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[h5md-user] tentative of synthesis: parameters, box size, particle numbe
Pierre de Buyl
[h5md-user] tentative of synthesis: parameters, box size, particle number
Wed, 14 Sep 2011 09:39:27 +0200
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 "/
- 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://
- 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 [:]
- 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.
- [h5md-user] tentative of synthesis: parameters, box size, particle number,
Pierre de Buyl <=