Re: [petsc-users] DMGetCoordinatesLocal and DMPlexGetCellCoordinates in PETSc > 3.18

2023-05-22 Thread Matthew Knepley 
On Mon, May 22, 2023 at 4:41 AM Berend van Wachem 
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
> > 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
> > 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
> > mailto:berend.vanwac...@ovgu.de>
> > >
> >  >  >   >  >  >  >
> >  >  > 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
> >  >  >  >  >   > >  > 
> >  >  > >>  >   > >
> >  >  >  >   >

Re: [petsc-users] DMGetCoordinatesLocal and DMPlexGetCellCoordinates in PETSc > 3.18

2023-05-22 Thread Berend van Wachem 

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 
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
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
mailto:berend.vanwac...@ovgu.de>
>
 >            >
 >      >     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
 >      >      > 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);
 >   

Re: [petsc-users] DMGetCoordinatesLocal and DMPlexGetCellCoordinates in PETSc > 3.18

2023-05-17 Thread Matthew Knepley 
On Wed, May 17, 2023 at 2:01 PM Berend van Wachem 
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 > 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 
> > >>
> 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
> >  >  > mailto:berend.vanwac...@ovgu.de>
>  > >  
> >  >  >  >  >
> >  >  > 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
> >  >  >

Re: [petsc-users] DMGetCoordinatesLocal and DMPlexGetCellCoordinates in PETSc > 3.18

2023-05-17 Thread Berend van Wachem 

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?

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 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 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
 >      > mailto:berend.vanwac...@ovgu.de> 
> 
 >           >
 >      >     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.
 >      >
 > 

Re: [petsc-users] DMGetCoordinatesLocal and DMPlexGetCellCoordinates in PETSc > 3.18

2023-05-17 Thread Matthew Knepley 
On Wed, May 17, 2023 at 11:20 AM Berend van Wachem 
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 > 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
> >  > 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/> <
> 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/

Re: [petsc-users] DMGetCoordinatesLocal and DMPlexGetCellCoordinates in PETSc > 3.18

2023-05-17 Thread Berend van Wachem 

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.


Best regards, Berend.

On 5/17/23 16:35, Matthew Knepley wrote:

On Wed, May 17, 2023 at 10:21 AM Berend van Wachem 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
 > 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/ 
 >



--
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/

Re: [petsc-users] DMGetCoordinatesLocal and DMPlexGetCellCoordinates in PETSc > 3.18

2023-05-17 Thread Matthew Knepley 
On Wed, May 17, 2023 at 10:21 AM Berend van Wachem 
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
> > 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/ <
> 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/

Re: [petsc-users] DMGetCoordinatesLocal and DMPlexGetCellCoordinates in PETSc > 3.18

2023-05-17 Thread Berend van Wachem 

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?

Thanks, Berend.



On 5/17/23 16:10, Matthew Knepley wrote:
On Wed, May 17, 2023 at 10:02 AM Berend van Wachem 
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/

Re: [petsc-users] DMGetCoordinatesLocal and DMPlexGetCellCoordinates in PETSc > 3.18

2023-05-17 Thread Matthew Knepley 
On Wed, May 17, 2023 at 10:02 AM Berend van Wachem 
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/

[petsc-users] DMGetCoordinatesLocal and DMPlexGetCellCoordinates in PETSc > 3.18

2023-05-17 Thread Berend van Wachem 

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?


Many thanks, Berend.