
>> --with-cgns=0 --with-memkind=0 --with-p4est=0 --with-saws=0 --with-yaml=0
>> --with-libjpeg=0 --with-cxx-dialect=C++11
>> --with-superlu_dist-include=/users/home/vergnet/apps/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9.3.0/superlu-dist-6.4.0-bagymefhq7s7gerf7jxwiv4fv7szoljh/include
>> --with-superlu_dist-lib=/users/home/vergnet/apps/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9.3.0/superlu-dist-6.4.0-bagymefhq7s7gerf7jxwiv4fv7szoljh/lib/libsuperlu_dist.a
>> --with-superlu_dist=1 --with-suitesparse=0 --with-ptscotch=0
>> --with-hdf5-include=/users/home/vergnet/apps/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9.3.0/hdf5-1.10.7-dkfs4ir3hlahyfs5z4xcmsf4ogklimji/include
>> --with-hdf5-lib=/users/home/vergnet/apps/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9.3.0/hdf5-1.10.7-dkfs4ir3hlahyfs5z4xcmsf4ogklimji/lib/libhdf5.so
>> --with-hdf5=1
>> --with-zlib-include=/users/home/vergnet/apps/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9.3.0/zlib-1.2.11-2pwsgfxppopolmjj6tf34k5jsaqzpodo/include
>> --with-zlib-lib=/users/home/vergnet/apps/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-9.3.0/zlib-1.2.11-2pwsgfxppopolmjj6tf34k5jsaqzpodo/lib/libz.so
>> --with-zlib=1
>> [0]PETSC ERROR: #1 DMPlexUninterpolate() line 1514 in
>> /tmp/vergnet/spack-stage/spack-stage-petsc-3.14.4-xtae5tcwlzkb4oiifbayj77bqlz5nngk/spack-src/src/dm/impls/plex/plexinterpolate.c
>> [0]PETSC ERROR: #2 assemble_mass() line 59 in
>> /users/home/vergnet/codes/cilia/cilia/cpp/assembling.hpp
>>
>> ----------
>>
>> Attached are a minimal working example, a mesh file and a makefile.
>>
>> Any ideas or suggestions are more than welcome !
>>
>> Regards,
>> Fabien
>>
>>
>>
>>
>
> --
> Stefano
>
>
>

-- 
Stefano
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