[petsc-users] indices into Vec/Mat associated to a DMPlex

[Matthew Knepley]

On Wed, Nov 15, 2017 at 6:09 AM, Matteo Semplice <matteo.semplice at unito.it>
wrote:

> On 15/11/2017 11:39, Matthew Knepley wrote:
>
> On Wed, Nov 15, 2017 at 3:11 AM, Matteo Semplice <matteo.semplice at unito.it
> > wrote:
>
>> Hi.
>>
>> I am struggling with indices into matrices associated to a DMPLex mesh. I
>> can explain my problem to the following minimal example.
>>
>> Let's say I want to assemble the matrix to solve an equation (say
>> Laplace) with data attached to cells and the finite volume method. In
>> principle I
>>
>> - loop over the faces of the DMPlex (height=1)
>>
>> - for each face, find neighbouring cells (say points i and j in the
>> DMPlex) and compute the contributions coming from that face (in the example
>> it would be something like (u_j-u_i)*<x_j-x_i,n> with x=centroids, n=scaled
>> normal to face and <,> the inner product)
>>
>> - insert the contributions +/-<x_j-x_i,n> in rows/columns n(i) and n(j)
>> of the matrix where n(k) is the index into Vec/Mat of the unknown
>> associated to the k-th cell
>>
>> My problem is how to find out n(k). I assume that the Section should be
>> able to tell me, but I cannot find the correct function to call. I see that
>> FEM methods can use DMPlexMatSetClosure but here we'd need a
>> DMPlexMatSetCone...
>>
>
> Everything always reduces to raw Section calls. For instance, for cell c
>
>   PetscSectionGetDof(sec, c, &dof);
>   PetscSectionGetOffset(sec, c, &off);
>
> give the number of degrees of freedom on the cell, and the offset into
> storage (a local vector for the local section, and global vector for the
> global section).
> The Closure stuff just calls this for every point in the closure.
>
>
> All right, so the offset is also the (global) index and that is to be used
> in calls to MatSetValues.
>

Not quite. For all owned dofs, it is (in the global section). For all
unowned dofs, it is -(off+1), so you have
to convert it if you want to set off-process values.

  Thanks,

    Matt


> Thanks a lot!
>
>     Matteo
>



-- 
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.caam.rice.edu/~mk51/>
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