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Re: [h5md-user] Offset

From: Pierre de Buyl
Subject: Re: [h5md-user] Offset
Date: Tue, 10 Sep 2013 12:04:02 -0400
User-agent: Internet Messaging Program (IMP) H4 (5.0.21)

Konrad Hinsen <address@hidden> a écrit :

My converter for protein trajectories is making good progress: for
non-periodic simulations, it seems to work.

While working on periodic boxes, I hit a problem: I don't understand
what the "offset" value is supposed to contain, nor even why it
exists. The periodicity of a system in space is fully described by
three lattice vectors, which are stored in "edges".

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.


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