Re: [h5md-user] H5MD discussions

[Felix Höfling]

Salut Pierre, Hallo Peter,

So let me start the dicussion on this provisional "list".

I have still some issues with the trajectory group of H5MD:

1) Rigid particles (like true colloids, not composed of many particles)  
have additional degrees of freedom. I suggest to optionally extend the  
trajectory group by groups "orientation" (a unit vector,  or angles? The  
vector appears less ambiguous than definitions of Euler angles) and  
"angular_velocity" (this is an axial vector, so actually a traceless,  
symmetric tensor of rank 2, but can be stored as a vector).

2) In NTP simulations, for example, the volume of the simulation box  
fluctuates. This shall be supported by a generic MD file format. (I'm not  
sure whether and how periodic boundaries are applied in this case, maybe  
they are not used in all directions.)

My suggestion is a separate data group "box" in trajectory along with its  
own timestamp, which may contain a single entry only if the box remains  
fixed. The relevant value of box at a given point in time is determined  
from the latest stored value before or at that point in time.

3) Specification of a box with non-orthogonal edges requires more than  
giving just two corners, it also requires some information about the  
angles. To me, it appears more direct if the edge vectors of the box would  
be stored for this general case. This would imply two datasets: "offset"  
and "edges", where the latter is a d×d matrix with the edge vectors as  
rows. For a cuboid box of lengths L_x, L_y, L_z centered around the  
origin, one would have:

offset (-L_x/2, -L_y/2, -L_z/2)
edges ((L_x, 0, 0), (0, L_y, 0), (0, 0, L_z))
time (0)
step (0)

This suggestion contains some redundancy (e.g., the zeros), but appears  
the most general and manageable to me.

Please let me know what you think about these ideas.

Cheers,
Felix


Am 16.06.2011, 20:26 Uhr, schrieb Peter Colberg  
<address@hidden>:

> Hello Felix, hello Pierre,
>
> by this mail, I shall officially establish contact between both of you
> to discuss the first specification of H5MD, while the public H5MD
> mailing list is still pending. Be sure to include me in CC:.
>
> Peter


--
Dr. Felix Höfling
Max Planck Institute for Intelligent Systems
(formerly Max Planck Institute for Metals Research)
Heisenbergstr. 3
70569 Stuttgart
Germany

Phone:  +49 711 689 1938
Fax:    +49 711 689 1922