[petsc-users] Question about DMPLEX/P4EST with different Sections

[Berend van Wachem]

Dear Matt,

Thanks for your response. My understanding of the DM and DMClone is the 
same - and I have tested this with a DMPLEX DM without problems.

However, for some reason, I cannot change/set the section of a P4EST dm. 
In the attached example code, I get an error in line 140, where I try to 
create a new section from the cloned P4EST DM. Is it not possible to 
create/set a section on a P4EST DM? Or maybe I am doing something else 
wrong? Do you suggest a workaround?

Many thanks, Berend.


On 2020-03-13 00:19, Matthew Knepley wrote:
> On Thu, Mar 12, 2020 at 7:40 AM Berend van Wachem 
> <berend.vanwachem at ovgu.de <mailto:berend.vanwachem at ovgu.de>> wrote:
> 
>     Dear All,
> 
>     I have started to use DMPLEX with P4EST for a computational fluid
>     dynamics application. I am solving a coupled system of 4 discretised
>     equations (for 3 velocity components and one pressure) on a mesh.
>     However, next to these 4 variables, I also have a few single field
>     variables (such as density and viscosity) defined over the mesh,
>     which I
>     don't solve for (they should not be part of the matrix with unknowns).
>     Most of these variables are at the cell centers, but in a few cases, it
>     want to define them at cell faces.
> 
>     With just DMPLEX, I solve this by:
> 
>     DMPlexCreateMesh, so I get an initial DM
>     DMPlexCreateSection, indicating the need for 4 variables
>     DMSetLocalSection
>     DMCreateGlobalVector (and Matrix), so I get an Unknown vector, a RHS
>     vector, and a matrix for the 4 variables.
> 
>     To get a vector for a single variable at the cell center or the cell
>     face, I clone the original DM, I define a new Section on it, and then
>     create the vector from that which I need (e.g. for density,
>     viscosity or
>     a velocity at the cell face).
> 
>     Then I loop over the mesh, and with MatSetValuesLocal, I set the
>     coefficients. After that, I solve the system for multiple timesteps
>     (sequential solves) and get the solution vector with the 4 variables
>     after each solve.
> 
>     So-far, this works fine with DMPLEX. However, now I want to use P4EST,
>     and I have difficulty defining a variable vector other than the
>     original 4.
> 
>     I have changed the code structure:
> 
>     DMPlexCreateMesh, so I get an initial DM
>     DMPlexCreateSection, indicating the need for 4 variables
>     DMSetLocalSection
>     DMForestSetBaseDM(DM, DMForest) to create a DMForest
>     DMCreateGlobalVector (and Matrix), so I get a Unknown vector, a RHS
>     vector, and a matrix for the 4 variables
> 
>     then I perform multiple time-steps,
>         DMForestTemplate(DMForest ->  DMForestPost)
>         Adapt DMForestPost
>         DMCreateGlovalVector(DMForestPost, RefinedUnknownVector)
>         DMForestTransferVec(UnknownVector , RefinedUnknownVector)
>         DMForestPost -> DMForest
>     and then DMConvert(DMForest,DMPLEX,DM)
>     and I can solve the system as usual. That also seems to work.
> 
>     But my conceptual question: how can I convert the other variable
>     vectors
>     (obtained with a different section on the same DM) such as density and
>     viscosity and faceVelocity within this framework?
> 
> 
> Here is my current thinking about DMs. A DM is a function space 
> overlaying a topology. Much to my dismay, we
> do not have a topology object, so it hides inside DM. DMClone() creates 
> a shallow copy of the topology. We use
> this to have any number of data layouts through PetscSection, laying 
> over the same underlying topology.
> 
> So for each layout you have, make a separate clone. Then things like 
> TransferVec() will respond to the layout in
> that clone. Certainly it works this way in Plex. I admit to not having 
> tried this for TransferVec(), but let me know if
> you have any problems.
> 
> BTW, I usually use a dm for the solution, which I give to the solver, 
> say SNESSetDM(snes, dm), and then clone
> it as dmAux which has the layout for all the auxiliary fields that are 
> not involved in the solve. The Plex examples
> all use this form.
> 
>    Thanks,
> 
>       Matt
> 
>     The DMForest has the same Section as the original DM and will thus have
>     the space for exactly 4 variables per cell. I tried pushing another
>     section on the DMForest and DMForestPost, but that does not seem to
>     work. Please find attached a working example with code to do this,
>     but I
>     get the error:
> 
>     PETSC ERROR: PetscSectionGetChart() line 513 in
>     /usr/local/petsc-3.12.4/src/vec/is/section/interface/section.c Wrong
>     type of object: Parameter # 1
> 
>     So, I is there a way to DMForestTransferVec my other vectors from one
>     DMForest to DMForestPost. How can I do this?
> 
>     Many thanks for your help!
> 
>     Best wishes, Berend.
> 
> 
> 
> -- 
> 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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