<head><!-- BaNnErBlUrFlE-HeAdEr-start -->
<style>
#pfptBannerfo726oo { all: revert !important; display: block !important;
visibility: visible !important; opacity: 1 !important;
background-color: #D0D8DC !important;
max-width: none !important; max-height: none !important }
.pfptPrimaryButtonfo726oo:hover, .pfptPrimaryButtonfo726oo:focus {
background-color: #b4c1c7 !important; }
.pfptPrimaryButtonfo726oo: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;">
On Sun, May 19, 2024 at 8: 25 PM Barry Smith <bsmith@ petsc. dev> wrote: You can call MatSetOption(mat,MAT_NEW_NONZERO_LOCATION_ERR) then insert the new values. If it is just a handful of new insertions the extra time should be small. Making
</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="pfptBannerfo726oo" 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="pfptBannerfo726oo" style="all: unset !important; float:left !important; display:block !important; margin: 0px 0px 1px 0px !important; max-width: 600px !important;">
<div id="pfptBannerfo726oo" 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="pfptBannerfo726oo" 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="ltr"><div dir="ltr">On Sun, May 19, 2024 at 8:25 PM Barry Smith <<a href="mailto:bsmith@petsc.dev">bsmith@petsc.dev</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 class="msg3902608206431091064">
<div style="font-size:1px;color:rgb(255,255,255);line-height:1px;height:0px;max-height:0px;opacity:0;overflow:hidden;display:none">
You can call MatSetOption(mat,MAT_NEW_NONZERO_LOCATION_ERR) then insert the new values. If it is just a handful of new insertions the extra time should be small. Making a copy of the matrix won't give you a new matrix that is any faster to
</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_3902608206431091064pfptBannergqdbr2p" 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_3902608206431091064pfptBannergqdbr2p" style="float:left;display:block;margin:0px 0px 1px;max-width:600px">
<div id="m_3902608206431091064pfptBannergqdbr2p" 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_3902608206431091064pfptBannergqdbr2p" 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><div><br></div> You can call MatSetOption(mat,MAT_NEW_NONZERO_LOCATION_ERR) then insert the new values. If it is just a handful of new insertions the extra time should be small.<div><br></div><div> Making a copy of the matrix won't give you a new matrix that is any faster to insert into so best to just use the same matrix.</div></div></div></blockquote><div><br></div><div>Let me add to Barry's answer. The preallocation infrastructure is now not strictly necessary. It is possible to just add all your nonzeros in and assembly, and the performance will be pretty good (uses hashing etc). So if just adding a few nonzeros does not work, we can go this route.</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 class="msg3902608206431091064"><div><div> Barry</div><div><br id="m_3902608206431091064lineBreakAtBeginningOfMessage"><div><br><blockquote type="cite"><div>On May 19, 2024, at 7:44 PM, Adrian Croucher <<a href="mailto:a.croucher@auckland.ac.nz" target="_blank">a.croucher@auckland.ac.nz</a>> wrote:</div><br><div><div dir="ltr" id="m_3902608206431091064pfptBannerk8ad5io" style="writing-mode:revert;color:revert;font-family:revert;font-feature-settings:revert;font-kerning:revert;font-size:revert;font-stretch:revert;font-variant-alternates:revert;font-variant-caps:revert;font-variant-east-asian:revert;font-variant-ligatures:revert;font-variant-numeric:revert;font-weight:revert;text-orientation:revert;zoom:revert;letter-spacing:revert;background-blend-mode:revert;background-image:revert;background-position:revert;background-repeat:revert;background-size:revert;border-collapse:revert;box-sizing:revert;break-after:revert;break-before:revert;break-inside:revert;caption-side:revert;clear:revert;columns:revert;column-fill:revert;column-gap:revert;column-rule:revert;column-span:revert;empty-cells:revert;float:revert;image-orientation:revert;isolation:revert;line-break:revert;line-height:revert;list-style:revert;mix-blend-mode:revert;object-fit:revert;object-position:revert;outline:revert;overflow:revert;quotes:revert;table-layout:revert;text-align:left;text-align-last:revert;text-decoration:revert;text-emphasis:revert;text-indent:revert;text-overflow:revert;text-transform:revert;text-underline-position:revert;vertical-align:revert;white-space:revert;word-break:revert;border-spacing:revert;word-spacing:revert;background-clip:revert;background-origin:revert;text-combine-upright:revert;display:block;opacity:revert;background-color:rgb(208,216,220);border-bottom:revert;border-left:revert;border-right:revert;height:revert;max-height:revert;max-width:revert;min-height:revert;width:revert;margin:16px 0px;padding:8px 16px;border-radius:4px;min-width:200px;border-top:4px solid rgb(144,164,174)"><div id="m_3902608206431091064pfptBannerk8ad5io" style="writing-mode:unset;color:unset;font-family:unset;font-feature-settings:unset;font-kerning:unset;font-size:unset;font-stretch:unset;font-variant-alternates:unset;font-variant-caps:unset;font-variant-east-asian:unset;font-variant-ligatures:unset;font-variant-numeric:unset;font-weight:unset;text-orientation:unset;zoom:unset;letter-spacing:unset;background:unset;background-blend-mode:unset;border-collapse:unset;border:unset;box-sizing:unset;break-after:unset;break-before:unset;break-inside:unset;caption-side:unset;clear:unset;columns:unset;column-fill:unset;column-gap:unset;column-rule:unset;column-span:unset;empty-cells:unset;float:left;image-orientation:unset;isolation:unset;line-break:unset;line-height:unset;list-style:unset;mix-blend-mode:unset;object-fit:unset;object-position:unset;outline:unset;overflow:unset;quotes:unset;table-layout:unset;text-align:unset;text-align-last:unset;text-decoration:unset;text-emphasis:unset;text-indent:unset;text-overflow:unset;text-transform:unset;text-underline-position:unset;vertical-align:unset;white-space:unset;word-break:unset;border-spacing:unset;word-spacing:unset;text-combine-upright:unset;display:block;opacity:unset;border-radius:unset;height:unset;max-height:unset;min-height:unset;min-width:unset;padding:unset;width:unset;margin:0px 0px 1px;max-width:600px"><div id="m_3902608206431091064pfptBannerk8ad5io" style="writing-mode:unset;font-family:Arial,sans-serif;font-feature-settings:unset;font-kerning:unset;font-size:14px;font-stretch:unset;font-variant-alternates:unset;font-variant-caps:unset;font-variant-east-asian:unset;font-variant-ligatures:unset;font-variant-numeric:unset;font-weight:bold;text-orientation:unset;zoom:unset;letter-spacing:unset;background-blend-mode:unset;background-image:unset;background-position:unset;background-repeat:unset;background-size:unset;border-collapse:unset;border:unset;box-sizing:unset;break-after:unset;break-before:unset;break-inside:unset;caption-side:unset;clear:unset;columns:unset;column-fill:unset;column-gap:unset;column-rule:unset;column-span:unset;empty-cells:unset;float:unset;image-orientation:unset;isolation:unset;line-break:unset;line-height:18px;list-style:unset;mix-blend-mode:unset;object-fit:unset;object-position:unset;outline:unset;overflow:unset;quotes:unset;table-layout:unset;text-align:unset;text-align-last:unset;text-decoration:unset;text-emphasis:unset;text-indent:unset;text-overflow:unset;text-transform:unset;text-underline-position:unset;vertical-align:unset;white-space:unset;word-break:unset;border-spacing:unset;word-spacing:unset;background-clip:unset;background-origin:unset;text-combine-upright:unset;display:block;opacity:unset;background-color:rgb(208,216,220);border-radius:unset;height:unset;margin:unset;max-height:unset;max-width:unset;min-height:unset;min-width:unset;padding:unset;width:unset">This Message Is From an External Sender</div><div id="m_3902608206431091064pfptBannerk8ad5io" style="writing-mode:unset;font-family:Arial,sans-serif;font-feature-settings:unset;font-kerning:unset;font-size:12px;font-stretch:unset;font-variant-alternates:unset;font-variant-caps:unset;font-variant-east-asian:unset;font-variant-ligatures:unset;font-variant-numeric:unset;font-weight:unset;text-orientation:unset;zoom:unset;letter-spacing:unset;background-blend-mode:unset;background-image:unset;background-position:unset;background-repeat:unset;background-size:unset;border-collapse:unset;border:unset;box-sizing:unset;break-after:unset;break-before:unset;break-inside:unset;caption-side:unset;clear:unset;columns:unset;column-fill:unset;column-gap:unset;column-rule:unset;column-span:unset;empty-cells:unset;float:unset;image-orientation:unset;isolation:unset;line-break:unset;line-height:18px;list-style:unset;mix-blend-mode:unset;object-fit:unset;object-position:unset;outline:unset;overflow:unset;quotes:unset;table-layout:unset;text-align:unset;text-align-last:unset;text-decoration:unset;text-emphasis:unset;text-indent:unset;text-overflow:unset;text-transform:unset;text-underline-position:unset;vertical-align:unset;white-space:unset;word-break:unset;border-spacing:unset;word-spacing:unset;background-clip:unset;background-origin:unset;text-combine-upright:unset;display:block;opacity:unset;background-color:rgb(208,216,220);border-radius:unset;height:unset;margin-bottom:unset;margin-left:unset;margin-right:unset;max-height:unset;max-width:unset;min-height:unset;min-width:unset;padding:unset;width:unset;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><pre style="font-size:18px;font-style:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;word-spacing:0px;text-decoration:none;font-family:sans-serif;white-space:pre-wrap">hi,
I have a Jacobian matrix created using DMCreateMatrix(). What would be
the best way to add extra nonzero entries into it?
I'm guessing that DMCreateMatrix() allocates the storage so the nonzero
structure can't really be easily modified. Would it be a case of
creating a new matrix, copying the nonzero entries from the original one
and then adding the extra ones, before calling MatSetUp() or similar? If
so, how exactly would you copy the nonzero structure from the original
matrix?
Background: the flow problem I'm solving (on a DMPlex with finite volume
method) has complex source terms that depend on the solution (e.g.
pressure), and can also depend on other source terms. A simple example
is when fluid is extracted from one location, with a pressure-dependent
flow rate, and some of it is then reinjected in another location. This
can result in poor nonlinear solver convergence. I think the reason is
that there are effectively missing Jacobian entries in the row for the
reinjection cell, which should have an additional dependence on the
solution in the cell where fluid is extracted.
- Adrian
--
Dr Adrian Croucher
Senior Research Fellow
Department of Engineering Science
Waipapa Taumata Rau / University of Auckland, New Zealand
email: <a href="mailto:a.croucher@auckland.ac.nz" target="_blank">a.croucher@auckland.ac.nz</a>
tel: +64 (0)9 923 4611
</pre><br></div></blockquote></div><br></div></div></div></blockquote></div><br clear="all"><div><br></div><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!ZAicuPSGpbQ0tcP9ZNf7TPN7b-DE4XuRcqUtAUEsr_yk9p2EAWn5wSAIdkxE7SYHsDeBftI_qWDRw4vwJWdb$" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br></div></div></div></div></div></div></div></div>