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

From: Pierre de Buyl
Subject: [h5md-user] tentative of synthesis: parameters, box size, particle number
Date: Wed, 14 Sep 2011 09:39:27 +0200

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.


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