[petsc-users] Periodic domains in DMPlex / petsc4py

[Stefano Zampini]

What do you mean by "I always get the first numbering"?
I understand you are using GMSH right? To have PETSc read the periodic
section of the .msh file, you need to pass -dm_plex_gmsh_periodic
Note that DMLocalizeCoordinates will localize coordinates ONLY if you use
DMSetPerioidicity(), which is done in the GMSH reader

Il giorno mer 12 dic 2018 alle ore 17:17 Artur Palha Da Silva Clérigo - LR
via petsc-users <petsc-users at mcs.anl.gov> ha scritto:

>
>
> On 12 Dec 2018, at 15:14, Matthew Knepley <knepley at gmail.com> wrote:
>
> 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.
>
>
> Yes, I agree. That happens yes. What I meant was that for both the
> periodic and non-periodic case I always get the first numbering. Is this
> because I miss DMLocalizeCoordinates?
>
>
>
>
>   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/>
>
>
>

-- 
Stefano
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