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

Mon Feb 22 06:09:12 CST 2021

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 <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 <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 <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 <mailto: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 <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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