<div dir="ltr">... and for the low-level table code we (or somebody else :-) still need to sit down and work through the math how we should specify tolerances (that are used to set spacing) for arbitrary cases where the tabulated function or its derivative has a zero-value in the relevant range.<div><br></div><div>Cheers,</div><div><br></div><div>Erik </div></div><br><div class="gmail_quote"><div dir="ltr">On Wed, Nov 14, 2018 at 2:12 AM Berk Hess <<a href="mailto:hess@kth.se">hess@kth.se</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
<div class="m_4502320658897670284moz-cite-prefix">Hi,<br>
<br>
I don't really think we need a usecase, but more people motivated
to work on it.<br>
<br>
We have delayed the work also because we are waiting for a new
non-bonded kernel structure. But we just as well start without
that, since it will not take much work to port the additional
tabulated kernels to a new framework.<br>
<br>
What is a dependency is a selecting the table index based on atom
type (pairs). We want to get rid of the (mis)use of energy groups
for this purpose in the group scheme.<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 13/11/2018 23.53, Mark Abraham wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi,
<div><br>
</div>
<div>Not much has happened. I did some basic cleanup, and Erik
has worked on some table classes in src/gromacs/tables.
Alfredo has some old GPU kernels buried somewhere on Gerrit.</div>
<div><br>
</div>
<div>It would be good to identify a use case that someone has
interest in to e.g. contribute coding time, test cases, design
idea sounding board. AFAIK none of the GROMACS core developers
uses this feature, so their priorities tend to align
elsewhere. However, we know it's useful to people, so we'd
like to find a group that can work together to make it happen!</div>
<div><br>
</div>
<div>Some of those dot points are a bit out of date, but the
general list of things to do is about right.</div>
<div><br>
</div>
<div>Mark</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr">On Tue, Nov 13, 2018 at 3:48 PM Adriaan Riet <<a href="mailto:adriaan.riet@case.edu" target="_blank">adriaan.riet@case.edu</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hello everyone,
<div><br>
</div>
<div>I know that Feature #1347 talks about the necessary
steps to get tables into Verlet (pasted below). I'm
curious to know where this sits. I'm happy to contribute
where (if) I can, but don't see clearly where to jump in.
Have the points of the list been integrated into redmine
feature requests? Have any of these been implemented yet?</div>
<div><br>
</div>
<div>Thanks,</div>
<div>Adriaan Riet</div>
<div><br>
</div>
<div>
<p style="color:rgb(51,51,51);font-family:Verdana,sans-serif;font-size:12px">Things
to do (roughly in order):</p>
<ul style="margin-bottom:1em;color:rgb(51,51,51);font-family:Verdana,sans-serif;font-size:12px">
<li>support regressiontests being able to read tables
from grompp or mdrun, so that new functionality in the
code doesn't need matching changes to the other repo
for valid testing in the few cases where they use
tables (<code>*CSTab*</code> in
group-scheme kernels)</li>
<li>add integration tests, e.g. a Martini-style(?)
non-bonded, and several kinds of bonded interactions</li>
<li>extract code from mdlib (particularly init_forcerec)
so that it is callable at grompp time, make sure
grompp can issue all notes and warnings, permit mdrun
to repeat any of those that it might need to. Keep
code for making hardware-specific layout decisions in
mdrun, because we won't know whether the kernels need
tables for CPUs or GPUs until then. If we can do it
without significant loss of accuracy, grompp should
handle any regularization of the user input (e.g. by
constructing and testing CPU and GPU tables, if
necessary).</li>
<li>move e.g. dihedral-interaction table reading to
grompp, bump .tpr version, write to .tpr, read in
mdrun, add infrastructure to support gmx check and gmx
dump on new .tpr contents</li>
<li>move angle- and bond-interaction table reading to
grompp, probably another .tpr version bump</li>
<li>move short-range interaction tables to grompp for
group scheme</li>
<li>extend <code>[pairs]</code> to
permit atom-type pairs to use an interaction shape
read from a table, e.g. from a file named on that line
of the topology. Should we have a per-pair-type
scaling parameter? Requirements for simulations that
use only user tables, and those that mix user tables
with normal short-ranged interaction types probably
differ.</li>
<li>add Verlet-scheme table-support infrastructure</li>
<li>add CPU kernels (hopefully in new scheme)</li>
<li>add GPU kernels (recycle from Alfredo's patch in
gerrit)</li>
<li>after some time passes and master branch rebases
enough, remove workaround from regressiontests (which
is anyway only needed for group-scheme kernel testing)</li>
</ul>
</div>
</div>
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