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

Mark Abraham Mark.Abraham at anu.edu.au
Wed Apr 11 02:24:38 CEST 2012

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 Of course, a static guide will go out of date as the code changes.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.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20120411/459094b0/attachment.html>

More information about the gromacs.org_gmx-developers mailing list