[petsc-users] Periodic boundary conditions using swarm

[Matthew Knepley]

On Sun, Apr 21, 2024 at 9:38 AM MIGUEL MOLINOS PEREZ <mmolinos at us.es> wrote:

> Dear Matt,
>
> Thank you for your answer. In addition to your suggestion I solved a bug
> in the test (I was not updating the local size integer during the time
> loop). Indeed if I turn off periodicity it works. Furthermore, if I use
> instead DM_BOUNDARY_TWIST instead, it works too.
>
> However, if I turn on DM_BOUNDARY_PERIODIC, I got an error in the search
> algorithm I implemented for the domain decomposition inspired by (
> https://urldefense.us/v3/__https://petsc.org/main/src/dm/tutorials/swarm_ex3.c.html__;!!G_uCfscf7eWS!flWhzJ-Vd_S7zFFxywsQXO7UelXYvJprWVsqngT5k0SlO7wMjGMHQ_D_3lQ-2_FNdN9pw-ztQ4gVIcl8_Lle$ ). The algorithm
> is not capable of finding some of the particles at the initial stage of the
> simulation (without transport).
>
> Looks like the error is on my end, however it is puzzling why it works for
> DM_BOUNDARY_TWIST but not for DM_BOUNDARY_PERIODIC.
>

I usually solve these things by making a simple example. We could make
another test in Swarm test ex1 that uses periodicity. If you send a draft
over that fails, I can help you debug it. It would make a fantastic
contribution to PETSc.

   Thanks,

     Matt


> Thanks,
> Miguel
>
> On 21 Apr 2024, at 14:53, Matthew Knepley <knepley at gmail.com> wrote:
>
> On Thu, Apr 18, 2024 at 8:23 AM MIGUEL MOLINOS PEREZ <mmolinos at us.es>
> wrote:
>
>>  Dear all, I am working on the implementation of periodic bcc using a
>> discretisation (PIC-style). I am working with a test case which consists on
>> solving the advection of a set of particles inside of a box (DMDA mesh)
>> with periodic bcc on
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>> Dear all,
>>
>> I am working on the implementation of periodic bcc using a discretisation
>> (PIC-style). I am working with a test case which consists on solving the
>> advection of a set of particles inside of a box (DMDA mesh) with periodic
>> bcc on the x axis.
>>
>> My implementation updates the position of each particle with a velocity
>> field, afterwards I check if the particle is inside, or not, the supercell
>> (periodic box). If not, I correct the position using bcc conditions. Once
>> this step is done, I call Dmswarmmigrate.
>>
>> It works in serial, but crashes in parallel with MPI (see attached nohup
>> file). I have checked some of the Dmswarmmigrate examples, and they
>> looks similar to my implementation. However they do not use periodic bcc.
>>
>> I am missing any step in addition to Dmswarmmigrate?
>>
>
> It does not sound like it. We do have parallel examples of periodic
> migration, such as Swarm ex9.
>
> What happens if you turn off periodicity and just let particles fall out
> of the box? Does it still crash?
>
>   Thanks,
>
>     Matt
>
>
>> Best regards
>> Miguel
>>
>>
>
> --
> 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
>
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>
>
>

-- 
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

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