[gmx-developers] Small hack regarding dihedrals

[Berk Hess]

But note that in 4.6 with SIMD (SSE/AVX) enablebd, dihedrals mostly 
(when only forces, no energies are needed) get calculated by a special 
SIMD dihedral function. You will need modifiy the conditional such that 
the plain C function always gets called.

Cheers,

Berk

On 09/26/2013 08:04 AM, MURAT OZTURK wrote:
> Thank you very much. I need to build a toy system to test it, but 
> sounds just about right. I might even hard-code the square of 
> threshold to save another flop, following your philosophy. A flop is a 
> flop :)
>
> Again, thank you.
>
> Murat
>
>
> On Thu, Sep 26, 2013 at 12:10 AM, Bogdan Costescu <bcostescu at gmail.com 
> <mailto:bcostescu at gmail.com>> wrote:
>
>     On Wed, Sep 25, 2013 at 5:29 PM, MURAT OZTURK <murozturk at ku.edu.tr
>     <mailto:murozturk at ku.edu.tr>> wrote:
>     > Is it OK to intorduce the conditional into pdihs(), and bypass
>     even calling
>     > dopdihs() if r_kj  ( as reported by calling dih_angle() ) is
>     less then
>     > threshold?
>
>     Yes. It makes sense to abort calculating as soon as you have enough
>     information to make the decision. You can place your test immediately
>     after calling dih_angle(), as it gives you r_jk. The code could look
>     like (based on your own proposal):
>
>     /* outside of the loop */
>     threshold2 = threshold * threshold;
>
>     for (i = 0; (i < nbonds); )
>     {
>       ...
>       phi = dih_angle(...)
>       midDist2 = iprod(r_jk, r_jk);
>       if (midDist2 > threshold2)
>         continue;
>       ...
>     }
>
>     Please note the comparison done on the squares of distances instead of
>     distances, saving some CPU cycles.
>
>     Good luck!
>     Bogdan
>     --
>     gmx-developers mailing list
>     gmx-developers at gromacs.org <mailto:gmx-developers at gromacs.org>
>     http://lists.gromacs.org/mailman/listinfo/gmx-developers
>     Please don't post (un)subscribe requests to the list. Use the
>     www interface or send it to gmx-developers-request at gromacs.org
>     <mailto:gmx-developers-request at gromacs.org>.
>
>
>
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20130926/eb23d3bd/attachment.html>