[petsc-users] Mass matrix with PetscFE

[Matthew Knepley]

On Wed, Feb 24, 2016 at 7:47 AM, Julian Andrej <juan at tf.uni-kiel.de> wrote:

> I'm now using the petsc git master branch.
>
> I tried adding my code to the ex12
>
>   DM dm_mass;
>   PetscDS prob_mass;
>   PetscFE fe;
>   Mat M;
>   PetscFECreateDefault(dm, user.dim, 1, PETSC_TRUE, NULL, -1, &fe);
>
>   DMClone(dm, &dm_mass);
>   DMGetDS(dm_mass, &prob_mass);
>   PetscDSSetDiscretization(prob_mass, 0, (PetscObject) fe);
>   PetscDSSetJacobian(prob_mass, 0, 0, mass_kernel, NULL, NULL, NULL);
>   DMCreateMatrix(dm_mass, &M);
>
>   MatSetOptionsPrefix(M, "M_";)
>
> and receive the error on running
> ./exe -interpolate -refinement_limit 0.0125 -petscspace_order 2
> -M_mat_view binary
>
> WARNING! There are options you set that were not used!
> WARNING! could be spelling mistake, etc!
> Option left: name:-M_mat_view value: binary
>
> I don't know if the matrix is actually there and assembled or if the
> option is ommitted because something is wrong.
>

Its difficult to know when I cannot see the whole code. You can always
insert

  MatViewFromOptions(M, NULL, "-mat_view");


> Using
> MatView(M, PETSC_VIEWER_STDOUT_WORLD);
>
> gives me a reasonable output to stdout.
>

Good.


> But saving the matrix and analysing it in matlab, results in an all zero
> matrix.
>
> PetscViewerBinaryOpen(PETSC_COMM_WORLD, "Mout",FILE_MODE_WRITE, &viewer);
> MatView(M, viewer);
>

I cannot explain this, but it has to be something like you are viewing the
matrix before it is
actually assembled. Feel free to send the code. It sounds like it is mostly
working.

  Matt


> Any hints?
>
>
> On 24.02.2016 13:58, Matthew Knepley wrote:
>
>> On Wed, Feb 24, 2016 at 6:47 AM, Julian Andrej <juan at tf.uni-kiel.de
>> <mailto:juan at tf.uni-kiel.de>> wrote:
>>
>>     Hi,
>>
>>     i'm trying to assemble a mass matrix with the PetscFE/DMPlex
>>     interface. I found something in the examples of TAO
>>
>>
>> https://bitbucket.org/petsc/petsc/src/da8116b0e8d067e39fd79740a8a864b0fe207998/src/tao/examples/tutorials/ex3.c?at=master&fileviewer=file-view-default
>>
>>     but using the lines
>>
>>     DMClone(dm, &dm_mass);
>>     DMSetNumFields(dm_mass, 1);
>>     DMPlexCopyCoordinates(dm, dm_mass);
>>     DMGetDS(dm_mass, &prob_mass);
>>     PetscDSSetJacobian(prob_mass, 0, 0, mass_kernel, NULL, NULL, NULL);
>>     PetscDSSetDiscretization(prob_mass, 0, (PetscObject) fe);
>>     DMPlexSNESComputeJacobianFEM(dm_mass, u, M, M, NULL);
>>     DMCreateMatrix(dm_mass, &M);
>>
>>     leads to errors in DMPlexSNESComputeJacobianFEM (u is a global
>> vector).
>>
>>     I don't can understand the necessary commands until
>>     DMPlexSNESComputeJacobianFEM. What does it do and why is it
>>     necessary? (especially why does the naming involve SNES?)
>>
>>     Is there another/easier/better way to create a mass matrix (the
>>     inner product of the function space and the test space)?
>>
>>
>> 1) That example needs updating. First, look at SNES ex12 which is up to
>> date.
>>
>> 2) I assume you are using 3.6. If you use the development version, you
>> can remove DMPlexCopyCoordinates().
>>
>> 3) You need to create the matrix BEFORE calling the assembly
>>
>> 4) Always always always send the entire error messge
>>
>>    Matt
>>
>>     Regards
>>     Julian Andrej
>>
>>
>>
>>
>> --
>> 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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