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Re: [h5md-user] Finalization of units module


From: Felix Höfling
Subject: Re: [h5md-user] Finalization of units module
Date: Fri, 20 Dec 2013 00:00:22 +0100
User-agent: Opera Mail/12.16 (Linux)

Am 19.12.2013, 22:26 Uhr, schrieb Pierre de Buyl <address@hidden>:

On Thu, Dec 19, 2013 at 05:08:49PM +0100, Felix Höfling wrote:

The collision between hour and Planck's constant is really unfortunate. I
copied the latter from Mosaic, but I'm not aware of an immediate
application in semi-classical MD simulations. So way may drop it. BTW, wth
sufficient knowledge about physical dimensions, the two symbols can not
really be confused---but this can't be expected from automated parsing as
in udunits.

Having "erg" but "dyne" out is a bit inconsistent, I would blame udunits
for this. Dalton and Poise are frequently encountered in scientific
literature, to specify polymer weights and fluid viscosities,
respectively. Anyway, for version 1.0 we may blindly follow udunits and
drop them too if it helps.

For the "degree" issue: I found "degC" in the XML file. We may equally use the longer form or use the extended ASCII character °, both are listed in
udunits2.

Actually, an idea would be to use udunits2 without the data from
udunits2-common.xml that includes completely irrelevant (for us) units such as
"bps" of confusing units such as "cc" (cm+3).

The result would be a comprehensive combination of SI units and commonly used
units ("eV" for instance).

Reducing the set is useful also to avoid backwards compatibility problems.
However, to allows for domain specific uses, it would be good to add an
attribute "system", of simple scalar dataspace and of VL string datatype, to be
complete :-), the value being "SI" for the current set.

P


Such an attribute seems useful to ensure backwards compatibility in the future. Otherwise, we could only extend the set of units in future versions (and could have no contradicting symbols like hour and Planck's constant).

The selection of non-SI-units in udunits appears a bit random, I'm not sure whether we should stick verbatim to this library. For the SI base and derived units, everything is fine though. We could restrict to this set of units, which would be denoted by the value "SI" for the system attribute. However, I'm afraid that many people will dislike the idea to strictly stick to SI.

Other non-SI units may be added later (with appropriately extended values of the system attribute).

As an alternative, we may give up direct interoperability with udunits. Then, the current status would still be a useful description of units which IMO covers most of the research with molecular data in physics, chemistry, and biology. Maybe udunits could even receive an update to support the missing symbols.

I'll be on vacation from tomorrow on, so please go ahead and choose whatever appears more practical.

Merry Christmas,

Felix



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