[petsc-users] Any examples to output a dmplex mesh as a hdf5 file?

[Fande Kong]

Hi Matt,

Is it possible to send me  some printed hdf5 and xdmf files (representing a
simple mesh)  that can be visualized by Paraview?  Similarly like that
printed by pylith. From these files I think I can figure out how to write a
hdf5 viewer by myself.

Sorry for bothering you.

Thanks,


On Wed, Jun 25, 2014 at 11:46 PM, Matthew Knepley <knepley at gmail.com> wrote:

> On Tue, Jun 24, 2014 at 7:50 AM, Fande Kong <fd.kong at siat.ac.cn> wrote:
>
>> Hi all,
>>
>> There are some functions called DMPlex_load_hdf5 and DMPlex_view_hdf5 in
>> petsc-dev.  They are really good functions for outputting the solution as a
>> hdf5 file in parallel. Are there any examples to show how  to use these
>> functions? Or are there some printed hdf5 and xdmf files that can be
>> visualized by paraview?
>>
>
> This is very new code. I plan to write a manual section as soon as the
> functionality solidifies. However, here is how I am currently using it.
> Anywhere that you think about viewing something add
>
>     ierr = PetscObjectViewFromOptions((PetscObject) obj, prefix,
> "-my_obj_view");CHKERRQ(ierr);
>
> Then you can use the standard option style
>
>   -my_obj_view hdf5:my.h5
>
> This extends nicely to many objects. Here is what I use for my magma
> dynamics output
>
>   -dm_view hdf5:sol_solver_debug.h5 -magma_view_solution
> hdf5:sol_solver_debug.h5::append -compaction_vec_view
> hdf5:sol_solver_debug.h5:HDF5_VIZ:append
>
> There is still a problem in that you cannot choose multiple formats using
> this method. I am going to extend
> the view options format
>
>   type:file:format:mode
>
> to allow
>
>   type:file:format,format,format:mode
>
> to handle this.
>
>   Thanks,
>
>       Matt
>
>
>> Thanks,
>>
>> Fande,
>>
>>
>>
>
>
> --
> 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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