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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:
http://thread.gmane.org/gmane.science.simulation.h5md.user/422
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.
Regards,
Peter