[gmx-developers] Increase the scope of dd domains

Berk Hess hess at kth.se
Fri Aug 28 20:25:55 CEST 2015


If rlist=1, you should have access to all pairs up to 1 nm.

One more question:
You do check/print the pairs on all ranks, not only on the master rank?



On 08/28/2015 08:15 PM, Xingcheng Lin wrote:
> Hi Berk,
> Yes, I think I was calling that after the coordinate communication. 
> The place where I code it in is after the command:
>    if (bDoForces)
>    {
>       post_process_forces(fplog, cr, step, nrnb, wcycle,
>         top, box, x, f, vir_force, mdatoms, graph, fr, vsite,
>         flags);
>    }
> After that I use a
> if(bNS){
>       if (DOMAINDECOMP(cr)){
> to make sure it is done every neighboring list step.
> Is this correct? BTW, I was coding that in gromacs4.6.3 version (this 
> is for historical reason because I have coded other unrelated things 
> in other files).
> I have checked that the ga2la_get_home in the first loop find all ai 
> atoms, but the second loop ga2la_get missed some aj atoms. One of the 
> reasons I guess is because the missing atom pairs are too far apart 
> (but less than 6 angstroms) in Cartesian space from each other, so 
> that even by including all cells of the home node it still could not 
> find it. That could be a problem, but I don't know exactly how -dd 
> find this pair partner in its neighboring cells.
> Thank you,
> Xingcheng

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