[petsc-users] Mat indices for DMPlex jacobian

[Matteo Semplice]

On 23/09/2024 17:16, Matthew Knepley wrote:
> On Mon, Sep 23, 2024 at 5:33 AM Matteo Semplice via petsc-users 
> <petsc-users at mcs.anl.gov> wrote:
>
>     Dear petsc,
>
>          I need to hand-code a jacobian and I can't figure out how to
>     translate the DMplex points/fields to matrix indices.
>
>     My DMPlex has a section with m fields per cell (which makes for
>     n>m dof
>     per cell since some fields are vector). Say I want to insert an nxn
>     block for the row corresponding to cell c and coloumn of its
>     neighbour
>     d. I guess that I should call either
>     MatSetValues/MatSetValuesLocal or
>     the blocked variants, but how do I find the row/col indices to
>     pass in
>     starting from the c/d dmplex points? And, while I am at it, which
>     MatSetValues version standard/Local standard/blocked is best?
>
>     I looked for a petsc example, but fails to find it: if there's
>     one, can
>     you just point me to it?
>
>
> 1. In FEM, the main unit of indices is usually the closure, so we provide
>
> https://urldefense.us/v3/__https://petsc.org/main/manualpages/DMPlex/DMPlexGetClosureIndices/__;!!G_uCfscf7eWS!YwF8ebZtFAZdHXKPu98AWB7KPuScfxMu4dRoe8ZqVaPVoEO_nX_qJa-zS6pOWHnPUs2ME6GB7l_SlHBl8ypyOPOQXzbVSC9xXhd8tw$ 
>
> which is what is used inside of
>
> https://urldefense.us/v3/__https://petsc.org/main/manualpages/DMPlex/DMPlexMatSetClosure/__;!!G_uCfscf7eWS!YwF8ebZtFAZdHXKPu98AWB7KPuScfxMu4dRoe8ZqVaPVoEO_nX_qJa-zS6pOWHnPUs2ME6GB7l_SlHBl8ypyOPOQXzbVSC8i-x5AVA$ 
>
> 2. These indices are calculated using the global section, so you can just
>
>   DMGetGlobalSection(dm, &gs);
>
> and then use PetscSectionGetDof() and PetscSectionGetOffset(), knowing 
> that
> off-process values are encoded as -(off + 1), so you need to convert 
> those.
>
> Does this make sense?

Yes! Thank you!

Matteo
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