[gmx-developers] Use of invsqrt with tables

[Berk Hess]

Hi,

I tried to explain that this doesn't work. If rsq is GMX_REAL_MIN you 
still get overflows during later operations.
For float you can do:
invr = invsqrt(r2 + 1e-38)

Berk

On 2016-03-23 14:06, Mark Abraham wrote:
> Hi,
>
> 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:
>
> rsqmod = (rsq == 0) ? smallnumber : rsq;
> rinv = invsqrt(rsqmod);
> rinv = (rsq == 0) ? 0 : rinv;
>
> and maybe a mask on energies also.
>
> 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.
>
> Mark
>
> On Wed, Mar 23, 2016 at 1:42 PM David van der Spoel 
> <spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>> wrote:
>
>     On 23/03/16 13:31, Berk Hess wrote:
>     > Hi,
>     >
>     > But avoiding the inversion is not possible, since you need to
>     multiply
>     > the scaling force by the normalized distance vector.
>     The force should be zero at r=0 for symmetry reasons and hence the
>     code
>     should not crash.
>     >
>     > Berk
>     >
>     > On 2016-03-23 13:00, David van der Spoel wrote:
>     >> Hi,
>     >>
>     >> In all versions of gromacs the distance between two nonbonded
>     atoms is
>     >> computed as
>     >>             rinv00           = gmx_invsqrt(rsq00);
>     >>             r00              = rsq00*rinv00;
>     >>
>     >> This is fine when we use Lennard Jones and Coulomb, but not
>     when using
>     >> table potentials which do not necessarily have singularities at
>     r = 0.
>     >> I would therefore propose to replace the statements by a normal
>     sqrt
>     >> in all innerloops using tables.
>     >>
>     >> Thoughts?
>     >
>
>
>     --
>     David van der Spoel, Ph.D., Professor of Biology
>     Dept. of Cell & Molec. Biol., Uppsala University.
>     Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>     spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
>     http://folding.bmc.uu.se
>     --
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