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Re: [h5md-user] Update on H5MD from Stuttgart

From: Felix Höfling
Subject: Re: [h5md-user] Update on H5MD from Stuttgart
Date: Thu, 18 Jul 2013 09:04:22 +0200
User-agent: Opera Mail/12.15 (Linux)

Am 17.07.2013, 21:25 Uhr, schrieb Pierre de Buyl <address@hidden>:

On Wed, Jul 17, 2013 at 11:30:54AM -0400, Peter Colberg wrote:
On Wed, Jul 17, 2013 at 02:28:28PM +0200, Pierre de Buyl wrote:

> Within the box description, the nature of the boundaries of the box were still > missing, although discussed on the list. "type" is to be replaced by "geometry" > and "boundary" is to be added, with the value "open" or "periodic" in each
> dimension.

What is the value of “boundary” in the presence of walls?

Note the definition of a closed system in thermodynamics: The system
is closed with regard to flow of mass, but open with regard to flow
of work and heat. Maybe it should be made explicit that “closed” and
“open” only refers to the flow of mass through the boundaries.

"open" was chosen to specify "non-periodic". Indeed, a lot of the discussion of this morning was about avoiding confusion and ambiguities. A solution would be
to have
- "open": no wall and no pbc
- "closed": walls, not specifying (yet) what kind of wall it is.
- "periodic": periodic

Hi Peter and Pierre,

before we start to distinguish between "open" and "closed", I would like to remark that walls are a certain form of an external potential. (It does not even matter whether the walls are made up of particles or are given as a potential in closed analytic form). Another example for an external potential is a random (but smooth) energy landscape.

The presence of an external potential does not affect the boundary conditions and vice versa. If the particles are hindered by the potential to reach the end of the box, fine. (Then, the BC does not even matter). On the other hand, an external potential may be combined with periodic BCs.

Instead of "open BC" I have also encountered the terminus "free BC" (check Google for this). In the context of partial differential equations this means that there is no constraint at the boundary, which is precisely the meaning we intended.

Best regards,


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