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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)
? If so, the mesh connectivity is like the one of a torus, then
how does it work with the cells/faces coordinates ?</p>
<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>
<p><br>
</p>
<p>Pierre<br>
</p>
<br>
<div class="moz-cite-prefix">On 15/10/21 15:33, Pierre Seize wrote:<br>
</div>
<blockquote type="cite"
cite="mid:8ff9d951-6958-aa1a-b875-e7488bb6b30b@onera.fr">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<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 class="moz-cite-prefix">On 15/10/21 14:03, Matthew Knepley
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAMYG4Gk+ibpcAdCrCByUebYt6p=dRS9fE3xjA04VeMkmQS65wg@mail.gmail.com">
<div dir="ltr">
<div dir="ltr">On Fri, Oct 15, 2021 at 7:31 AM Pierre Seize
<<a href="mailto:pierre.seize@onera.fr"
moz-do-not-send="true">pierre.seize@onera.fr</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 bgcolor="#FFFFFF">
<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>
</div>
</blockquote>
<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>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF">
<p>Pierre<br>
</p>
<br>
<div>On 15/10/21 13:25, Matthew Knepley wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<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>
<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">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>
</blockquote>
<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>
<blockquote class="gmail_quote" style="margin:0px
0px 0px 0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex"> Pierre Seize<br>
</blockquote>
</div>
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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
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target="_blank"
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<br>
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-- <br>
<div dir="ltr" class="gmail_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/%7Eknepley/"
target="_blank" moz-do-not-send="true">https://www.cse.buffalo.edu/~knepley/</a><br>
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