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Re: [h5md-user] boundary conditions (again)
From: |
Peter Colberg |
Subject: |
Re: [h5md-user] boundary conditions (again) |
Date: |
Thu, 1 Aug 2013 11:52:34 -0400 |
User-agent: |
Mutt/1.5.21 (2010-09-15) |
On Thu, Aug 01, 2013 at 11:06:40AM -0400, Peter Colberg wrote:
> On Thu, Aug 01, 2013 at 02:19:13PM +0200, Felix Höfling wrote:
> > Am 01.08.2013, 14:11 Uhr, schrieb Pierre de Buyl
> > <address@hidden>:
> >
> > >On Thu, Aug 01, 2013 at 10:50:25AM +0200, Felix Höfling wrote:
> > >>"cuboid" is to be understood as "hypercuboid" with a straightforward
> > >>generalisation to dimensions lower and higher than 3. I think the
> > >>main purpose of these attributes is to discriminate between the
> > >>various shapes of edges: a vector for cuboid, and a set of vectors
> > >>for triclinic.
> > >>
> > >>What about dropping the "geometry" attribute and interpreting
> > >>"edges" according to its shape? See the attached patch for details.
> > >>I have also included a scalar shape for a natural support of the
> > >>simplest and very common case: cubic boxes.
> > >>
> > >
> > >cuboid and triclinic are 3D but the specifications then refers to
> > >D-dimensional
> > >data so that there is no confusion.
> > >
> > >Interpreting "edges" to infer "geometry" is an opposite way of
> > >working than what
> > >you suggested in the past :-)
> > >I can live with both situations but keeping "geometry" seems more
> > >simple to me.
> > >
> >
> > I was in favour of the "dimension" attribute since the dimension is of
> > interest in different situations, independently of the box edges.
> >
> > The "geometry" attribute, on the other hand, appears to have a useful
> > interpretation only in conjuction with the values in edges. So one has to
> > read "edges" anyway. This motivated the suggested modification.
>
> I am also in favour of dropping the geometry attribute. Felix, please
> go ahead with the changes, including the boundary values "periodic"
> and "none".
I missed the detail of a scalar shape for cubic boxes.
I sort of prefer edges to convey the dimensionality of the box (apart
from the dimension attribute), and have one common dimension with the
offset attribute. Therefore I suggest to leave it at the choice of a
vector or a matrix shape for edges.
Peter