[petsc-users] Domain decomposition in PETSc for Molecular Dynamics

[Matthew Knepley]

On Sat, Nov 4, 2023 at 8:40 AM Mark Adams <mfadams at lbl.gov> wrote:

> Hi MIGUEL,
>
> This might be a good place to start: https://petsc.org/main/manual/vec/
> Feel free to ask more specific questions, but the docs are a good place to
> start.
>
> Thanks,
> Mark
>
> On Fri, Nov 3, 2023 at 5:19 AM MIGUEL MOLINOS PEREZ <mmolinos at us.es>
> wrote:
>
>> Dear all,
>>
>> I am currently working on the development of a in-house molecular
>> dynamics code using PETSc and C++. So far the code works great, however it
>> is a little bit slow since I am not exploiting MPI for PETSc vectors. I was
>> wondering if there is a way to perform the domain decomposition efficiently
>> using some PETSc functionality. Any feedback is highly appreciated.
>>
>
It sounds like you mean "is there a way to specify a communication
construct that can send my particle
information automatically". We use PetscSF for that. You can see how this
works with the DMSwarm class, which represents a particle discretization.
You can either use that, or if it does not work for you, do the same things
with your class.

  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

https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
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