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On 15/10/21 22:30, Matthew Knepley wrote:<br>
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cite="mid:CAMYG4GnhLHEbJCfcULZ5dcc9uN+5jyvDLe+HPZw4tpMtttC_pg@mail.gmail.com">
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<div dir="ltr">On Fri, Oct 15, 2021 at 10:16 AM Pierre Seize
<<a href="mailto:pierre.seize@onera.fr"
moz-do-not-send="true">pierre.seize@onera.fr</a>> wrote:<br>
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<p>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) ?</p>
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<div>Yes, the DAG would be modified if you want it for some
particular mesh that we cannot read automatically. For
example, we can read periodic GMsh meshes. </div>
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<p> If so, the mesh connectivity is like the one of a
torus, then how does it work with the cells/faces
coordinates ?</p>
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<div>You let the coordinate field be in a DG space, so that it
can have jumps. <br>
</div>
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I'm not sure I fully understand this, what I'll do is that I will
experiment with a periodic GMSH mesh.<br>
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<p>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.</p>
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<div>It is more complicated. We make the LocalToGlobalMap by
looking at the PetscSection (essentially if gives function
space information) and deciding which unknowns are removed
from the global space.</div>
<div>You would need to decide that unknowns constrained by
periodicity are not present in the global space. Actually,
this is not hard. You just mark them as constrained in the
PetscSection, and all the layout</div>
<div>functions will function correctly. However, then the
LocalToGlobalMap will not be exactly right because the
constrained unknowns will not be filled in (just like
Dirichlet conditions). You would augment the</div>
<div>map so that it fills those in by looking up their
periodic counterparts. Jed has argued for this type of
periodicity.</div>
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I also don't understand. One one side of my mesh I have : | ghost1
| cell1 | cell2 | ... and on the other | cell_n-1 | cell_n |
ghost_n |. Are not the ghosts (from DMPlexConstructGhostCells)
already constrained ?<br>
I experimented on that too, I did:<br>
<br>
DMGetSectionSF<br>
PetscSFGetGraph<br>
augment the graph by adding the local ghost cells to the leaves, and
the correct remote "true" cells to the roots<br>
PetscSFSetGraph<br>
<br>
and it seems to do what I want. Is this what you meant ? Is this a
correct way to use the PETSc objects ? Or is this just hacky and I'm
lucky it works ?<br>
<br>
Pierre<br>
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<div>To me, the first kind is much more straightforward, but
maybe this is because I find the topology code more clear.</div>
<div><br>
</div>
<div> Thanks,</div>
<div><br>
</div>
<div> Matt</div>
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<p>Pierre<br>
</p>
<br>
<div>On 15/10/21 15:33, Pierre Seize wrote:<br>
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<p>When I first tried to handle the periodicity, I found
the <tt>DMPlexCreateBoxMesh</tt> function (I cannot
find the cylinder one).</p>
<p>From reading the sources, I understand that we do
some work either in <tt>DMPlexCreateCubeMesh_Internal</tt>
or with <tt>DMSetPeriodicity</tt>.</p>
<p>I tried to use <tt>DMSetPeriodicity</tt> before, for
example with a 2x2 box on length 10. I did something
like:<br>
</p>
<tt> const PetscReal maxCell[] = {2, 2};</tt><tt><br>
</tt><tt>const PetscReal L[] = {10, 10};</tt><tt><br>
</tt><tt>const DMBoundaryType bd[] =
{DM_BOUNDARY_PERIODIC, DM_BOUNDARY_PERIODIC}</tt><tt>;<br>
</tt><tt>DMSetPeriodicity(dm, PETSC_TRUE, maxCell, L,
bd);<br>
</tt><tt>// or:<br>
</tt><tt>DMSetPeriodicity(dm, PETSC_TRUE, NULL, L, bd);</tt><br>
<p>but it did not work: <br>
</p>
<tt>VecSet(X, 1);<br>
DMGetLocalVector(dm, &locX);</tt><tt><br>
</tt><tt>VecZeroEntries(locX);</tt><tt><br>
</tt><tt>DMGlobalToLocalBegin(dm, X, INSERT_VALUES,
locX);</tt><tt><br>
</tt><tt>DMGlobalToLocalEnd(dm, X, INSERT_VALUES, locX);</tt><br>
<tt>VecView(locX, PETSC_VIEWER_STDOUT_WORLD);</tt>
<p>but the ghost cells values are all 0, only the real
cells are 1. So I guess <tt>DMSetPeriodicity</tt>
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 <tt>DMGlobalToLocalBegin/</tt><tt>DMGlobalToLocalEnd</tt>
do exchange values between procs AND exchange the
periodic values?</p>
<p><br>
</p>
<p>Thanks for the help</p>
<p><br>
</p>
<p>Pierre<br>
</p>
<br>
<div>On 15/10/21 14:03, Matthew Knepley wrote:<br>
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<div dir="ltr">On Fri, Oct 15, 2021 at 7:31 AM
Pierre Seize <<a
href="mailto:pierre.seize@onera.fr"
target="_blank" moz-do-not-send="true">pierre.seize@onera.fr</a>>
wrote:<br>
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<p>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 ?<br>
</p>
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<div>The first way is implemented for example in
DMPlexCreateBoxMesh() and
DMPlexCreateCylinderMesh(). The second is not
implemented since</div>
<div>there did not seem to be a general way to do
it. I would help if you wanted to try coding it
up.</div>
<div><br>
</div>
<div> Thanks,</div>
<div><br>
</div>
<div> Matt </div>
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<p>Pierre<br>
</p>
<br>
<div>On 15/10/21 13:25, Matthew Knepley wrote:<br>
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<div dir="ltr">On Fri, Oct 15, 2021 at
7:08 AM Pierre Seize <<a
href="mailto:pierre.seize@onera.fr"
target="_blank" moz-do-not-send="true">pierre.seize@onera.fr</a>>
wrote:<br>
</div>
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<blockquote class="gmail_quote"
style="margin:0px 0px 0px
0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">Hi,<br>
<br>
I'm writing a code using PETSc to
solve NS equations with FV on an <br>
unstructured mesh. Therefore I use
DMPlex.<br>
<br>
Regarding periodicity, I manage to
implement it this way:<br>
<br>
- for each couple of boundaries
that is linked with periodicity, I <br>
create a buffer vector with an
ISLocalToGlobalMapping<br>
<br>
- then, when I need to fill the
ghost cells corresponding to the <br>
periodicity, the i "true" cell of the
local vector fills the buffer <br>
vector on location i with
VecSetValuesBlockedLocal, then <br>
VecAssemblyBegin/VecAssemblyEnd ensure
each value is send to the correct <br>
location thanks to the mapping, then
the i "ghost" cell of the local <br>
vector reads the vector on location i
to get it's value.<br>
<br>
<br>
It works, but it seems to me there is
a better way, with maybe PetscSF, <br>
VecScatter, or something I don't know
yet. Does anyone have any advice ?<br>
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<div><br>
</div>
<div>There are at least two other ways
to handle this. First, the method that
is advocated in</div>
<div>Plex is to actually make a periodic
geometry, meaning connect the cells
that are meant</div>
<div>to be connected. Then, if you
partition with overlap = 1,
PetscGlobalToLocal() will fill in</div>
<div>these cell values automatically.</div>
<div><br>
</div>
<div>Second, you could use a
non-periodic geometry, but alter the
LocalToGlobal map such</div>
<div>that the cells gets filled in
anyway. Many codes use this scheme and
it is straightforward</div>
<div>with Plex just by augmenting the
map it makes automatically.</div>
<div><br>
</div>
<div>Does this make sense?</div>
<div><br>
</div>
<div> Thanks,</div>
<div><br>
</div>
<div> Matt</div>
<div> </div>
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Pierre Seize<br>
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<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>
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<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/%7Eknepley/"
target="_blank"
moz-do-not-send="true">https://www.cse.buffalo.edu/~knepley/</a><br>
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-- <br>
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<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/%7Eknepley/"
target="_blank" moz-do-not-send="true">https://www.cse.buffalo.edu/~knepley/</a><br>
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