[petsc-users] Loading PETSC Grid

[Matthew Knepley]

On Wed, Jul 14, 2021 at 3:47 PM Alfredo J Duarte Gomez <aduarteg at utexas.edu>
wrote:

> Good morning,
>
> We are currently developing a PETSC application on a structured grid,
> however, we are applying a curvilinear transformation so that the physical
> domain is not a rectangle (the computational domain is).
>
> As a result we are trying to load in a mesh into the PETSC dmda object to
> create easy visualizations. I have successfully done this through the
> following code:
>
>
> ierr=VecCreateMPI(PETSC_COMM_WORLD,PETSC_DECIDE,6400,&co);CHKERRQ(ierr);
>      ierr=PetscObjectSetName((PetscObject) co,
> "coordinates");CHKERRQ(ierr);
>
> ierr=PetscViewerHDF5Open(PETSC_COMM_WORLD,"coord2d.h5",FILE_MODE_READ,&viewer);CHKERRQ(ierr);
>      ierr=VecLoad(co,viewer);CHKERRQ(ierr);
>      ierr=PetscViewerDestroy(&viewer);CHKERRQ(ierr);
>      ierr=DMSetCoordinates(da,co);CHKERRQ(ierr);
>
> Where my coordinate vector in HDF5 format is a single column vector in the
> order x1,y1,x2,y2,...xN,yN,etc. where 1 is the lower left corner and N.
> However this seems like a rather crude way of doing it, it seems like using
> the DMGetCoordinateDM() and DMCreateGlobalVector() is a more sophisticated
> way of leveraging the dmda object, however when I use:
>
> DMGetCoordinateDM(da, &cda);
> DMCreateGlobalVector(cda, &co);
> ierr=PetscObjectSetName((PetscObject) co, "coordinates");CHKERRQ(ierr);
>
> ierr=PetscViewerHDF5Open(PETSC_COMM_WORLD,"coord2d.h5",FILE_MODE_READ,&viewer);CHKERRQ(ierr);
> ierr=VecLoad(co,viewer);CHKERRQ(ierr);
> ierr=PetscViewerDestroy(&viewer);CHKERRQ(ierr);
> ierr=DMSetCoordinates(da,co);CHKERRQ(ierr);
>
> The loading function complains about the structure/format of my data. I
> haven't been able to find the format that this coordinate dmda expects from
> an HDF5 file in any of the documentation. Is there anywhere I could find
> this information?
>

Yes, I agree that it should work that way. You have to show me the
complaint, or a small example that I can run. Perhaps
it is the fact that the coordinate vector will have a block size (the
spatial dimension), which your HDF5 data may be missing.

  Thanks,

     Matt


> Thank you,
>
> -Alfredo
>
>
>
>
>
> --
> Alfredo Duarte
> Graduate Research Assistant
> The University of Texas at Austin
>


-- 
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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