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

[Stefano Zampini]

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
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