[petsc-users] Including constrained dofs in a matrix/vector created with DMCreateXXXX()

[Matthew Knepley]

On Tue, Feb 19, 2019 at 1:13 AM Jordan Wagner via petsc-users <
petsc-users at mcs.anl.gov> wrote:

> Hi,
>
> Over the past few months, I have implemented dmplex/section in my
> preexisting finite element code. We already had our own implementations for
> things like the finite element space, boundary conditions, projections,
> etc, so I am mostly using dmplex/section at its lowest level; no DT/DS
> stuff for the moment. Everything is working fine at this level, and I am
> overall very happy with how it ties into the code that we already have.
>
> I am currently doing my own preallocation for the system Jacobian but am
> wanting to use DMCreateMatrix() instead, as it seems pointless to keep
> using my own crappy function when this one is just sitting there waiting.
> However, I dislike how I am currently implementing this and was hoping to
> get some suggestions or some advice. My problem is handling nicely the
> Dirichlet dofs. My code takes the approach of first assembling the entire
> Jacobian matrix and load vector as if no constraints are imposed. We then
> have a function that applies the essential conditions after assembly and
> extracts a submatrix and subvector similar to the way ex49
> <https://www.mcs.anl.gov/petsc/petsc-current/src/ksp/ksp/examples/tutorials/ex49.c.html>
> is doing.
>
> Since DMCreateMatrix() automatically partitions out the constraints
> specified in the section, I find myself having to create two nearly
> identical sections: one that has constraints and one that does not, and
> then I clone the DM and set the default section of each respectively. I can
> then use DMCreateMatrix() on the one dm/section with no constraints to
> preallocate the larger matrix that I am assembling. Then I use the
> dm/section with constraints to do all of my boundary condition and
> projection operations on the previously created matrix and vector.
> Essentially, I am using an unconstrained section only for allocation and a
> constrained section for most everything else.
>
> This process actually works fine for me, but its pretty ugly, and I am
> sure there is a better way. I am wondering if I am missing something that
> could keep me from having to go through this process of creating two
> sections that differ only in the constraints. It seems to me if there were
> an option for DMCreateMatrix()/DMCreateVector() to either include or not
> include the dofs, that would completely solve my problem. That way, I can
> use the same section for both creation and allocation.
>
> So, the main question I have is just whether there is a function or option
> that I am missing like DMCreateXXXX() but with the ability to retain the
> constrained rows and columns rather than compressing them out.
>
> I do not completely understand the above, but here is how Section works. A
_local_ Section contains all dofs and is intended for assembly using local
Vecs. To communicate with the solver, you make a _global_ Section using
PetscSectionCreateGlobalSection(). This has an option to include or exclude
constraints. For example, I make a global Section with constraints when I
output for visualization. Maybe you can use that to do what you want.

What I do not understand is why you do not just use a global Section
without constraints to assemble your matrix, rather than eliminating the
rows/columns later. The global Section gives back negative indices for
unknown that are constrained or not owned. These are ignored by
MatSetValues() and VecSetValues(). This is how the default Plex assembly
makes operators without constrained variables.

  Thanks,

     Matt

> Thanks a lot, as always.
>


-- 
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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