[petsc-users] PetscFE questions

[Matthew Knepley]

On Fri, Oct 21, 2016 at 2:26 AM, Julian Andrej <juan at tf.uni-kiel.de> wrote:

> On Thu, Oct 20, 2016 at 5:18 PM, Matthew Knepley <knepley at gmail.com>
> wrote:
> > On Thu, Oct 20, 2016 at 9:42 AM, Julian Andrej <juan at tf.uni-kiel.de>
> wrote:
> >>
> >> Thanks for the suggestion. I guess DMCreateSubDM can work, but is
> >> cumbersome to handle for the normal solution process since the mass
> >> matrix for example is not a seperate field.
> >
> >
> > I did not understand what you meant by "parts of the physics". If you
> just
> > want to make a different operator, then swap out the PetscDS from the DM.
> > That holds the pointwise functions and discretizations.
> >
>
> Yes, its basically a different operator! Thats a really smart design,
> i can just create different PetscDS objects and stick them in to
> assemble the operator.
>
>   /* Assemble mass operator */
>   DMSetDS(dm, ds_mass);
>   DMPlexSNESComputeJacobianFEM(dm, dummy, ctx->M, ctx->M, NULL);
>   /* Assemble laplacian operator */
>   DMSetDS(dm, ds_laplacian);
>   DMPlexSNESComputeJacobianFEM(dm, dummy, ctx->J, ctx->J, NULL);
>
> There is one thing that bothers me just a bit. Everytime you call
> DMSetDS the old PetscDS object is destroyed and you have to reacreate
> the object in case you want to reassemble that operator.
>
> src/dm/interface/dm.c:3889:  ierr = PetscDSDestroy(&dm->prob);
> CHKERRQ(ierr);
>
> Maybe it is just my specific use case but something to think about.


If you want to keep them around, you should do this

DMGetDS(dm, &oldds);
PetscObjectReference(oldds);
DMSetDS(dm, newds);
<do  stuff>
DMSetDS(dm, oldds);
PetscObjectDeferefence(oldds);

  Thanks,

     Matt


> >>
> >> src/snes/examples/tutorials/ex77 handles a seperate field for the
> >> nullspace, if anyone is interested in that.
> >>
> >> An intuitive way was just copying the DM and describing a new problem on
> >> it.
> >>
> >>   DM dm_mass;
> >>   PetscDS ds_mass;
> >>   Vec dummy;
> >>   PetscInt id = 1;
> >>   petsc_call(DMCreateGlobalVector(dm, &dummy));
> >>   petsc_call(DMClone(ctx->dm, &dm_mass));
> >>   petsc_call(DMGetDS(dm_mass, &ds_mass));
> >>   petsc_call(PetscDSSetDiscretization(ds_mass, 0, (PetscObject)fe));
> >>   petsc_call(PetscDSSetJacobian(ds_mass, 0, 0, mass_kernel, NULL, NULL,
> >> NULL));
> >>   petsc_call(PetscDSAddBoundary(ds_mass, PETSC_TRUE, "wall", "marker",
> >> 0, 0, NULL, (void (*)())ctx->exact_funcs[0], 1, &id, ctx));
> >>   petsc_call(DMCreateMatrix(dm_mass, &ctx->M));
> >>   petsc_call(DMPlexSNESComputeJacobianFEM(dm_mass, dummy, ctx->M,
> >> ctx->M, NULL));
> >>
> >> is this an intended way to assemble a jacobian based on a weak form?
> >> The memory overhead for a DM copy isn't huge on the first sight.
> >
> >
> > Its O(1).
> >
> >>
> >> And a much more important question. Is there any mathematical
> >> description how exactly you handle dirichlet boundary conditions here?
> >
> >
> > Right now, you can do two things:
> >
> >   1) Handle it yourself
> >
> > or
> >
> >   2) eliminate particular dofs
> >
> > If you use 2), these dofs are eliminated from the global vector. They
> remain
> > in the
> > local vector, and boundary values are inserted before local vectors are
> > passed to
> > assembly routines.
> >
> >    Matt
> >
>
> Thank you again for your help and suggestions.
>
> Regards
> Julian
>
> >>
> >> On first sight it looks like condensing the nodes only to
> >> non-essential nodes and then projecting them back in the solution
> >> vector. If thats teh case I don't understand how you "augment" the
> >> solution with the boundary nodes.
> >>
> >> Regards
> >> Julian
> >>
> >>
> >> On Wed, Oct 19, 2016 at 11:51 AM, Matthew Knepley <knepley at gmail.com>
> >> wrote:
> >> > On Tue, Oct 18, 2016 at 7:38 AM, Julian Andrej <juan at tf.uni-kiel.de>
> >> > wrote:
> >> >>
> >> >> Hi,
> >> >>
> >> >> i have general question about PetscFE. When i want to assemble
> certain
> >> >> parts of physics separately, how can i do that? I basically want to
> >> >> assemble matrices/vectors from the weak forms on the same DM (and
> >> >> avoid copying the DM) and use them afterwards. Is there a convenient
> >> >> way for doing that?
> >> >>
> >> >> The "workflow" i'm approaching is something like:
> >> >>
> >> >> - Setup the DM
> >> >> - Setup discretization (spaces and quadrature) for each weak form i
> >> >> want to compute
> >> >> - Compute just the weak form i want right now for a specific
> >> >> discretization and field.
> >> >>
> >> >> The reason is i need certain parts of the "complete" Jacobian for
> >> >> computations of eigenproblems and like to avoid computing those more
> >> >> often than needed.
> >> >
> >> >
> >> > The way I envision this working is to use DMCreateSubDM(). It should
> >> > extract
> >> > everything correctly for the subset of fields you select. However, I
> >> > have
> >> > not
> >> > extensively tested, so if something is wrong let me know.
> >> >
> >> >   Thanks,
> >> >
> >> >      Matt
> >> >
> >> >>
> >> >> Regards
> >> >> Julian
> >> >
> >> >
> >> >
> >> >
> >> > --
> >> > 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
> >
> >
> >
> >
> > --
> > 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
>



-- 
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
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