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Re: [h5md-user] Offset

From: Felix Höfling
Subject: Re: [h5md-user] Offset
Date: Mon, 23 Sep 2013 15:27:01 +0200
User-agent: Opera Mail/12.15 (Linux)

Am 11.09.2013, 13:13 Uhr, schrieb Konrad Hinsen <address@hidden>:

Pierre de Buyl writes:

 > Some people work with [-L/2:L/2], others with [0:L].
 > offset is there so that users may dump their position data without
 > operation between memory and file, whatever box convention they use.

Do I conclude then that "offset" is supposed to be -L/2 in the first
case, and 0 in the second?

Olaf Lenz writes:

> I was always wondering about the offset, but I didn't want to start that
 > discussion. Thanks, Konrad. :-/
 > The offset is mathematically irrelevant.

I agree.

 > I also do not see what the offset is needed for in the file.

I'd look at this from a different point of view: if it's there, what
information does it convey? What conclusion can a trajectory reader
draw from it?

 > The only case that I can think of where the offset might be useful is,
 > when it is somehow guaranteed that the positions are all within the
 > primary image that is defined by the offset and the edges.


 > Therefore, from my point of view, the offset is useless and can be
 > removed from the specs.

Or add a guarantee about the positions being in the primary image to
the specs. From my experience, that can be useful information to have.


The purpose of the offset was precisely this guarantee, although it got lost in the course of time. Originally, we had minimum and maximum coordinates for the particle positions which where then replaced by the offset (plus edge lengths).

The current draft says that particle positions are stored "as periodically wrapped or unwrapped coordinate vectors". What decides whether they are wrapped or not? (BTW, if the word "folded" is more common the spec should use it.) If the positions are wrapped, then it is easy to add the guarantee that they are within the primary box.


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