[petsc-users] Mass matrix with PetscFE

[juan]

I attached another example which creates the correct mass matrix
but also overwrites the DM for the SNES solve. Somehow i cannot manage
to really copy the DM to dm_mass and use that. If i try to do that with
DMClone(dm, &dm_mass) i get a smaller mass matrix (which is not of size 
A).

Maybe this helps in the discussion.

Relevant code starts at line 455.

On 2016-02-24 15:03, Julian Andrej wrote:
> Thanks Matt,
> 
> I attached the modified example.
> 
> the corresponding code (and only changes to ex12) is starting at line 
> 832.
> 
> It also seems that the mass matrix is of size 169x169 and the
> stiffness matrix is of dimension 225x225. I'd assume that if i
> multiply test and trial function i'd get a matrix of same size (if the
> space/quadrature is the same for the stiffness matrix)
> 
> On 24.02.2016 14:56, Matthew Knepley wrote:
>> On Wed, Feb 24, 2016 at 7:47 AM, Julian Andrej <juan at tf.uni-kiel.de
>> <mailto: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 <tel:24.02.2016%2013>: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>
>>         <mailto: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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