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Re: [h5md-user] attribute modification_time

From: Felix Höfling
Subject: Re: [h5md-user] attribute modification_time
Date: Wed, 29 May 2013 17:36:09 +0200
User-agent: Opera Mail/12.15 (Linux)

Am 29.05.2013, 16:51 Uhr, schrieb Peter Colberg <address@hidden>:

On Wed, May 29, 2013 at 01:07:36PM +0200, Felix Höfling wrote:
the /h5md group contains the attribute "creation_time". I suggest to
provide "modification_time" (or "last_modified") as well to document
manipulations of the H5MD file after the initial simulation. The
description could be:

modification_time: The time when then file was modified last. It
uses the same format as "creation_time". H5MD writers are advised to
update the field just before closing the file.

What do you think?

When a simulation has finished successfully, I `chmod 444` the input
and output files and never write to them again. That practice should
be standard for molecular simulations.

Of course users are free to modify their files after the fact, but
should this behaviour be encouraged by the specification?


Just some examples:

A user may decide to continue a simulation and to append the results to the same file.

One may want to delete some unneeded data groups after a while (data that should not have been written in the first place).

A H5MD file may also facilitate the setup of more complex systems und therefore undergo further processing: first equilibrate a homogeneous system, then cut out a region and replace it by something else. Or bringing two separate systems into contact.

Of course, these things could be split across several files which is at some variance to the HDF5 idea of having everything in one file. And for such cases, it makes sense to record what happened. As this easily opens Pandora's box we may forget about it for the upcoming first release.


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