[petsc-users] DMPlex for cell centred finite volume

[Edoardo alinovi]

Sounds good, i will take a look. Thanks!

On Tue, 27 Aug 2019, 12:28 Nathan Collier, <nathaniel.collier at gmail.com>
wrote:

> Here is a example of what I think you need:
>
>
> https://github.com/TDycores-Project/toy-problems/blob/master/TracyProblem/Richards.c
>
> It is written to solve Richard's equation using a simple two-point flux,
> but it may be helpful to look at the setup and residual loop.
>
> Nate
>
>
> On Tue, Aug 27, 2019 at 6:55 AM Matthew Knepley via petsc-users <
> petsc-users at mcs.anl.gov> wrote:
>
>> On Tue, Aug 27, 2019 at 4:54 AM Edoardo alinovi <
>> edoardo.alinovi at gmail.com> wrote:
>>
>>> Hello Matt,
>>>
>>> Thanks for your kind replay. Using DMplex and changing the data
>>> structure is not a straightforward task as you can imagine. Up to now I am
>>> in the preliminaries and I am trying to understand how to reuse most of all
>>> my subroutines (I am using fortran) such as fluxes and coeffs assembly,
>>> numerical schemes  and so o in order to avoid to rewrite all the code :p I
>>> will start with your first two suggestions and see if it is  an affordable
>>> task :)
>>>
>>> For the face value, I am not interested in Reimann solvers. Being
>>> incompressible I am using Central difference, QUICK, SOU, Upwind or
>>> TVD-family schemes, but maybe I can use my stuff to get it.
>>>
>>> I think I can be happy enough having the ghost cell centers available
>>> and some way to deal with the BC (I guess this will be the most tricky
>>> part).  Basically I would like to use DMplex at low level just to have a
>>> support for the parallel mesh management.
>>> Have you got some example for P0 finite elements and overlap=1?
>>>
>>
>> This is one group already using PETSc in exactly this way for a FV code.
>>
>> Maybe it would help if I gave a high-level overview of this usage pattern.
>>
>> 1) Hopefully replacing your current mesh topology/geometry with Plex is
>> not hard. Let me know if you have any questions about this.
>>
>> 2) If you give overlap=1 on distribution, then support(face) for any
>> regular face gives the two cells on either side. You
>>     probably want to screen out faces between two ghost cells. There is a
>> DMLabel for doing that.
>>
>> 3) A PetscSection just gives the data layout over a mesh. The idea here
>> is to make it describe _exactly_ the layout you already have.
>>     The DMGetGlobalVector() and DMGetLocalVector() should produce vectors
>> in your existing order and you can reuse all your code.
>>
>>   Thanks,
>>
>>      Matt
>>
>>
>>> Thank you! :)
>>>
>>> Il giorno mar 27 ago 2019 alle ore 09:33 Matthew Knepley <
>>> knepley at gmail.com> ha scritto:
>>>
>>>> On Tue, Aug 27, 2019 at 4:07 AM Edoardo alinovi via petsc-users <
>>>> petsc-users at mcs.anl.gov> wrote:
>>>>
>>>>> Hello PETSc users and developers,
>>>>> I hope you are doing well! Today I have a general question about
>>>>> DMplex to see if it can be usefull to me or not.
>>>>>
>>>>> I have my fancy finite volume solver (cell centered, incompressible
>>>>> NS) which uses petsc as linear solver engine. Thanks to your suggestions so
>>>>> far it is now running well :)
>>>>>
>>>>> I would like to see if I can do another step incapsulatng in petsc
>>>>> also the mesh managment part. I think that Dmplex is the way to go since my
>>>>> code is fully unstructured.
>>>>>
>>>>> I have red some papers and lectures by Matt around the web, but still
>>>>> I have not found an answer to this question:
>>>>> Can dmplex dial with cell centered data arrangement and provide some
>>>>> support for basic operation (e. g. interpolation between partitions, face
>>>>> value calculation etc)?
>>>>>
>>>>
>>>> 1) Cell centered data
>>>>
>>>> Definitely yes. This is the same data layout as P0 finite elements. You
>>>> just assign the PetscSection k dofs per cell.
>>>>
>>>> 2) Interpolation between partitions
>>>>
>>>> I assume you mean ghost values from other parallel partitions. You can
>>>> do this by using overlap=1 in DMPlexDisrtibute().
>>>>
>>>> 3) Face value calculation
>>>>
>>>> You can do Riemann solves by looping over faces, grabbing values from
>>>> the neighboring cells, doing the calculation, and
>>>> updating cell values. We carry out this kind of computation in TS ex11.
>>>> That example attempts to do everything, so it is
>>>> messy, but we can help you understand what it is doing in any part that
>>>> is unclear.
>>>>
>>>> 4) FV boundary conditions
>>>>
>>>> You can use DMPlexConstructGhostCells() to put artificial cells around
>>>> the boundary that you use to prescribe fluxes.
>>>>
>>>>   Thanks,
>>>>
>>>>      Matt
>>>>
>>>>
>>>>> Thank you very much!
>>>>>
>>>>> Edo
>>>>>
>>>>
>>>>
>>>> --
>>>> 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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