<div dir="ltr">Hi,<div><br></div><div>This isn't related to using tables per se, but rather with using potentials that lack singularities that prevent r=0 in practice. I think such kernels should rather use an approach like that we use for exclusions:</div><div><br></div><div>rsqmod = (rsq == 0) ? smallnumber : rsq;</div><div>rinv = invsqrt(rsqmod);</div><div>rinv = (rsq == 0) ? 0 : rinv;</div><div><br></div><div>and maybe a mask on energies also.</div><div><br></div><div>gmx::sqrt in the SIMD module is also an option that implements the same kind of conditionality, but doesn't solve the need to have a functional rinv.</div><div><br></div><div>Mark</div></div><br><div class="gmail_quote"><div dir="ltr">On Wed, Mar 23, 2016 at 1:42 PM David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">On 23/03/16 13:31, Berk Hess wrote:<br>
> Hi,<br>
><br>
> But avoiding the inversion is not possible, since you need to multiply<br>
> the scaling force by the normalized distance vector.<br>
The force should be zero at r=0 for symmetry reasons and hence the code<br>
should not crash.<br>
><br>
> Berk<br>
><br>
> On 2016-03-23 13:00, David van der Spoel wrote:<br>
>> Hi,<br>
>><br>
>> In all versions of gromacs the distance between two nonbonded atoms is<br>
>> computed as<br>
>> rinv00 = gmx_invsqrt(rsq00);<br>
>> r00 = rsq00*rinv00;<br>
>><br>
>> This is fine when we use Lennard Jones and Coulomb, but not when using<br>
>> table potentials which do not necessarily have singularities at r = 0.<br>
>> I would therefore propose to replace the statements by a normal sqrt<br>
>> in all innerloops using tables.<br>
>><br>
>> Thoughts?<br>
><br>
<br>
<br>
--<br>
David van der Spoel, Ph.D., Professor of Biology<br>
Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br>
<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se" rel="noreferrer" target="_blank">http://folding.bmc.uu.se</a><br>
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