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hi, I've been trying creating a matrix with DMCreateMatrix() and then adding extra blocks of nonzeros into it using MatSetValuesBlocked(), but getting some unexpected results if I set the matrix type to BAIJ. It seems to behave as expected
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<p>hi,</p>
<p>I've been trying creating a matrix with DMCreateMatrix() and then
adding extra blocks of nonzeros into it using
MatSetValuesBlocked(), but getting some unexpected results if I
set the matrix type to BAIJ. It seems to behave as expected if I
use matrix type AIJ.</p>
<p>I've attached a minimal example program. It reads in the DMPlex
from file, sets up a section on it, creates a matrix (blocksize 2)
and then inserts a single 2x2 block at global block indices (0,7).
It views the matrix before and after the insertion.<br>
</p>
<p>If I run with "-dm_mat_type aij" it gives the expected results,
but with "-dm_mat_type baij" it doesn't - e.g. if run in serial,
it adds the new nonzeros in the right place but also adds a whole
lot of other duplicated entries in block row 0.<br>
</p>
<p>Is there something I'm not understanding about BAIJ, or about
MatSetValuesBlocked()? or possibly some other mistake?<br>
</p>
<p>- Adrian<br>
</p>
<div class="moz-cite-prefix">On 20/05/24 12:24 pm, Barry Smith
wrote:<br>
</div>
<blockquote type="cite" cite="mid:4368DA96-759E-4831-8BCF-710F265A4728@petsc.dev">
<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><br>
</div>
<div> Barry</div>
<div><br id="lineBreakAtBeginningOfMessage">
<div><br>
<blockquote type="cite">
<div>On May 19, 2024, at 7:44 PM, Adrian Croucher
<a class="moz-txt-link-rfc2396E" href="mailto:a.croucher@auckland.ac.nz"><a.croucher@auckland.ac.nz></a> wrote:</div>
<br class="Apple-interchange-newline">
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-webkit-user-modify: unset !important; -webkit-user-select: unset !important; word-spacing: unset !important; background-clip: unset !important; background-origin: unset !important; box-shadow: unset !important; mask-composite: unset !important; mask-mode: unset !important; text-combine-upright: unset !important; -webkit-backdrop-filter: unset !important; -webkit-background-clip: unset !important; -webkit-background-origin: unset !important; -webkit-box-shadow: unset !important; mask-size: unset !important; -webkit-mask: unset !important; -webkit-mask-composite: unset !important; -webkit-mask-source-type: unset !important; -webkit-text-combine: unset !important; display: block !important; visibility: visible !important; opacity: unset !important; background-color: rgb(208, 216, 220) !important; block-size: unset !important; border-block: unset !important; border-radius: unset !important; border-end-end-radius: unset !important; border-end-start-radius: unset !important; border-inline: unset !important; border-start-end-radius: unset !important; border-start-start-radius: unset !important; inset: unset !important; contain-intrinsic-block-size: unset !important; contain-intrinsic-size: unset !important; contain-intrinsic-inline-size: unset !important; height: unset !important; inline-size: unset !important; inset-block: unset !important; inset-inline: unset !important; margin-block: unset !important; margin-bottom: unset !important; margin-inline: unset !important; margin-left: unset !important; margin-right: unset !important; max-block-size: unset !important; max-height: unset !important; max-inline-size: unset !important; max-width: unset !important; min-block-size: unset !important; min-height: unset !important; min-inline-size: unset !important; min-width: unset !important; overscroll-behavior-block: unset !important; overscroll-behavior-inline: unset !important; overscroll-behavior: unset !important; padding-block: unset !important; padding: unset !important; padding-inline: unset !important; scroll-margin-block: unset !important; scroll-margin: unset !important; scroll-margin-inline: unset !important; scroll-padding-block: unset !important; scroll-padding: unset !important; scroll-padding-inline: unset !important; width: unset !important; margin-top: 2px !important;">This
message came from outside your organization.</div>
</div>
</div>
<pre style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: sans-serif; white-space: pre-wrap; overflow-wrap: break-word;">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" moz-do-not-send="true" class="moz-txt-link-freetext">a.croucher@auckland.ac.nz</a>
tel: +64 (0)9 923 4611
</pre>
<br class="Apple-interchange-newline">
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</div>
</blockquote>
<pre class="moz-signature" cols="72">--
Dr Adrian Croucher
Senior Research Fellow
Department of Engineering Science
Waipapa Taumata Rau / University of Auckland, New Zealand
email: <a class="moz-txt-link-abbreviated" href="mailto:a.croucher@auckland.ac.nz">a.croucher@auckland.ac.nz</a>
tel: +64 (0)9 923 4611</pre>
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