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Re: [h5md-user] The Box Story

From: Pierre de Buyl
Subject: Re: [h5md-user] The Box Story
Date: Fri, 27 Sep 2013 21:36:28 +0200
User-agent: Mutt/1.5.21 (2010-09-15)


Thanks Konrad for proposing this "poll" method. Sorry for not following Peter's
thread but the propositions were lost.

On Thu, Sep 26, 2013 at 09:19:36AM +0200, Konrad Hinsen wrote:
> Proposition 1: Store a single time series with box information for the
> whole trajectory. It must cover at least those steps for which any
> position information is stored. The box information for a given step
> must be retrieved by binary search for random-access step
> retrieval. For sequential traversal of the trajectory, more efficient
> methods are available.
>  + Simplicity. Easy to understand, easy to check.
>  + Efficient storage: no duplication of box data.
>  - Box information retrieval is less efficient.
>  - Parallel writing (in the sense of parallel I/O) of independent
>    position time series requires coordination between processes.

   - Cannot accomodate parallel tempering simulations.

> Proposition 2: With every position time series, store a box time
> series at exactly the same step numbers. If multiple such box time
> series are identical, links can be used to avoid duplicating the data.
>  + Efficient random read access to positions with matching box information.

   + Can accomodate parallel tempering simulations.

   + Allows to separate easily a sub-trajectory.

>  - Efficient writing (without data duplication) requires some effort
>    and careful thought.

I was at first strongly in favour of having only /observables/box (mostly
because it is a O(1) data). As some parts of /particles/<my super particles
group name> might need the box data (among other reasons for visualizations), I
prefer /particles/<mspgn>/box
So, in the end, I prefer 2 above.

I have mentioned parallel tempering, but there could also be systems that
consist of coupled parts that each have their box.

In addition, there is still some box info in observables.


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