[gmx-developers] local atom number from global atom number

[Mark Abraham]

On 11/04/2012 7:28 AM, Dmitry Nerukh wrote:
>
> Hi,
>
> When using MPI, how do I calculate the local atom number from the 
> global one?  The code given here
>
> http://www.gromacs.org/Developer_Zone/Programming_Guide/Programmer%27s_Guide#local_index
>
> does not work for the latest gromacs 4.5.5 which I need.  Also, if I 
> understand correctly, the given code only works for domain 
> decomposition.  I need a universal method... Thanks!
>

Then you'll have to see how particle decomposition (and current DD) does 
it by looking at the code. It won't be any harder than the snippet there 
suggests. Of course, a static guide will go out of date as the code changes.

> My ultimate goal is to hack mdrun such that I can output only a few 
> atoms' positions and velocities, say atoms 0,1, and 3, but fairly 
> frequently (say, every 10 steps).
>

nstxtcout, xtc_precision and xtc_grps can solve this problem already.

Mark
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