[petsc-users] DMGetCoordinatesLocal and DMPlexGetCellCoordinates in PETSc > 3.18
Matthew Knepley
knepley at gmail.com
Mon May 22 05:10:08 CDT 2023
On Mon, May 22, 2023 at 4:41 AM Berend van Wachem <berend.vanwachem at ovgu.de>
wrote:
> Dear Matt,
>
> I'm really sorry for this stupid bug!
>
No problem. You have really helped me get the bugs out of Plex.
Thanks,
Matt
> I can confirm that setting the coordinates with both
> CellCoordinatesLocal and CoordinatesLocal works.
>
> Best regards, Berend.
>
> Many thanks and best regards, Berend.
>
> On 5/17/23 23:04, Matthew Knepley wrote:
> > On Wed, May 17, 2023 at 2:01 PM Berend van Wachem
> > <berend.vanwachem at ovgu.de <mailto:berend.vanwachem at ovgu.de>> wrote:
> >
> > Dear Matt,
> >
> > I tried it, but it doesn't seem to work.
> > Attached is a very small working example illustrating the problem.
> > I create a DMPlexBox Mesh, periodic in the Y direction. I then scale
> > the Y coordinates with a factor 10, and add 1.0 to it. Both
> > DMGetCoordinatesLocal and DMGetCellCoordinatesLocal.
> > Then I evaluate the coordinates with DMPlexGetCellCoordinates. Most
> > of the Y coordinates are correct, but not all of them - for
> > instance, the minimum Y coordinate is 0.0, and this should be 1.0.
> >
> > Am I doing something wrong?
> >
> >
> > Quickly, I see that
> >
> > a *= 10.0 + 1.0;
> >
> > is the same as
> >
> > a *= 11.0;
> >
> > not multiply by 10 and add 1. I will send it back when I get everything
> > the way I want.
> >
> > Thanks,
> >
> > Matt
> >
> > Thanks and best regards,
> >
> > Berend.
> >
> > On 5/17/23 17:58, Matthew Knepley wrote:
> > > On Wed, May 17, 2023 at 11:20 AM Berend van Wachem
> > <berend.vanwachem at ovgu.de <mailto:berend.vanwachem at ovgu.de>
> > <mailto:berend.vanwachem at ovgu.de <mailto:berend.vanwachem at ovgu.de>>>
> > wrote:
> > >
> > > Dear Matt,
> > >
> > > Is there a way to 'redo' the DMLocalizeCoordinates() ? Or to
> > undo it?
> > > Alternatively, can we make the calling of
> > DMLocalizeCoordinates() in the DMPlexCreate...() routines optional?
> > >
> > > Otherwise, we would have to copy all arrays of coordinates
> > from DMGetCoordinatesLocal() and DMGetCellCoordinatesLocal() before
> > > scaling them.
> > >
> > >
> > > I am likely not being clear. I think all you have to do is the
> > following:
> > >
> > > DMGetCoordinatesLocal(dm, &xl);
> > > VecScale(xl, scale);
> > > DMSetCoordinatesLocal(dm, xl);
> > > DMGetCellCoordinatesLocal(dm, &xl);
> > > VecScale(xl, scale);
> > > DMSetCellCoordinatesLocal(dm, xl);
> > >
> > > Does this not work?
> > >
> > > Thanks,
> > >
> > > Matt
> > >
> > > Best regards, Berend.
> > >
> > > On 5/17/23 16:35, Matthew Knepley wrote:
> > > > On Wed, May 17, 2023 at 10:21 AM Berend van Wachem
> > <berend.vanwachem at ovgu.de <mailto:berend.vanwachem at ovgu.de>
> > <mailto:berend.vanwachem at ovgu.de <mailto:berend.vanwachem at ovgu.de>>
> > > <mailto:berend.vanwachem at ovgu.de
> > <mailto:berend.vanwachem at ovgu.de> <mailto:berend.vanwachem at ovgu.de
> > <mailto:berend.vanwachem at ovgu.de>>>> wrote:
> > > >
> > > > Dear Matt,
> > > >
> > > > Thanks for getting back to me so quickly.
> > > >
> > > > If I scale each of the coordinates of the mesh (say, I
> > want to cube each
> > > > co-ordinate), and I do this for both:
> > > >
> > > > DMGetCoordinatesLocal();
> > > > DMGetCellCoordinatesLocal();
> > > >
> > > > How do I know I am not cubing one coordinate multiple
> > times?
> > > >
> > > >
> > > > Good question. Right now, the only connection between the
> > two sets of coordinates is DMLocalizeCoordinates(). Since
> > > sometimes
> > > > people want to do non-trivial things to
> > > > coordinates, I prefer not to push in an API for "just"
> > scaling, but I could be convinced
> > > > the other way.
> > > >
> > > > Thanks,
> > > >
> > > > Matt
> > > >
> > > > Thanks, Berend.
> > > >
> > > > On 5/17/23 16:10, Matthew Knepley wrote:
> > > > > On Wed, May 17, 2023 at 10:02 AM Berend van Wachem
> > > > > <berend.vanwachem at ovgu.de
> > <mailto:berend.vanwachem at ovgu.de> <mailto:berend.vanwachem at ovgu.de
> > <mailto:berend.vanwachem at ovgu.de>> <mailto:berend.vanwachem at ovgu.de
> > <mailto:berend.vanwachem at ovgu.de>
> > > <mailto:berend.vanwachem at ovgu.de
> > <mailto:berend.vanwachem at ovgu.de>>> <mailto:berend.vanwachem at ovgu.de
> > <mailto:berend.vanwachem at ovgu.de> <mailto:berend.vanwachem at ovgu.de
> > <mailto:berend.vanwachem at ovgu.de>>
> > > > <mailto:berend.vanwachem at ovgu.de
> > <mailto:berend.vanwachem at ovgu.de> <mailto:berend.vanwachem at ovgu.de
> > <mailto:berend.vanwachem at ovgu.de>>>>> wrote:
> > > > >
> > > > > Dear PETSc Team,
> > > > >
> > > > > We are using DMPlex, and we create a mesh using
> > > > >
> > > > > DMPlexCreateBoxMesh (.... );
> > > > >
> > > > > and get a uniform mesh. The mesh is periodic.
> > > > >
> > > > > We typically want to "scale" the coordinates
> > (vertices) of the mesh,
> > > > > and
> > > > > to achieve this, we call
> > > > >
> > > > > DMGetCoordinatesLocal(dm, &coordinates);
> > > > >
> > > > > and scale the entries in the Vector coordinates
> > appropriately.
> > > > >
> > > > > and then
> > > > >
> > > > > DMSetCoordinatesLocal(dm, coordinates);
> > > > >
> > > > >
> > > > > After this, we localise the coordinates by
> calling
> > > > >
> > > > > DMLocalizeCoordinates(dm);
> > > > >
> > > > > This worked fine up to PETSc 3.18, but with
> > versions after this, the
> > > > > coordinates we get from the call
> > > > >
> > > > > DMPlexGetCellCoordinates(dm, CellID, &isDG,
> > &CoordSize,
> > > > > &ArrayCoordinates, &Coordinates);
> > > > >
> > > > > are no longer correct if the mesh is periodic.
> > A number of the
> > > > > coordinates returned from calling
> > DMPlexGetCellCoordinates are wrong.
> > > > >
> > > > > I think, this is because DMLocalizeCoordinates
> > is now automatically
> > > > > called within the routine DMPlexCreateBoxMesh.
> > > > >
> > > > > So, my question is: How should we scale the
> > coordinates from a periodic
> > > > > DMPlex mesh so that they are reflected
> > correctly when calling both
> > > > > DMGetCoordinatesLocal and
> > DMPlexGetCellCoordinates, with PETSc versions
> > > > > >= 3.18?
> > > > >
> > > > >
> > > > > I think we might have to add an API function. For
> > now, when you scale
> > > > > the coordinates,
> > > > > can you scale both copies?
> > > > >
> > > > > DMGetCoordinatesLocal()
> > > > > DMGetCellCoordinatesLocal();
> > > > >
> > > > > and then set them back.
> > > > >
> > > > > Thanks,
> > > > >
> > > > > Matt
> > > > >
> > > > > Many thanks, Berend.
> > > > >
> > > > > --
> > > > > 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/
> > <https://www.cse.buffalo.edu/~knepley/>
> > <https://www.cse.buffalo.edu/~knepley/
> > <https://www.cse.buffalo.edu/~knepley/>>
> > > <https://www.cse.buffalo.edu/~knepley/
> > <https://www.cse.buffalo.edu/~knepley/>
> > <https://www.cse.buffalo.edu/~knepley/
> > <https://www.cse.buffalo.edu/~knepley/>>>
> > <http://www.cse.buffalo.edu/~knepley/
> > <http://www.cse.buffalo.edu/~knepley/>
> > > <http://www.cse.buffalo.edu/~knepley/
> > <http://www.cse.buffalo.edu/~knepley/>>
> > > > <http://www.cse.buffalo.edu/~knepley/
> > <http://www.cse.buffalo.edu/~knepley/>
> > <http://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/
> > <https://www.cse.buffalo.edu/~knepley/>
> > <https://www.cse.buffalo.edu/~knepley/
> > <https://www.cse.buffalo.edu/~knepley/>>
> > <http://www.cse.buffalo.edu/~knepley/
> > <http://www.cse.buffalo.edu/~knepley/>
> > > <http://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/
> > <https://www.cse.buffalo.edu/~knepley/>
> > <http://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/>
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