<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head>
<body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
Hi Matthew,
<div class=""><br class="">
</div>
<div class="">So I’m discretizing via a tensor product of Lagrange polynomials co-located at the Gauss-Lobatto-Legendre (GLL) points. The polynomial order might range from 4 to 10 or something like that. The current problem is solved on 2D hexes. </div>
<div class="">
<div class=""><br class="">
</div>
<div class="">I had found DMPlexCreateSection, and followed plex/ex1to get things set up. You can see my attempt below. Basically I’ve got 4 fields (displacement, velocity, acceleration, and strain) over each element. Here I’ve tried to setup a tensor product
of 4th order (5 GLL points) Lagrange polynomials (line 11). This seemed to <i class="">
somewhat</i> achieve what I wanted — I created a global vector and wrote it to a vtk file with VecView, and the numbering seemed to make sense. You can also see my attempt at defining a boundary condition (it looked like DMPlexCreateFromExodus labeled side
sets as “Face Sets”, seems to have worked). </div>
<div class=""><br class="">
</div>
<div class="">Does this seem to be headed in the right direction?</div>
<div class=""><br class="">
</div>
<div class="">Cheers,</div>
<div class="">Mike.</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">DM</div>
<div class="">mesh::createSection(const DM &dm)</div>
<div class="">{</div>
<div class=""><br class="">
</div>
<div class="">01 // displacement, velocity, acceleration, strain</div>
<div class="">02 IS bcPointIs[1];</div>
<div class="">03 PetscInt numBc = 1;</div>
<div class="">04 PetscInt bcField[1];</div>
<div class="">05 PetscInt numFields = 4;</div>
<div class="">06 PetscInt dim; DMGetDimension(dm, &dim);</div>
<div class="">07 PetscInt numComp[numFields];</div>
<div class="">08 for (auto i=0; i<numFields; i++) {numComp[i] = dim;}</div>
<div class="">09 PetscInt numDof[numFields*(dim+1)];</div>
<div class="">10 for (auto i=0; i<numFields*(dim+1); i++) {numDof[i] = 0;}</div>
<div class="">11 for (auto i=0; i<numFields; i++) {numDof[i*(dim+1)+dim] = 5;}</div>
<div class="">12 bcField[0] = 0;</div>
<div class="">13 PetscSection section;</div>
<div class="">14 DMPlexGetStratumIS(dm, "Face Sets", 1, &bcPointIs[0]);</div>
<div class="">15 DMPlexCreateSection(dm, dim, numFields, numComp, numDof, numBc, bcField,</div>
<div class="">16 NULL, bcPointIs, NULL, §ion);</div>
<div class="">17 ISDestroy(&bcPointIs[0]);</div>
<div class="">18 PetscSectionSetFieldName(section, 0, "u");</div>
<div class="">19 PetscSectionSetFieldName(section, 1, "v");</div>
<div class="">20 PetscSectionSetFieldName(section, 2, "a");</div>
<div class="">21 PetscSectionSetFieldName(section, 3, "e");</div>
<div class="">22 DMSetDefaultSection(dm, section);</div>
<div class="">23 return dm;</div>
<div class="">}</div>
</div>
<div class=""><br class="">
<div apple-content-edited="true" class="">--<br class="">
Michael Afanasiev<br class="">
Ph.D. Candidate<br class="">
Computational Seismology<br class="">
Institut für Geophysik<br class="">
ETH Zürich<br class="">
<br class="">
Sonneggstrasse 5, NO H 39.2<br class="">
CH 8092 Zürich<br class="">
<a href="mailto:michael.afanasiev@erdw.ethz.ch" class="">michael.afanasiev@erdw.ethz.ch</a><br class="">
</div>
<br class="">
<div>
<blockquote type="cite" class="">
<div class="">On Oct 22, 2015, at 2:32 AM, Matthew Knepley <<a href="mailto:knepley@gmail.com" class="">knepley@gmail.com</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div dir="ltr" style="font-family: Optima-Regular; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<div class="gmail_extra">
<div class="gmail_quote">On Wed, Oct 21, 2015 at 3:07 PM, Dave May<span class="Apple-converted-space"> </span><span dir="ltr" class=""><<a href="mailto:dave.may@erdw.ethz.ch" target="_blank" class="">dave.may@erdw.ethz.ch</a>></span><span class="Apple-converted-space"> </span>wrote:<br class="">
<blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex;">
<div dir="ltr" class="">Hey Mike,<br class="">
<br class="">
<br class="">
<div class="gmail_extra"><br class="">
<div class="gmail_quote">On 21 October 2015 at 18:01, Afanasiev Michael<span class="Apple-converted-space"> </span><span dir="ltr" class=""><<a href="mailto:michael.afanasiev@erdw.ethz.ch" target="_blank" class="">michael.afanasiev@erdw.ethz.ch</a>></span><span class="Apple-converted-space"> </span>wrote:<br class="">
<blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-style: solid; border-left-color: rgb(204, 204, 204); padding-left: 1ex;">
<div style="word-wrap: break-word;" class="">Hey Dave,
<div class=""><br class="">
</div>
<div class="">So I’ve got a couple of days where there’s nothing pressing to work on… was thinking of ripping out the parallel routines (ugly) in my wave propagation code and replacing them with Petsc DM routines. I can read in my exodusii mesh with DMPLEX,
and partition it with chaco, which gives me a nicely partitioned DM. This takes me like 5 lines of code. That’s amazing.</div>
<div class=""><br class="">
</div>
<div class="">But here I’m stuck, and am having a whale of a time with the documentation. All I<span class="Apple-converted-space"> </span><i class="">think</i><span class="Apple-converted-space"> </span>I need is a way to modify the exodus-created DM, and
add to it the degrees of freedom that are introduced by my quadrature rule. This would be really neat. I can just treat each sub-domain as its own mesh, with its own global numbering. Then whenever necessary I can scatter stuff the the<span class="Apple-converted-space"> </span><i class="">real</i> global
degrees of freedom with something like VecLocToGlob. Most of the things I like about the code could stay the same (element-wise, matrix-free nature), just these parallel broadcasts would be infinitely nicer.</div>
<div class=""><br class="">
</div>
</div>
</blockquote>
<div class=""><br class="">
</div>
<div class="">First off - I don't use DMPLEX.</div>
</div>
</div>
</div>
</blockquote>
<div class=""><br class="">
</div>
<div class="">Dave is refreshingly candid about his shortcomings ;)</div>
<div class=""> </div>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex;">
<div dir="ltr" class="">
<div class="gmail_extra">
<div class="gmail_quote">
<div class=""> </div>
</div>
</div>
</div>
</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex;">
<div dir="ltr" class="">
<div class="gmail_extra">
<div class="gmail_quote">
<div class=""></div>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-style: solid; border-left-color: rgb(204, 204, 204); padding-left: 1ex;">
<div style="word-wrap: break-word;" class="">
<div class=""></div>
<div class="">But I just can’t figure out how to set this up. The main problem really boils down to: what’s the best way to add my quadrature points to an already-created DM, which was constructed with an exodus file? I guess I could do this after the file
is read, but before the partitioning. In this case though, what’s stopping the partitioner from cutting an element in half? It seems like it would be a lot cleaner to do this post-partitioning.</div>
<div class=""><br class="">
</div>
</div>
</blockquote>
<div class=""><br class="">
</div>
<div class="">Presumably what is read from exodus is just the vertices of the hexes, and what you want to do is define the function space (given by your GLL locations) on top of element geometry read in. Is that what you are asking about?</div>
</div>
</div>
</div>
</blockquote>
<div class=""><br class="">
</div>
<div class="">So Dave is right. We read in topology and geometry from ExodusII. Then you define a function space on top. How</div>
<div class="">exactly are you discretizing? In order to create vectors, do local to global, etc. Petsc really only need to know the</div>
<div class="">amount of data associated with each mesh piece. You can define this with PetscSection. If you give me an idea</div>
<div class="">what you want I can help you write the code easily I think.</div>
<div class=""><br class="">
</div>
<div class=""> Thanks,</div>
<div class=""><br class="">
</div>
<div class=""> Matt</div>
<div class=""> </div>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex;">
<div dir="ltr" class="">
<div class="gmail_extra">
<div class="gmail_quote">
<blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-style: solid; border-left-color: rgb(204, 204, 204); padding-left: 1ex;">
<div style="word-wrap: break-word;" class="">
<div class=""></div>
<div class="">Any hints here?</div>
</div>
</blockquote>
<div class=""><br class="">
</div>
<div class="">Actually I have no experience with this object.<br class="">
I would just send an email to<span class="Apple-converted-space"> </span><br class="">
</div>
<div class=""> <span class="Apple-converted-space"> </span><a href="mailto:petsc-users@mcs.anl.gov" target="_blank" class="">petsc-users@mcs.anl.gov</a><br class="">
</div>
<div class="">asking for help.<br class="">
</div>
<div class=""> <br class="">
</div>
<div class="">The developer of DMPLEX (Matt Knepley) will definitely answer within in 1 day.<br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Cheers,<br class="">
</div>
<div class=""> Dave<br class="">
</div>
<div class=""><br class="">
</div>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-style: solid; border-left-color: rgb(204, 204, 204); padding-left: 1ex;">
<div style="word-wrap: break-word;" class="">
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Mike.<span class="HOEnZb"><font color="#888888" class=""><br class="">
<div class="">--<br class="">
Michael Afanasiev<br class="">
Ph.D. Candidate<br class="">
Computational Seismology<br class="">
Institut für Geophysik<br class="">
ETH Zürich<br class="">
<br class="">
Sonneggstrasse 5, NO H 39.2<br class="">
CH 8092 Zürich<br class="">
<a href="mailto:michael.afanasiev@erdw.ethz.ch" target="_blank" class="">michael.afanasiev@erdw.ethz.ch</a><br class="">
</div>
<br class="">
</font></span></div>
</div>
</blockquote>
</div>
<br class="">
</div>
</div>
</blockquote>
</div>
<br class="">
<br clear="all" class="">
<div class=""><br class="">
</div>
--<span class="Apple-converted-space"> </span><br class="">
<div class="gmail_signature">What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br class="">
-- Norbert Wiener</div>
</div>
</div>
</div>
</blockquote>
</div>
<br class="">
</div>
</div>
</body>
</html>