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Re: [h5md-user] increasing order of "time" dataset

From: Peter Colberg
Subject: Re: [h5md-user] increasing order of "time" dataset
Date: Thu, 8 May 2014 14:54:42 -0400
User-agent: Mutt/1.5.23 (2014-03-12)

Hi Felix,

On Mon, May 05, 2014 at 05:05:22PM +0200, Felix Höfling wrote:
> I encountered an obstacle with the present specification of the "time"
> dataset of generic H5MD elements. It says "The values of the dataset are
> in monotonically increasing order."
> In specific use cases, it happens that the positions/velocities are
> modified without incrementing time. An example is rescaling of the
> velocities at the end of a run to match a prescribed kinetic energy. In
> the current H5MD spec it is not possible to store the data before and
> after the rescaling as time does not progress. (The step may be
> incremented by convention in such a case.)
> I suggest to relax the condition on the "time" dataset to "non-descreasing
> order". This would not impair binary search strategies in the "time"
> dataset. And time being a floating-point value should not be used to
> uniquely identify a simulation step anyway.

The “time” dataset constraint has been mentioned before:


I think it is good to have the implied uniqueness of the time values.

Could you provide insight why one stores the velocities both before
and after a rescaling? I consider the rescaling part of the MD step
and store the velocities after the rescaling.

> Would this change entail an issue I have overlooked?

Dropping the uniqueness is backwards-incompatible with readers.


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