[petsc-users] Outputting cell data in stead of point data while writing .vtr file

[Matthew Knepley]

On Thu, Mar 11, 2021 at 9:02 AM Smit Thijs <thijs.smit at hest.ethz.ch> wrote:

> Hi Matt,
>
>
>
> Oke, would a code change be difficult? I mean, feasible for me to do as a
> mechanical engineer? ;)
>

Sure. The hard part is determining what to do with a given vector. Here

  https://gitlab.com/petsc/petsc/-/blob/main/src/dm/impls/da/gr2.c#L677

you can see that we just save vectors until they are written out. You would
have to

  1) Enhance the DMCompatible() check to allow both cell and vertex meshes
here, and mark
      the cell vector somehow.

  2) Save that cell data mark when you save the vector

  3) Then when vectors are written here

    https://gitlab.com/petsc/petsc/-/blob/main/src/dm/impls/da/grvtk.c#L106

you have to add a <Cell data> section. I do not understand the structured
grid XML format, but I assume
you can look this up.

How does that sound?

  Thanks,

     Matt


> Or can I use an other version of PETSc where the output to ASCII VTK is
> still available?
>
>
>
> Best, Thijs
>
>
>
> *From:* Matthew Knepley <knepley at gmail.com>
> *Sent:* 11 March 2021 14:54
> *To:* Smit Thijs <thijs.smit at hest.ethz.ch>
> *Cc:* petsc-users at mcs.anl.gov
> *Subject:* Re: [petsc-users] Outputting cell data in stead of point data
> while writing .vtr file
>
>
>
> On Thu, Mar 11, 2021 at 8:17 AM Smit Thijs <thijs.smit at hest.ethz.ch>
> wrote:
>
> Hi Matt,
>
>
>
> Actually I have two 3D DMDA’s, one for the nodal data, where the FEM is
> solved on. The other DMDA is a cell centered one for the volume data, like
> the density of a particular voxel. Ideally I would like to write both point
> data (displacement field) and cell data (density) to the vtr.
>
>
>
> Code for DMDA.
>
>
>
>     DMBoundaryType bx = DM_BOUNDARY_NONE;
>
>     DMBoundaryType by = DM_BOUNDARY_NONE;
>
>     DMBoundaryType bz = DM_BOUNDARY_NONE;
>
>
>
>     DMDAStencilType stype = DMDA_STENCIL_BOX;
>
>
>
> PetscInt stencilwidth = 1;
>
>
>
>     // Create the nodal mesh
>
>     ierr = DMDACreate3d(PETSC_COMM_WORLD, bx, by, bz, stype, nx, ny, nz,
> PETSC_DECIDE, PETSC_DECIDE, PETSC_DECIDE,
>
>                         numnodaldof, stencilwidth, 0, 0, 0, &(da_nodes));
>
>     CHKERRQ(ierr);
>
>
>
>     DMSetFromOptions(da_nodes);
>
>     DMSetUp(da_nodes);
>
>
>
>     ierr = DMDASetUniformCoordinates(da_nodes, xmin, xmax, ymin, ymax,
> zmin, zmax);
>
>     CHKERRQ(ierr);
>
>
>
>     ierr = DMDASetElementType(da_nodes, DMDA_ELEMENT_Q1);
>
>     CHKERRQ(ierr);
>
>
>
> When I wrote the original version which output to ASCII VTK, we allowed
> switching between point data and cell data. It is
>
> fragile since you have to assure that the different grids match properly.
> When the viewer was rewritten to use the XML,
>
> all output was point data. It looks like it would take code changes to get
> this done.
>
>
>
>   Thanks,
>
>
>
>      Matt
>
>
>
> Best, Thijs
>
>
>
> *From:* Matthew Knepley <knepley at gmail.com>
> *Sent:* 11 March 2021 14:08
> *To:* Smit Thijs <thijs.smit at hest.ethz.ch>
> *Cc:* petsc-users at mcs.anl.gov
> *Subject:* Re: [petsc-users] Outputting cell data in stead of point data
> while writing .vtr file
>
>
>
> What kind of DM is it?
>
>
>
>   Thanks,
>
>
>
>      Matt
>
>
>
> On Thu, Mar 11, 2021 at 3:36 AM Smit Thijs <thijs.smit at hest.ethz.ch>
> wrote:
>
> Hi All,
>
>
>
> I am outputting several vectors to a .vtr file successfully for viewing in
> Paraview. At this moment the information is written to point data. How can
> I change this and make sure the data is written to cell data?
>
>
>
> The code I am currently using for outputting:
>
>
>
> PetscViewer viewer;
>
>
>
> ierr = PetscViewerVTKOpen(PETSC_COMM_WORLD, “test.vtr”, FILE_MODE_WRITE,
> &viewer);
>
> CHKERRQ(ierr);
>
>
>
> ierr = DMView(nd, viewer);
>
> CHKERRQ(ierr);
>
>
>
> PetscObjectSetName((PetscObject)xPhys,"xPhys");
>
> ierr = VecView(xPhys, viewer);
>
> CHKERRQ(ierr);
>
>
>
> PetscObjectSetName((PetscObject)S,"SvonMises");
>
> ierr = VecView(S, viewer);
>
> CHKERRQ(ierr);
>
>
>
> ierr = PetscViewerDestroy(&viewer);
>
> CHKERRQ(ierr);
>
>
>
> Best regards,
>
>
>
> Thijs Smit
>
>
>
> PhD Candidate
>
> ETH Zurich
>
> Institute for Biomechanics
>
>
>
>
>
>
> --
>
> 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/>
>
>
>
>
> --
>
> 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/>
>


-- 
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/>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20210311/0d1e6025/attachment.html>