<div dir="auto">Sounds good, i will take a look. Thanks! </div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, 27 Aug 2019, 12:28 Nathan Collier, <<a href="mailto:nathaniel.collier@gmail.com">nathaniel.collier@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Here is a example of what I think you need:<div><br></div><div><a href="https://github.com/TDycores-Project/toy-problems/blob/master/TracyProblem/Richards.c" target="_blank" rel="noreferrer">https://github.com/TDycores-Project/toy-problems/blob/master/TracyProblem/Richards.c</a><br></div><div><br></div><div>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. </div><div><br></div><div>Nate</div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Aug 27, 2019 at 6:55 AM Matthew Knepley via petsc-users <<a href="mailto:petsc-users@mcs.anl.gov" target="_blank" rel="noreferrer">petsc-users@mcs.anl.gov</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div dir="ltr">On Tue, Aug 27, 2019 at 4:54 AM Edoardo alinovi <<a href="mailto:edoardo.alinovi@gmail.com" target="_blank" rel="noreferrer">edoardo.alinovi@gmail.com</a>> wrote:<br></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Hello Matt, <div><br></div><div>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 :) </div><div><br></div><div>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.</div><div><br></div><div>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. </div><div>Have you got some example for P0 finite elements and overlap=1?</div></div></blockquote><div><br></div><div>This is one group already using PETSc in exactly this way for a FV code.</div><div><br></div><div>Maybe it would help if I gave a high-level overview of this usage pattern.</div><div><br></div><div>1) Hopefully replacing your current mesh topology/geometry with Plex is not hard. Let me know if you have any questions about this.</div><div><br></div><div>2) If you give overlap=1 on distribution, then support(face) for any regular face gives the two cells on either side. You</div><div> probably want to screen out faces between two ghost cells. There is a DMLabel for doing that.</div><div><br></div><div>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.</div><div> The DMGetGlobalVector() and DMGetLocalVector() should produce vectors in your existing order and you can reuse all your code.</div><div><br></div><div> Thanks,</div><div><br></div><div> Matt</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div>Thank you! :) </div><div><br></div></div><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Il giorno mar 27 ago 2019 alle ore 09:33 Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank" rel="noreferrer">knepley@gmail.com</a>> ha scritto:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div dir="ltr">On Tue, Aug 27, 2019 at 4:07 AM Edoardo alinovi via petsc-users <<a href="mailto:petsc-users@mcs.anl.gov" target="_blank" rel="noreferrer">petsc-users@mcs.anl.gov</a>> wrote:<br></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="auto">Hello PETSc users and developers,<div dir="auto">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.</div><div dir="auto"><br></div><div dir="auto">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 :)</div><div dir="auto"><br></div><div dir="auto">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.</div><div dir="auto"><br></div><div dir="auto">I have red some papers and lectures by Matt around the web, but still I have not found an answer to this question:</div><div dir="auto">Can dmplex dial with cell centered data arrangement and provide some support for basic operation (e. g. interpolation between partitions, face value calculation etc)?</div></div></blockquote><div><br></div><div>1) Cell centered data</div><div><br></div><div>Definitely yes. This is the same data layout as P0 finite elements. You just assign the PetscSection k dofs per cell.</div><div><br></div><div>2) Interpolation between partitions</div><div><br></div><div>I assume you mean ghost values from other parallel partitions. You can do this by using overlap=1 in DMPlexDisrtibute().</div><div><br></div><div>3) Face value calculation</div><div><br></div><div>You can do Riemann solves by looping over faces, grabbing values from the neighboring cells, doing the calculation, and</div><div>updating cell values. We carry out this kind of computation in TS ex11. That example attempts to do everything, so it is</div><div>messy, but we can help you understand what it is doing in any part that is unclear.</div><div><br></div><div>4) FV boundary conditions</div><div><br></div><div>You can use DMPlexConstructGhostCells() to put artificial cells around the boundary that you use to prescribe fluxes.</div><div><br></div><div> Thanks,</div><div><br></div><div> Matt</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="auto"><div dir="auto">Thank you very much!</div><div dir="auto"><br></div><div dir="auto">Edo</div></div>
</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="m_4266690838735366679gmail-m_830229942254562764gmail-m_-3559531205028374979gmail-m_-4856282592389270037gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>-- Norbert Wiener</div><div><br></div><div><a href="http://www.cse.buffalo.edu/~knepley/" target="_blank" rel="noreferrer">https://www.cse.buffalo.edu/~knepley/</a><br></div></div></div></div></div></div></div></div>
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</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="m_4266690838735366679gmail-m_830229942254562764gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>-- Norbert Wiener</div><div><br></div><div><a href="http://www.cse.buffalo.edu/~knepley/" target="_blank" rel="noreferrer">https://www.cse.buffalo.edu/~knepley/</a><br></div></div></div></div></div></div></div></div>
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