[petsc-users] interpolate HDF5 mesh

[Matthew Knepley]

On Thu, Dec 20, 2018 at 2:35 PM Yann JOBIC <yann.jobic at univ-amu.fr> wrote:

> Le 20/12/2018 à 19:05, Matthew Knepley a écrit :
>
> On Thu, Dec 20, 2018 at 12:56 PM Yann JOBIC <yann.jobic at univ-amu.fr>
> wrote:
>
>> Le 20/12/2018 à 16:40, Matthew Knepley a écrit :
>>
>> On Thu, Dec 20, 2018 at 9:33 AM Yann JOBIC via petsc-users <
>> petsc-users at mcs.anl.gov> wrote:
>>
>>> Dear Petsc Users,
>>>
>>> When i'm using DMPlexCreateBoxMesh, my code works fine. However, when i
>>> load the "exact" same mesh from an HDF5 file, it's not working anymore
>>> (Nonlinear solve did not converge due to DIVERGED_FNORM_NAN iterations
>>> 0).
>>>
>>> The mesh view when i use DMPlexCreateBoxMesh looks like (i labeled my
>>> boudary nodes):
>>>
>>> /* generated with DMPlexCreateBoxMesh */
>>> DM Object: Mesh 1 MPI processes
>>>    type: plex
>>> Mesh in 3 dimensions:
>>>    0-cells: 216
>>>    1-cells: 540
>>>    2-cells: 450
>>>    3-cells: 125
>>> Labels:
>>>    Faces: 6 strata with value/size (2 (121), 4 (121), 3 (121), 6 (121),
>>> 5 (121), 7 (121))
>>>    boundary: 1 strata with value/size (1 (602))
>>>    depth: 4 strata with value/size (0 (216), 1 (540), 2 (450), 3 (125))
>>>    Face Sets: 6 strata with value/size (6 (25), 5 (25), 3 (25), 4 (25),
>>> 1 (25), 2 (25))
>>>    marker: 1 strata with value/size (1 (450))
>>>
>>> And when i use DMPlexCreateFromFile, or DMLoad, i have :
>>>
>>> /* generated with H5 file */
>>> fin label DM
>>> DM Object: Mesh 1 MPI processes
>>>    type: plex
>>> Mesh in 3 dimensions:
>>>    0-cells: 216
>>>    1-cells: 540
>>>    2-cells: 450
>>>    3-cells: 125
>>> Labels:
>>>    Faces: 6 strata with value/size (2 (121), 4 (121), 6 (121), 7 (121),
>>> 5 (121), 3 (121))
>>>    boundary: 1 strata with value/size (1 (602))
>>>    depth: 4 strata with value/size (0 (216), 1 (540), 2 (450), 3 (125))
>>>
>>> It looks like my DM is not interpolated. Am i wrong ?
>>>
>>
>> Its interpolated (you have 4 kinds of k-cells, instead of 2). However,
>> you are missing your
>> Face Sets marker, which probably means boundary conditions are not
>> getting applied.
>>
>> My Face marker is label to 1, with the label  "boundary" (i used
>> DMPlexMarkBoundaryFaces)
>> After that, i create a new label, "Faces", with the number associated to
>> the boundary condition.
>> Faces = 0 -> ouest
>> Faces = 1 -> est
>> ...
>>
>> But you're right, I'm missing "Face Sets".
>>
>
> You are also missing "marker". Both of these are added by the mesh
> creation function. Do you know
> which one you are using (setting in a boundary condition)?
>
> I'm using DMPlexLoad_HDF5_Internal, which doesn't add those markers.
> I'm using the label "Faces", that i create, with has a different value
> defining the physical location of the boundary.
> Next, my using this label in order to define my boundary condition, as :
>   ierr = PetscDSAddBoundary(prob, DM_BC_ESSENTIAL, "wall", "Faces", 0,
> Ncomp, components, (void (*)(void)) zero, NInd, nord, NULL);CHKERRQ(ierr);
>   ierr = PetscDSAddBoundary(prob, DM_BC_ESSENTIAL, "wall", "Faces", 0,
> Ncomp, components, (void (*)(void)) zero, NInd, sud, NULL);CHKERRQ(ierr);
>   ierr = PetscDSAddBoundary(prob, DM_BC_ESSENTIAL, "wall", "Faces", 0,
> Ncomp, components, (void (*)(void)) zero, NInd, Back, NULL);CHKERRQ(ierr);
>   ierr = PetscDSAddBoundary(prob, DM_BC_ESSENTIAL, "wall", "Faces", 0,
> Ncomp, components, (void (*)(void)) zero, NInd, Top, NULL);CHKERRQ(ierr);
>   ierr = PetscDSAddBoundary(prob, DM_BC_ESSENTIAL, "in", "Faces", 0,
> Ncomp, components, (void (*)(void)) uIn, NInd, west, NULL);CHKERRQ(ierr);
> With:
>   const PetscInt Ncomp = 3; /*  dim = 3 */
>   const PetscInt components[] = {0,1,2};
>   const PetscInt NInd = 1;
>   const PetscInt west[] = {2}; /* (x=0) */
>   const PetscInt est[] = {3}; /* (x=L_x) */
>   const PetscInt sud[] = {4}; /* (y=0) */
>   const PetscInt nord[] = {5}; /* (y=L_y) */
>   const PetscInt Back[] = {6}; /* (z=0) */
>   const PetscInt Top[] = {7}; /* (z=L_z) */
>
> Is it the right way to do it ?
>

It looks right.


> Should i have a different label for each boundary condition ? I thought
> that the value was enough.
>

The next thing to do is compare residuals.

   Matt


> Thanks,
>
> Yann
>
>
>   Thanks,
>
>     Matt
>
>
>> I couldn't find the function which adds this label.
>> Is there one ? or do i have to do as in  DMPlexCreateCubeMesh_Internal?
>>
>> Thanks,
>>
>> Yann
>>
>>   Thanks,
>>
>>     Matt
>>
>>
>>> It's strange, because when i use DMPlexCreateFromFile, i put PETSC_TRUE
>>> for interpolation.
>>>
>>> Even after loading the mesh, i used DMPlexInterpolate, which return a
>>> new DM (not null).
>>>
>>> Do you know what's happening here ?
>>> Maybe my DIVERGED_FNORM_NAN comes from another part of the code ?
>>> (however only the mesh is changing)
>>>
>>> Thanks,
>>>
>>> Yann
>>>
>>
>

-- 
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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