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

[Matthew Knepley]

On Mon, Feb 22, 2021 at 6:28 AM Fabien Vergnet <
fabien.vergnet at sorbonne-universite.fr> wrote:

> 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);
>

I don't think you want this call. It is designed to pick out hypersurfaces.
If you just want part of a mesh, DMPlexFilter is better.


> 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.
>

The code does not seem to be attached.

As Stefano says, you can use DMPlexGetTransitiveClosure() to get vertices,
but if you actually want values attached to the
vertices, it is easier to use DMPlexVecGetClosure().

  Thanks,

     Matt


> Any ideas or suggestions are more than welcome !
>
> Regards,
> Fabien
>
>
>
>

-- 
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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