I read everything again, I think I did not understand you at first. The
first solution is to modify the DAG, so that the rightmost cell is
linked to the leftmost face, right ? To do that, do I have to manually
edit the DAG (the mesh is read from a file) ? If so, the mesh
connectivity is like the one of a torus, then how does it work with the
cells/faces coordinates ?
Now I think the second method may be more straightforward. What's the
idea ? Get the mapping with DMGetLocalToGlobalMapping, then create the
mapping corresponding to the periodicity with
ISLocalToGlobalMappingCreate, and finally
ISLocalToGlobalMappingConcatenate ? I'm not sure this is the way, and I
did not find something like DMSetLocalToGlobalMapping to restore the
modified mapping.
Pierre
On 15/10/21 15:33, Pierre Seize wrote:
When I first tried to handle the periodicity, I found the
DMPlexCreateBoxMesh function (I cannot find the cylinder one).
From reading the sources, I understand that we do some work either in
DMPlexCreateCubeMesh_Internal or with DMSetPeriodicity.
I tried to use DMSetPeriodicity before, for example with a 2x2 box on
length 10. I did something like:
const PetscReal maxCell[] = {2, 2};
const PetscReal L[] = {10, 10};
const DMBoundaryType bd[] = {DM_BOUNDARY_PERIODIC, DM_BOUNDARY_PERIODIC};
DMSetPeriodicity(dm, PETSC_TRUE, maxCell, L, bd);
// or:
DMSetPeriodicity(dm, PETSC_TRUE, NULL, L, bd);
but it did not work:
VecSet(X, 1);
DMGetLocalVector(dm, &locX);
VecZeroEntries(locX);
DMGlobalToLocalBegin(dm, X, INSERT_VALUES, locX);
DMGlobalToLocalEnd(dm, X, INSERT_VALUES, locX);
VecView(locX, PETSC_VIEWER_STDOUT_WORLD);
but the ghost cells values are all 0, only the real cells are 1. So I
guess DMSetPeriodicity alone is not sufficient to handle the
periodicity. Is there a way to do what I want ? That is set up my
DMPlex in a way that DMGlobalToLocalBegin/DMGlobalToLocalEnd do
exchange values between procs AND exchange the periodic values?
Thanks for the help
Pierre
On 15/10/21 14:03, Matthew Knepley wrote:
On Fri, Oct 15, 2021 at 7:31 AM Pierre Seize <[email protected]
<mailto:[email protected]>> wrote:
It makes sense, thank you. In fact, both ways seems better than
my way. The first one looks the most straightforward.
Unfortunately I do not know how to implement either of them.
Could you please direct me to the corresponding PETSc functions ?
The first way is implemented for example in DMPlexCreateBoxMesh() and
DMPlexCreateCylinderMesh(). The second is not implemented since
there did not seem to be a general way to do it. I would help if you
wanted to try coding it up.
Thanks,
Matt
Pierre
On 15/10/21 13:25, Matthew Knepley wrote:
On Fri, Oct 15, 2021 at 7:08 AM Pierre Seize
<[email protected] <mailto:[email protected]>> wrote:
Hi,
I'm writing a code using PETSc to solve NS equations with FV
on an
unstructured mesh. Therefore I use DMPlex.
Regarding periodicity, I manage to implement it this way:
- for each couple of boundaries that is linked with
periodicity, I
create a buffer vector with an ISLocalToGlobalMapping
- then, when I need to fill the ghost cells corresponding
to the
periodicity, the i "true" cell of the local vector fills the
buffer
vector on location i with VecSetValuesBlockedLocal, then
VecAssemblyBegin/VecAssemblyEnd ensure each value is send to
the correct
location thanks to the mapping, then the i "ghost" cell of
the local
vector reads the vector on location i to get it's value.
It works, but it seems to me there is a better way, with
maybe PetscSF,
VecScatter, or something I don't know yet. Does anyone have
any advice ?
There are at least two other ways to handle this. First, the
method that is advocated in
Plex is to actually make a periodic geometry, meaning connect
the cells that are meant
to be connected. Then, if you partition with overlap = 1,
PetscGlobalToLocal() will fill in
these cell values automatically.
Second, you could use a non-periodic geometry, but alter the
LocalToGlobal map such
that the cells gets filled in anyway. Many codes use this scheme
and it is straightforward
with Plex just by augmenting the map it makes automatically.
Does this make sense?
Thanks,
Matt
Pierre Seize
--
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/%7Eknepley/>
--
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/%7Eknepley/>
