<head><!-- BaNnErBlUrFlE-HeAdEr-start -->
<style>
#pfptBannerpjl7ft4 { all: revert !important; display: block !important;
visibility: visible !important; opacity: 1 !important;
background-color: #D0D8DC !important;
max-width: none !important; max-height: none !important }
.pfptPrimaryButtonpjl7ft4:hover, .pfptPrimaryButtonpjl7ft4:focus {
background-color: #b4c1c7 !important; }
.pfptPrimaryButtonpjl7ft4:active {
background-color: #90a4ae !important; }
</style>
<!-- BaNnErBlUrFlE-HeAdEr-end -->
</head><!-- BaNnErBlUrFlE-BoDy-start -->
<!-- Preheader Text : BEGIN -->
<div style="display:none !important;display:none;visibility:hidden;mso-hide:all;font-size:1px;color:#ffffff;line-height:1px;height:0px;max-height:0px;opacity:0;overflow:hidden;">
* they do have a vocal mesh, so perhaps They want DM Plex. * they want ghost particle communication, that also might want a mesh * DM swarm does not have a notion of ghost particle, as far as I know, but it could use one On Tue, Jul 30, 2024
</div>
<!-- Preheader Text : END -->
<!-- Email Banner : BEGIN -->
<div style="display:none !important;display:none;visibility:hidden;mso-hide:all;font-size:1px;color:#ffffff;line-height:1px;height:0px;max-height:0px;opacity:0;overflow:hidden;">ZjQcmQRYFpfptBannerStart</div>
<!--[if ((ie)|(mso))]>
<table border="0" cellspacing="0" cellpadding="0" width="100%" style="padding: 16px 0px 16px 0px; direction: ltr" ><tr><td>
<table border="0" cellspacing="0" cellpadding="0" style="padding: 0px 10px 5px 6px; width: 100%; border-radius:4px; border-top:4px solid #90a4ae;background-color:#D0D8DC;"><tr><td valign="top">
<table align="left" border="0" cellspacing="0" cellpadding="0" style="padding: 4px 8px 4px 8px">
<tr><td style="color:#000000; font-family: 'Arial', sans-serif; font-weight:bold; font-size:14px; direction: ltr">
This Message Is From an External Sender
</td></tr>
<tr><td style="color:#000000; font-weight:normal; font-family: 'Arial', sans-serif; font-size:12px; direction: ltr">
This message came from outside your organization.
</td></tr>
</table>
</td></tr></table>
</td></tr></table>
<![endif]-->
<![if !((ie)|(mso))]>
<div dir="ltr" id="pfptBannerpjl7ft4" style="all: revert !important; display:block !important; text-align: left !important; margin:16px 0px 16px 0px !important; padding:8px 16px 8px 16px !important; border-radius: 4px !important; min-width: 200px !important; background-color: #D0D8DC !important; background-color: #D0D8DC; border-top: 4px solid #90a4ae !important; border-top: 4px solid #90a4ae;">
<div id="pfptBannerpjl7ft4" style="all: unset !important; float:left !important; display:block !important; margin: 0px 0px 1px 0px !important; max-width: 600px !important;">
<div id="pfptBannerpjl7ft4" style="all: unset !important; display:block !important; visibility: visible !important; background-color: #D0D8DC !important; color:#000000 !important; color:#000000; font-family: 'Arial', sans-serif !important; font-family: 'Arial', sans-serif; font-weight:bold !important; font-weight:bold; font-size:14px !important; line-height:18px !important; line-height:18px">
This Message Is From an External Sender
</div>
<div id="pfptBannerpjl7ft4" style="all: unset !important; display:block !important; visibility: visible !important; background-color: #D0D8DC !important; color:#000000 !important; color:#000000; font-weight:normal; font-family: 'Arial', sans-serif !important; font-family: 'Arial', sans-serif; font-size:12px !important; line-height:18px !important; line-height:18px; margin-top:2px !important;">
This message came from outside your organization.
</div>
</div>
<div style="clear: both !important; display: block !important; visibility: hidden !important; line-height: 0 !important; font-size: 0.01px !important; height: 0px"> </div>
</div>
<![endif]>
<div style="display:none !important;display:none;visibility:hidden;mso-hide:all;font-size:1px;color:#ffffff;line-height:1px;height:0px;max-height:0px;opacity:0;overflow:hidden;">ZjQcmQRYFpfptBannerEnd</div>
<!-- Email Banner : END -->
<!-- BaNnErBlUrFlE-BoDy-end -->
<div dir="auto">* they do have a vocal mesh, so perhaps They want DM Plex.</div><div dir="auto"><br></div><div dir="auto">* they want ghost particle communication, that also might want a mesh</div><div dir="auto"><br></div><div dir="auto">* DM swarm does not have a notion of ghost particle, as far as I know, but it could use one</div><div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Jul 30, 2024 at 7:58 AM Matthew Knepley <<a href="mailto:knepley@gmail.com">knepley@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="display:none!important;display:none;font-size:1px;color:#ffffff;line-height:1px;height:0px;max-height:0px;opacity:0;overflow:hidden">
On Tue, Jul 30, 2024 at 12: 24 AM Marco Seiz <marco@ kit. ac. jp> wrote: Hello, I'd like to solve transient heat transport at a particle scale using TS, with the per-particle equation being something like dT_i / dt = (S(T_i) + sum(F(T_j,
</div>
<div style="display:none!important;display:none;font-size:1px;color:#ffffff;line-height:1px;height:0px;max-height:0px;opacity:0;overflow:hidden">ZjQcmQRYFpfptBannerStart</div>
<u></u>
<div dir="ltr" id="m_4390999247231378535pfptBanner1pz0wj5" style="display:block!important;text-align:left!important;margin:16px 0px 16px 0px!important;padding:8px 16px 8px 16px!important;border-radius:4px!important;min-width:200px!important;background-color:#d0d8dc!important;background-color:#d0d8dc;border-top:4px solid #90a4ae!important;border-top:4px solid #90a4ae">
<div id="m_4390999247231378535pfptBanner1pz0wj5" style="float:left!important;display:block!important;margin:0px 0px 1px 0px!important;max-width:600px!important">
<div id="m_4390999247231378535pfptBanner1pz0wj5" style="display:block!important;background-color:#d0d8dc!important;color:#000000!important;color:#000000;font-family:'Arial',sans-serif!important;font-family:'Arial',sans-serif;font-weight:bold!important;font-weight:bold;font-size:14px!important;line-height:18px!important;line-height:18px">
This Message Is From an External Sender
</div>
<div id="m_4390999247231378535pfptBanner1pz0wj5" style="display:block!important;background-color:#d0d8dc!important;color:#000000!important;color:#000000;font-weight:normal;font-family:'Arial',sans-serif!important;font-family:'Arial',sans-serif;font-size:12px!important;line-height:18px!important;line-height:18px;margin-top:2px!important">
This message came from outside your organization.
</div>
</div>
<div style="clear:both!important;display:block!important;line-height:0!important;font-size:0.01px!important;height:0px"> </div>
</div>
<u></u>
<div style="display:none!important;display:none;font-size:1px;color:#ffffff;line-height:1px;height:0px;max-height:0px;opacity:0;overflow:hidden">ZjQcmQRYFpfptBannerEnd</div>
<div dir="ltr"><div dir="ltr">On Tue, Jul 30, 2024 at 12:24 AM Marco Seiz <<a href="mailto:marco@kit.ac.jp" target="_blank">marco@kit.ac.jp</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><u></u>
<div style="font-size:1px;color:rgb(255,255,255);line-height:1px;height:0px;max-height:0px;opacity:0;overflow:hidden;display:none">
Hello, I'd like to solve transient heat transport at a particle scale using TS, with the per-particle equation being something like dT_i / dt = (S(T_i) + sum(F(T_j, T_i), j connecting to i)) with a nonlinear source term S and a conduction term
</div>
<div style="font-size:1px;color:rgb(255,255,255);line-height:1px;height:0px;max-height:0px;opacity:0;overflow:hidden;display:none">ZjQcmQRYFpfptBannerStart</div>
<u></u>
<div dir="ltr" id="m_4390999247231378535m_-1596636162298961751pfptBannerniaaxqr" style="display:block;text-align:left;margin:16px 0px;padding:8px 16px;border-radius:4px;min-width:200px;background-color:rgb(208,216,220);border-top:4px solid rgb(144,164,174)">
<div id="m_4390999247231378535m_-1596636162298961751pfptBannerniaaxqr" style="float:left;display:block;margin:0px 0px 1px;max-width:600px">
<div id="m_4390999247231378535m_-1596636162298961751pfptBannerniaaxqr" style="display:block;background-color:rgb(208,216,220);color:rgb(0,0,0);font-family:Arial,sans-serif;font-weight:bold;font-size:14px;line-height:18px">
This Message Is From an External Sender
</div>
<div id="m_4390999247231378535m_-1596636162298961751pfptBannerniaaxqr" style="font-weight:normal;display:block;background-color:rgb(208,216,220);color:rgb(0,0,0);font-family:Arial,sans-serif;font-size:12px;line-height:18px;margin-top:2px">
This message came from outside your organization.
</div>
</div>
<div style="height:0px;clear:both;display:block;line-height:0;font-size:0.01px"> </div>
</div>
<u></u>
<div style="font-size:1px;color:rgb(255,255,255);line-height:1px;height:0px;max-height:0px;opacity:0;overflow:hidden;display:none">ZjQcmQRYFpfptBannerEnd</div>
<div><pre style="font-family:sans-serif;font-size:100%;white-space:pre-wrap">Hello,
I'd like to solve transient heat transport at a particle scale using TS, with the per-particle equation being something like
dT_i / dt = (S(T_i) + sum(F(T_j, T_i), j connecting to i))
with a nonlinear source term S and a conduction term F. The particles can move, deform and grow/shrink/vanish on a voxel grid, but for the temperature a particle-scale resolution should be sufficient. The particles' connectivity will change during the simulation, but is assumed constant during a single timestep. I have a data structure tracking the particles' connectivity, so I can say which particles should conduct heat to each other. I exploit symmetry and so only save the "forward" edges, so e.g. for touching particles 1->2->3, I only store [[2], [3], []], from which the full list [[2], [1, 3], [2]] could be reconstructed but which I'd like to avoid. In parallel each worker would own some of the particle data, so e.g. for the 1->2->3 example and 2 workers, worker 0 could own [[2]] and worker 1 [[3],[]].
Looking over the DM variants, either DMNetwork or some manual mesh build with DMPlex seem suited for this. I'd especially like it if the adjacency information is handled by the DM automagically based on the edges so I don't have to deal with ghost particle communication myself. I already tried something basic with DMNetwork, though for some reason the offsets I get from DMNetworkGetGlobalVecOffset() are larger than the actual network. I've attached what I have so far but comparing to e.g. src/snes/tutorials/network/ex1.c I don't see what I'm doing wrong if I don't need data at the edges. I might not be seeing the trees for the forest though. The output with -dmnetwork_view looks reasonable to me. Any help in fixing this approach, or if it would seem suitable pointers to using DMPlex for this problem, would be appreciated.</pre></div></div></blockquote><div>To me, this sounds like you should built it with DMSwarm. Why?</div><div><br></div><div>1) We only have vertices and edges, so a mesh does not buy us anything.</div><div><br></div><div>2) You are managing the parallel particle connectivity, so DMPlex topology is not buying us anything. Unless I am misunderstanding.</div><div><br></div><div>3) DMNetwork has a lot of support for vertices with different characteristics. Your particles all have the same attributes, so this is unnecessary.</div><div><br></div><div>How would you set this up?</div><div><br></div><div>1) Declare all particle attributes. There are many Swarm examples, but say ex6 which simulates particles moving under a central force.</div><div><br></div><div>2) That example decides when to move particles using a parallel background mesh. However, you know which particles you want to move,</div><div> so you just change the _rank_ field to the new rank and call DMSwarmMigrate() with migration type _basic_.</div><div><br></div><div>It should be straightforward to setup a tiny example moving around a few particles to see if it does everything you want.</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"><div><div><pre style="font-family:sans-serif;font-size:100%;white-space:pre-wrap">Best regards,
Marco</pre></div></div></blockquote></div></div><div dir="ltr"><span class="gmail_signature_prefix">-- </span><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="https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!bLVHnoUGooYpdfGD8zNQrHTY2ln70W082hEc6pG7vdjA2fCvs77tcI9d7QOA0i_FjGK1of3nNOKXCE-4Rwb0$" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br></div></div></div></div></div></div></div></div>
</blockquote></div></div>