[petsc-users] DMPlex general questions

[Matthew Knepley]

On Sun, Jul 5, 2015 at 11:57 AM, Filippo Leonardi <
filippo.leonardi at sam.math.ethz.ch> wrote:

>  Hi all,
>
>
>
> I'm starting to migrate my code to DMDAs to use DMPlex but I have troubles
> that neither the documentation nor google can answer.
>
>
>
> 1) I want to to traverse the DAG associated to the DMPlex in the following
> way: assuming I have a DMPlex of dimension 2, I have a point representing a
> cell (2 dimensional) and I want to find all neighbouring 2-dim cells. A way
> to do this may be to GetCone and then follow the arrows in reverse in the
> DAG from height 2 to height 1. Any routine to do that? I looked at the DM
> documentation page but cannot find the proper one. I tried all the
> GetAdjacency routines but none of them seems to give the right
> implementation. I am thinking of something like GetCone or GetSupport, but
> from 2-dim cell to adjacent 2-dim cell.
>

You would use

http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/DM/DMPlexGetAdjacency.html

Note that the default is for FEM style adjacency. If you want FVM style,
you need to call


http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/DM/DMPlexSetAdjacencyUseClosure.html#DMPlexSetAdjacencyUseClosure

http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/DM/DMPlexGetAdjacencyUseCone.html#DMPlexGetAdjacencyUseCone


>
> 2) I've noticed that the numbering concerning the Height in the BFS search
> of the DMPlex section is a bit inconsistent. What I mean is that if want
> all the 2-dim cells of my DMPlex I should do:
>
> DMPlexGetHeightStratum(dm, d, &pStart, &pEnd);
>
> with d = 0, but if I'd like to call
>
> DMPlexCreateSection
>
> and create DOFs on the 2-dim cell, I have to do:
>
> numDof[f*(dim+1)+d] = 2;
>
> with d = 2.
>
> Is there any reason behind that? I was trying with some mock example and
> fell into this trap a couple of times.
>

There are two measures, the 'depth' which matches the idea of dimension,
and the 'height' which matches
the idea of co-dimension. In CreateSection() I have gone with input by
depth, mostly because a prior
implementation in the FIAT package did it that way.


> 3) This brings me to the following: I've noticed that the documentation is
> a bit "sparse", and I'd really like to contribute, especially improving the
> APIs documentation. I am not native speaker and new to all the DMPlex
> business but if you devs think this may be useful, I'll be glad to help.
>
> Would this be of any use to you?
>

Sure, pull requests are the best way to do this since we can review them. I
am trying to have all
the functions documented. I do hold off on some of the more experimental
ones in order to see
how we like the interface before advertising it.


> 4) I had problems loading meshes from Gmsh and, as far as I understood, it
> seems that is not PETSc preferred mesher (got problems with boundaries IS).
> PETSc seems to like this ExodusII format, any suggestion of a tool similar
> to Gmsh that creates ExodusII meshes?
>

The Gmsh problems should be fixed in the latest release due to hard work
from MIchael Lange. Report the problems
and we will see what can be done.

  Thanks,

     Matt


> Sorry for the length and thanks in advance.
>
>
>
> Best,
>
> Filippo
>



-- 
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
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