h5md-user
[Top][All Lists]
Advanced

[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [h5md-user] fix remaining imprecisions - particle position


From: Olaf Lenz
Subject: Re: [h5md-user] fix remaining imprecisions - particle position
Date: Fri, 10 Jan 2014 16:21:52 +0100

2014/1/10 Pierre de Buyl <address@hidden>:
> For those components where `boundary` is set to "none", any value of
> `edges` or `image` must be silently ignored.

Any value of `image` then. Edges only play a role if 'image' is different from
zero.
 
No! That is exactly *not* true. It makes perfect sense to specify periodic boundary conditions, an edge, but no image! This is exactly the case when you use what I call absolute coordinates, where the positions may be outside the box.

To clarify, let me try to make some examples of possible cases, all of which do make sense! I am now specifying only one dimension and a single particle with a position x=20.3. In the periodic case, the edge is 10.0.

Case 1: Open boundaries

  boundary = "none"
  position[0] = 20.3

In this case, any value of 'edge' or 'image' has to be ignored.

Case 2: Periodic boundaries, with folded positions and image specification

  boundary = "periodic"
  edge[0] = 10.0
  position[0] = 0.3
  image[0] = 2

This is probably the standard case that most people think of.

Case 3: Periodic boundaries, with absolute positions and without image

  boundary = "periodic"
  edge[0] = 10.0
  position[0] = 20.3

This case also makes sense when a software never explicitly computes the image the particle is in.

Case 4: Periodic boundaries, with folded positions that may lie outside the primary image ("mixed")

  boundary = "periodic"
  edge[0] = 10.0
  position[0] = 10.3
  image[0] = 1

This case might look weird, but it does make perfect sense in some simulation packages.

Olaf

--
Dr. rer. nat. Olaf Lenz
Institut für Computerphysik, Allmandring 3, D-70569 Stuttgart
Phone: +49-711-685-63607

reply via email to

[Prev in Thread] Current Thread [Next in Thread]