[petsc-users] Mass matrix with PetscFE

Thu Jul 21 08:04:57 CDT 2016

On Mon, Mar 7, 2016 at 6:21 PM, Julian Andrej <juan at tf.uni-kiel.de> wrote:

> Any news about this? I've seen you merged the dmforest branch into next.

I am going through my mail, and see that this might have been dropped. Has
your
problem been solved?

  Sorry for the delay,

     Matt

>
> On 2016-02-26 01:22, Matthew Knepley wrote:
>
>> I am sorry about the delay. I have your example working but it exposed
>> a bug in Plex so I need to push the fix first. I should have
>> everything for you early next week.
>>
>>   Thanks
>>
>>      Matt
>>
>> On Feb 25, 2016 2:04 AM, "Julian Andrej" <juan at tf.uni-kiel.de> wrote:
>>
>> After a bit of rethinking the problem, the discrepancy between the
>>> size of matrix A and the mass matrix M arises because of the
>>> Dirichlet boundary conditions. So why aren't the BCs not imposed on
>>> the mass matrix? Do I need to handle Dirichlet BCs differently in
>>> this context (like zero rows and put one the diagonal?)
>>>
>>> On 24.02.2016 20 [1]:54, juan wrote:
>>> 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 [2]: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 [3] <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
>>>
>>
>>
>> Links:
>> ------
>> [1] tel:24.02.2016%2020
>> [2] tel:24.02.2016%2014
>> [3] tel:24.02.2016%2013
>>
>

-- 
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20160721/dc401004/attachment-0001.html>