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

[MIGUEL MOLINOS PEREZ]

Thank you Mark! I will have a look to it.

Best,
Miguel


On 4 Nov 2023, at 13:54, Matthew Knepley <knepley at gmail.com> wrote:


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