<!-- 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;">
Thanks again Matt, that makes a lot more sense !! Just to check that we are on the same page. You are saying: 1. create a field define a field called "owner rank" for each particle. 2. Identify the phantom particles and modify the
</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="pfptBanner4pso0j7" 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="pfptBanner4pso0j7" style="all: unset !important; float:left !important; display:block !important; margin: 0px 0px 1px 0px !important; max-width: 600px !important;">
<div id="pfptBanner4pso0j7" 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="pfptBanner4pso0j7" 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 -->
<html>
<head><!-- BaNnErBlUrFlE-HeAdEr-start -->
<style>
#pfptBanner4pso0j7 { all: revert !important; display: block !important;
visibility: visible !important; opacity: 1 !important;
background-color: #D0D8DC !important;
max-width: none !important; max-height: none !important }
.pfptPrimaryButton4pso0j7:hover, .pfptPrimaryButton4pso0j7:focus {
background-color: #b4c1c7 !important; }
.pfptPrimaryButton4pso0j7:active {
background-color: #90a4ae !important; }
</style>
<!-- BaNnErBlUrFlE-HeAdEr-end -->
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head>
<body style="overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;">
<div>
<div>Thanks again Matt, that makes a lot more sense !!</div>
<div><br>
</div>
<div>Just to check that we are on the same page. You are saying: </div>
<div><br>
</div>
<div>1. create a field define a field called "owner rank" for each particle. </div>
<div><br>
</div>
<div>2. Identify the phantom particles and modify the internal variable defined by the DMSwarmField_rank variable. </div>
<div><br>
</div>
<div>3. Call DMSwarmMigrate(*,PETSC_FALSE), do the calculations using the new local vector including the ghost particles. </div>
<div><br>
</div>
<div>4. Then, once the calculations are done, rename the DMSwarmField_rank variable using the "owner rank" variable and call DMSwarmMigrate(*,PETSC_FALSE) once again.</div>
<div><br>
</div>
<div>Thank you,</div>
<div>Miguel</div>
<div><br>
</div>
<div><br>
</div>
<div>
<blockquote type="cite">
<div>On Aug 2, 2024, at 5:33 PM, Matthew Knepley <knepley@gmail.com> wrote:</div>
<br class="Apple-interchange-newline">
<div>
<div dir="ltr" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;">
<div dir="ltr">On Fri, Aug 2, 2024 at 11:15 AM MIGUEL MOLINOS PEREZ <<a href="mailto:mmolinos@us.es">mmolinos@us.es</a>> wrote:<br>
</div>
<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>Thank you Matt for your time,
<div><br>
</div>
<div>What you describe seems to me the ideal approach. </div>
<div><br>
</div>
<div>
<blockquote type="cite">
<div dir="ltr">
<div class="gmail_quote">
<div>1) Add a particle field 'ghost' that identifies ghost vs owned particles. I think it needs options OWNED, OVERLAP, and GHOST</div>
</div>
</div>
</blockquote>
<div>This means, locally, I need to allocate Nlocal + ghost particles (duplicated) for my model?</div>
</div>
</div>
</blockquote>
<div><br>
</div>
<div>I would do it another way. I would allocate the particles with no overlap and set them up. Then I would identify the halo particles, mark them as OVERLAP, call DMSwarmMigrate(), and mark the migrated particles as GHOST, then unmark the OVERLAP particles.
Shoot! That marking will not work since we cannot tell the difference between particles we received and particles we sent. Okay, instead of the `ghost` field we need an `owner rank` field. So then we</div>
<div><br>
</div>
<div>1) Setup the non-overlapping particles</div>
<div><br>
</div>
<div>2) Identify the halo particles</div>
<div><br>
</div>
<div>3) Change the `rank`, but not the `owner rank`</div>
<div><br>
</div>
<div>4) Call DMSwarmMigrate()</div>
<div><br>
</div>
<div>Now we can identify ghost particles by the `owner rank`</div>
<div> </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>
<div>
<div>If that so, how to do the communication between the ghost particles living in the rank i and their “real” counterpart in the rank j.</div>
</div>
<div><br>
</div>
<div>Algo, as an alternative, what about:</div>
<div>1) Use an IS tag which contains,<span style=""> </span><span style="">for each rank,</span><span style=""> a </span>list of the global index of the neighbors particles outside of the rank. </div>
<div>2) Use <span style="color: rgb(75, 81, 1); font-family: Menlo, Monaco, "Courier New", monospace; white-space: pre-wrap; background-color: rgb(255, 255, 255);">VecCreateGhost t</span>o create a new vector which contains extra local space for the ghost components
of the vector. </div>
<div>3) Use <font color="#4e4900" style="font-family: Menlo, Monaco, "Courier New", monospace; white-space: pre-wrap; background-color: rgb(255, 255, 255);">VecScatterCreate,
</font><span style="font-family: Menlo, Monaco, "Courier New", monospace; white-space: pre-wrap; background-color: rgb(255, 255, 255); color: rgb(78, 73, 0);">VecScatterBegin, and
</span><span style="font-family: Menlo, Monaco, "Courier New", monospace; white-space: pre-wrap; background-color: rgb(255, 255, 255); color: rgb(78, 73, 0);">VecScatterEnd
</span>to do the transference of data between a vector obtained with<span class="Apple-converted-space"> </span><span style="color: rgb(99, 99, 36); font-family: Menlo, Monaco, "Courier New", monospace; white-space: pre-wrap; background-color: rgb(255, 255, 255);">
DMSwarmCreateGlobalVectorFromField</span> </div>
<div>4) Do necessary computations using the vectors created with <span style="color: rgb(75, 81, 1); font-family: Menlo, Monaco, "Courier New", monospace; white-space: pre-wrap; background-color: rgb(255, 255, 255);">VecCreateGhost</span>.</div>
</div>
</blockquote>
<div><br>
</div>
<div>This is essentially what Migrate() does. I was trying to reuse the code.</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-width: 1px; border-left-style: solid; border-left-color: rgb(204, 204, 204); padding-left: 1ex;">
<div>
<div>Thanks,</div>
<div>Miguel</div>
<div>
<div><br>
<blockquote type="cite">
<div>On Aug 2, 2024, at 8:58 AM, Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>> wrote:</div>
<br>
<div>
<div dir="ltr">
<div dir="ltr">On Thu, Aug 1, 2024 at 4:40 PM MIGUEL MOLINOS PEREZ <<a href="mailto:mmolinos@us.es" target="_blank">mmolinos@us.es</a>> wrote:<br>
</div>
<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><u></u><u></u>
<div dir="ltr" id="m_5114540859675030278m_6853013589290146639pfptBanner8j38xab" 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-width: 4px; border-top-style: solid; border-top-color: rgb(144, 164, 174);">
<div id="m_5114540859675030278m_6853013589290146639pfptBanner8j38xab" style="float: left; display: block; margin: 0px 0px 1px; max-width: 600px;">
<div id="m_5114540859675030278m_6853013589290146639pfptBanner8j38xab" style="display: block; background-color: rgb(208, 216, 220); font-family: Arial, sans-serif; font-weight: bold; font-size: 14px; line-height: 18px;">
This Message Is From an External Sender<span class="Apple-converted-space"> </span></div>
<div id="m_5114540859675030278m_6853013589290146639pfptBanner8j38xab" style="font-weight: normal; display: block; background-color: rgb(208, 216, 220); font-family: Arial, sans-serif; font-size: 12px; line-height: 18px; margin-top: 2px;">
This message came from outside your organization.<span class="Apple-converted-space"> </span></div>
</div>
<div style="height: 0px; clear: both; display: block; line-height: 0; font-size: 0.01px;">
</div>
</div>
<u></u>
<div>
<pre style="font-family: sans-serif; font-size: 12px; white-space: pre-wrap;">Dear all,
I am implementing a Molecular Dynamics (MD) code using the DMSWARM interface. In the MD simulations we evaluate on each particle (atoms) some kind of scalar functional using data from the neighbouring atoms. My problem lies in the parallel implementation of the model, because sometimes, some of these neighbours lie on a different processor.
This is usually solved by using ghost particles. A similar approach (with nodes instead) is already implemented for other PETSc mesh structures like DMPlexConstructGhostCells. Unfortunately, I don't see this kind of constructs for DMSWARM. Am I missing something?
I this could be done by applying a buffer region by exploiting the background DMDA mesh that I already use to do domain decomposition. Then using the buffer region of each cell to locate the ghost particles and finally using VecCreateGhost. Is this feasible? Or is there an easier approach using other PETSc functions.</pre>
</div>
</div>
</blockquote>
<div><br>
</div>
<div>This is feasible, but it would be good to develop a set of best practices, since we have been mainly focused on the case of non-redundant particles. Here is how I think I would do what you want.</div>
<div><br>
</div>
<div>1) Add a particle field 'ghost' that identifies ghost vs owned particles. I think it needs options OWNED, OVERLAP, and GHOST</div>
<div><br>
</div>
<div>2) At some interval identify particles that should be sent to other processes as ghosts. I would call these "overlap particles". The determination</div>
<div> seems application specific, so I would leave this determination to the user right now. We do two things to these particles</div>
<div><br>
</div>
<div> a) Mark chosen particles as OVERLAP</div>
<div><br>
</div>
<div> b) Change rank to process we are sending to</div>
<div><br>
</div>
<div>3) Call DMSwarmMigrate with PETSC_FALSE for the particle deletion flag</div>
<div><br>
</div>
<div>4) Mark OVERLAP particles as GHOST when they arrive</div>
<div><br>
</div>
<div>There is one problem in the above algorithm. It does not allow sending particles to multiple ranks. We would have to do this</div>
<div>in phases right now, or make a small adjustment to the interface allowing replication of particles when a set of ranks is specified.</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-width: 1px; border-left-style: solid; border-left-color: rgb(204, 204, 204); padding-left: 1ex;">
<div>
<div>
<pre style="font-family: sans-serif; font-size: 12px; white-space: pre-wrap;">Thank you,
Miguel
</pre>
</div>
</div>
</blockquote>
</div>
<br clear="all">
<div><br>
</div>
<span class="gmail_signature_prefix">--<span class="Apple-converted-space"> </span></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!YUCXV0Md1eeDXw0O-sIM1ttHyCHlD3L9TKHf-ojo81xTW1wSCAlD3ilqjvUp-jFdEJos7OcgQNHzLbZZLJUNUA$" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</div>
</blockquote>
</div>
<br clear="all">
<div><br>
</div>
<span class="gmail_signature_prefix">--<span class="Apple-converted-space"> </span></span><br>
<div dir="ltr" class="gmail_signature">
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
-- Norbert Wiener</div>
<div><br>
</div>
<div><a href="https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!YUCXV0Md1eeDXw0O-sIM1ttHyCHlD3L9TKHf-ojo81xTW1wSCAlD3ilqjvUp-jFdEJos7OcgQNHzLbZZLJUNUA$" target="_blank">https://www.cse.buffalo.edu/~knepley/</a></div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</body>
</html>