[gmx-developers] accessing atoms position with domain decomposition

[Berk Hess]

Hi,

If you do not want to  compromise parallel efficiency,
your code should be parallel as well.
A good example might be the pull code.
Here only one global operation is required, a sum to determine the centers
of mass of one ore more groups of atoms. All the rest of the pull code 
works locally.
For the pull code there the local pull groups are constructed each time 
the domain
decomposition is repartitioned.
There is a ga2la struct in gmx_domdec_t with which you can ask if a certain
global atom index is locally present and what its local number is,
see http://wiki.gromacs.org/index.php/Data_Structures#gmx_ga2la_t

But if you operate on very many atoms, this can be an expensive 
operation, since it requires
access to a global index over the whole system.

If you are lucky, your algorithms might work similar to the pull code,
so you can look at how the pull code is implemented with domain 
decomposition.

Berk

Massimiliano Bonomi wrote:
> Dear Gromacs Developers,
>
> I would like to make the external plugin PLUMED working with
> gromacs 4 and the domain decomposition.
> This plugin adds additional forces on selected atoms.
> For this reason, the plugin needs to access to the position of these 
> atoms
> at every time step.
>
> Is there an efficient way to accomplish this when using domain 
> decomposition?
>
> Since this is a problem related to many computational technique, such as
> steering, umbrella sampling..., have you planned to develop a general 
> interface
> which makes the position of a list of atoms available at request 
> without compromising
> the parallel efficiency of the code?
>
> Best regards,
> Massimiliano
>
> -------------------------------------------------------------------------------------------------------- 
>
> ETH Zürich
> Massimiliano Bonomi
> Computational Science, Department of Chemistry and Applied Biosciences,
> c/o USI Campus, via Giuseppe Buffi 13,
> CH-6900 Lugano, Switzerland
>
> mbonomi at ethz.ch
> massimiliano.bonomi at gmail.com
>
> http://www.rgp.ethz.ch
>
> +41 58 666 48 03           phone
> +41 58 666 48 17           fax
> massimiliano.bonomi    skype
>
>
>
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