[petsc-users] dmplex extruded layers

[Matthew Knepley]

On Mon, Nov 22, 2021 at 12:10 PM Bhargav Subramanya <
bhargav.subramanya at kaust.edu.sa> wrote:

> Dear All,
>
> I have a prismatic mesh generated by extruding a base icosahedron
> spherical surface mesh. The mesh is distributed on 2 processes after
> extrusion. The dof for my problem are defined only on the simplices of the
> spherical layers.
>
> 1. For a given spherical layer, I want to get points, which are basically
> simplices, lying on that layer only. DMPlexGetHeightStratum returns the
> points on all the spherical Layers. I can probably use DMPlexFindVertices
> (based on the radius of the spherical layer) and
> DMPlexGetSimplexOrBoxCells. Could you suggest if there is a better way to
> retrieve the points (which are simplices) on a given spherical layer in the
> extruded mesh?
>

DMPlexGetHeightStratum() refers to height in the Hasse Diagram, which is a
DAG, not in the mesh. For example, height 0 points are the cells, height 1
are the faces, etc.

I believe the default numbering for extrusion (in the main branch), is that
all vertices produced from a given vertex be in order. This would mean that
if v were the vertex point number, then

  (v - vStart) % Nl == l

where Nl is the number of layers and l is the layer of that vertex. It is
also the same for triangles. So if you want to segregate each shell, after
extrusion, make a label that gives triangles this marker, and then use
DMPlexLabelComplete(). Then after refinement you will still have the shells
labeled correctly.

I would be happy to help you make an example that does this. It seems cool.


> 2. I am able to visualize the entire mesh using dm_view. Is there a way to
> get the mesh file for the local dm from a specific process?
>

You can use -dm_partition_view which outputs a field with the process
number. Then use Clip inside Paraview and clip to the process number you
want,
or just view that field so each process has a different color.


> 3. One of my previous emails might have got lost as I mistakenly attached
> a large mesh file and sent it. So I am repeating the question here.
> DMPlexExtrude gives the following error after distributing the base 2D
> spherical mesh. Both refinement or/and extrusion after dm distribution does
> not work for me. In fact, I tried with src/dm/impls/plex/tutorials/ex10.c
> also. Although the mesh is distributed after the extrusion in ex10.c (which
> is working fine for me), I tried to distribute before extrusion, and I get
> the following error. Could you please suggest where I might be making a
> mistake?
>

So you want to distribute the mesh before extruding. For that small example
(using the main branch), I run

  mpiexec -n 3 ./meshtest -dm_plex_shape sphere -dm_refine_pre 2
-dm_distribute -dm_partition_view -dm_view hdf5:mesh.h5 -dm_extrude 3

and I get the attached picture.

  Thanks,

    Matt


> [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [0]PETSC ERROR: Object is in wrong state
> [0]PETSC ERROR: This DMPlex is distributed but its PointSF has no graph set
> [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
> [0]PETSC ERROR: Petsc Release Version 3.16.1, unknown
> [0]PETSC ERROR: ./cavity_flow.out on a arch-darwin-c-debug named kl-21859
> by subrambm Mon Nov 22 19:47:14 2021
> [0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++
> --with-fc=gfortran --download-mpich --download-fblaslapack
> --download-superlu_dist --download-hypre --download-fiat
> --download-generator --download-triangle --download-tetgen --download-chaco
> --download-make -download-boost --download-cmake --download-ml
> --download-mumps=https://bitbucket.org/petsc/pkg-mumps.git
> --download-mumps-commit=v5.4.1-p1 --download-scalapack --download-ptscotch
> --download-hdf5 --force
> [0]PETSC ERROR: #1 DMPlexCheckPointSF() at
> /Users/subrambm/petsc/src/dm/impls/plex/plex.c:8554
> [0]PETSC ERROR: #2 DMPlexOrientInterface_Internal() at
> /Users/subrambm/petsc/src/dm/impls/plex/plexinterpolate.c:595
> [0]PETSC ERROR: #3 DMPlexInterpolate() at
> /Users/subrambm/petsc/src/dm/impls/plex/plexinterpolate.c:1357
> [0]PETSC ERROR: #4 DMPlexExtrude() at
> /Users/subrambm/petsc/src/dm/impls/plex/plexcreate.c:1543
> [0]PETSC ERROR: #5 CreateMesh() at ex10.c:161
> [0]PETSC ERROR: #6 main() at ex10.c:180
> [0]PETSC ERROR: PETSc Option Table entries:
> [0]PETSC ERROR: -dm_plex_extrude_layers 3
> [0]PETSC ERROR: -dm_view vtk:mesh.vtk
> [0]PETSC ERROR: -init_dm_plex_dim 2
> [0]PETSC ERROR: -petscpartitioner_type simple
> [0]PETSC ERROR: -srf_dm_distribute
> [0]PETSC ERROR: -srf_dm_refine 0
> [0]PETSC ERROR: ----------------End of Error Message -------send entire
> error message to petsc-maint at mcs.anl.gov----------
>
> Thanks,
> Bhargav
>
>
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-- 
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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