[petsc-users] DMPlex ghost cell indexing

[Mark Adams]

I think you want
https://petsc.org/main/docs/manualpages/DMPLEX/DMPlexConstructGhostCells

Mark


On Sat, Jul 2, 2022 at 6:20 PM Nicholas Arnold-Medabalimi <
narnoldm at umich.edu> wrote:

> Dear PETSc users,
>
> I have some general novice questions regarding how to properly access a
> distributed DMPLEX vector that has ghost cells for a finite volume use case.
>
> My process for setup
> 1) generated a simple box mesh using DMPlexCreateBoxMesh
> 2) distribute the mesh using DMPlexDistribute (at this point everything
> looks fine when I View (as paraview file) and I can see the partitions)
> 3) I generate a section with 5 variables located at the cells. (I don't
> think it matters if I use 5 fields or 1 field with 5 components?) I can
> alternatively do this using the PetscFV variable with 5 components.
> 4)  I then have the dm setup properly (with no ghost cells at this point)
> and I use DMCreateGlobalVector and DMCreateLocalVector to get the Vectors
> to work with
> 5) I'm just setting a quadratic IC. The overall loop over the cells is
> constructed via getting the cell stratum which has the Cell point list and
> then using the SectionOffset to assign each of the components at each cell
> using DMPlexComputeCellGeometryFVM to get the cell centroid.
>
> As far as I can tell this is an adequate solution but now I'm moving into
> learning how to access neighboring cells for flux calculations which isn't
> just the local cell but requires access to neighboring cells which at some
> point will be located on neighboring processors and synched to be
> accessible. When I did this for a DMDA it was pretty straightforward
> insofar as I just needed to call DMDAGetCorners and the LocalVector
> indexing would allow the stencil to extend gracefully into the ghost
> values.
>
> My general question is how do I achieve a similar loop structure for
> DMPlex as far as the indexing over the owned cells while being able to
> access the neighbor halo cells. I have been looking at example 52 and 11 in
> the ts tutorial examples but I'm struggling to extract exactly what I need.
>
> To boil it down into 3 starting questions
> 1) What is the preferred way to setup the cells and then access the
> internal cells for say N cell halos for the boundaries between processors
> in a DMPlex?
> 2) What is the distinction between the overlap argument in
> DMPlexDistribute and DMPlexConstructGhostCells (which I see used in the
> examples)? (at least based on my tests it seems GhostCells is generating
> cells at the overall boundaries not the internal partition boundaries?)
> 3) Once I do have a DMPlex object that has the appropriate halos, how
> would I get the access range for those cells? Based on my current
> assumption the Stratum range for the Cells would include the ghost cells as
> well which I would like to avoid? (Ultimately in the examples I see cases
> where there is the synch step for Local to Global and vice versa but I'm
> trying to just get to the point where I have the DM setup properly to
> handle the internal mesh boundaries and have the correct indexing from the
> StratumGet commands.)
>
> Any advice and corrections would be welcome.
>
> Sincerely
> Nicholas
>
> --
> Nicholas Arnold-Medabalimi
>
>
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