[petsc-users] interpolate HDF5 mesh

[Yann JOBIC]

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

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
>>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20181220/88d49d44/attachment-0001.html>