[h5md-user] tentative of synthesis: parameters, box size, particle number

[Pierre de Buyl]

Hi everyone,

There has been a lot of traffic on the list and I couldn't keep up.  
I'll try to make a synthesis of my suggestions, remarks and questions.

Please, if possible, keep the discussion in this single thread so as  
to remain focused on these items.

1. parameters "subgroups"
     - I think it is a good idea to devise a few (let us keep it to  
a minimum) shared parameters and to put program parameters in "/ 
parameters/program_name".
     - In my opinion, time-dependent information should not be in  
"parameters" but in "observables".

2. box size
    - The offset should be given, each in their "H5MD containter"  
with step and time.
    - How different is what we do with respect to, for instance, PDB  
or gromacs ?
       see the manual of gromacs, chapter 3, §3.1 and §3.2 at http:// 
www.gromacs.org/ second news item or direct link ftp:// 
ftp.gromacs.org/pub/manual/manual-4.5.4.pdf
      pdb http://www.wwpdb.org/documentation/format33/sect8.html
    - If we put all of that in "observables" (not parameters), then  
a H5MD file with only the trajectory group will be useless. Do we  
agree on that ?
    - can one on Konrad or Felix synthetize the result?
    - I am not in favour of storing in fractional coordinates, for  
my data at least. How would that work ?
    - Peter, do you have comments ?
    - If I understood correctly, the latest suggestion is to store,  
for each time frame, a set of transformations and a shift ? How would  
it work if I sample very often a reduced set of coordinates (center  
of mass of a group of particles), I guess I need to have the  
transforms available at all times ?

3. particle numbers
    - I prefer the option where the data is in a single dataset [:] 
[N_species].
    - It should be in "observables".
    - It should not be mandatory, as some simulation/experiments may  
work with no "particle number" or with a fixed particle number, in  
this situtation having a time-dependent dataset is overkill.

Thanks for your various suggestions, and sorry if it looks like I'm  
not understanding everything. I am not familiar myself with non-cubic  
boxes, understand that they are very useful in many situations, and  
at the same time would like to keep "H5MD 0.1" simple enough.

Pierre