Dear Matt,
I'm really sorry for this stupid bug!
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.vanwac...@ovgu.de <mailto:berend.vanwac...@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.vanwac...@ovgu.de <mailto:berend.vanwac...@ovgu.de>
<mailto:berend.vanwac...@ovgu.de <mailto:berend.vanwac...@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.vanwac...@ovgu.de <mailto:berend.vanwac...@ovgu.de>
<mailto:berend.vanwac...@ovgu.de <mailto:berend.vanwac...@ovgu.de>>
> <mailto:berend.vanwac...@ovgu.de
<mailto:berend.vanwac...@ovgu.de> <mailto:berend.vanwac...@ovgu.de
<mailto:berend.vanwac...@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.vanwac...@ovgu.de
<mailto:berend.vanwac...@ovgu.de> <mailto:berend.vanwac...@ovgu.de
<mailto:berend.vanwac...@ovgu.de>> <mailto:berend.vanwac...@ovgu.de
<mailto:berend.vanwac...@ovgu.de>
> <mailto:berend.vanwac...@ovgu.de
<mailto:berend.vanwac...@ovgu.de>>> <mailto:berend.vanwac...@ovgu.de
<mailto:berend.vanwac...@ovgu.de> <mailto:berend.vanwac...@ovgu.de
<mailto:berend.vanwac...@ovgu.de>>
> > <mailto:berend.vanwac...@ovgu.de
<mailto:berend.vanwac...@ovgu.de> <mailto:berend.vanwac...@ovgu.de
<mailto:berend.vanwac...@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/>
