[petsc-users] Periodic domains in DMPlex / petsc4py

[Matthew Knepley]

On Wed, Dec 12, 2018 at 9:12 AM Artur Palha Da Silva Clérigo - LR <
A.PalhaDaSilvaClerigo at tudelft.nl> wrote:

> Dear Matt,
>
> Thank you for your quick reply. As for your question: "why would there be
> a difference? They should be numbered in the same way.”
>
> I see the degrees of freedom living on the periodic domain as the ones
> living at boundaries between interior elements. This is what I expect for
> non-periodic domain for nodal scalar field:
>
> Non-periodic:
>
> 1                3                5
> X-------------X-------------X
> |                  |                 |
> |                  |                 |
> |                  |                 |
> X-------------X-------------X
> 0                2                 4
>
> Periodic (vertical boundaries, topologically, the domain is a cylinder)
>
> 1                3                1
> X-------------X-------------X
> |                  |                 |
> |                  |                 |
> |                  |                 |
> X-------------X-------------X
> 0                2                 0
>
> This is not the expected behaviour?
>

What I mean is that each vertex in the periodic domain gets 1 dof. Same
procedure as non-periodic.
We do not duplicate vertices or anything like that.

  Thanks,

    Matt


> Once again thank you for your help.
>
> -artur palha
>
> On 12 Dec 2018, at 15:04, Matthew Knepley <knepley at gmail.com> wrote:
>
> On Wed, Dec 12, 2018 at 9:01 AM Artur Palha Da Silva Clérigo - LR via
> petsc-users <petsc-users at mcs.anl.gov> wrote:
>
>> Dear All,
>>
>> I having been trying to add periodic domain functionality to my code. I
>> am able to generate a periodic mesh with gmsh and load it using dmplex. The
>> problem is that I am unable to have a numbering of the degrees of freedom
>> that reflects the periodicity (they are numbered as if there was no
>> periodicity).
>>
>
> Why would there be a difference? They should be numbered in the same way.
>
>
>> I read this thread:
>> https://lists.mcs.anl.gov/mailman/htdig/petsc-users/2018-October/036539.html
>>
>> There it is mentioned that DMLocalizeCoordinates is required after
>> loading the mesh.
>>
>
> Yes, this makes cell-wise coordinates, which have a jump at the periodic
> boundary.
>
>
>> My questions are the following:
>>
>> 1. Is it correct that I need to run DMLocalizeCoordinates on my DM?
>>
>
> Yes.
>
>
>> 2. I am currently using petsc4py but I am unable to find
>> DMLocalizeCoordinates. Is this functionality missing or is there an
>> alternative to it?\
>>
>
> Its possible no wrapper has been written for this yet. Lisandro, is it
> missing? (I am at a meeting, or I would check).
>
>   Thanks,
>
>     Matt
>
>
>> Thank you for your time.
>>
>> Kind regards,
>>
>> -artur palha
>>
>
>
> --
> 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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