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Re: [h5md-user] Particle tracking

From: Pierre de Buyl
Subject: Re: [h5md-user] Particle tracking
Date: Sun, 01 Sep 2013 16:23:35 -0400
User-agent: Internet Messaging Program (IMP) H4 (5.0.21)

Peter Colberg <address@hidden> a écrit :
On Sun, Sep 01, 2013 at 02:15:41PM -0400, Pierre de Buyl wrote:
Did you consider variable length datatypes? It would allow to keep
the first dimension of datasets the time.

The same applies as for Array data types, it does not allow slicing.


Is it worth losing slicing?

As time-depedent data requires chunking anyway, what about using
H5S_UNLIMITED for the N (where N is the number of particles)
dimension of the datasets in the particles group. This would allow
for the storage of a (potentially) growing number of particles,
without having to (i) having to know N_max and (ii) storing unused

Coming back to my previous message and the use of "id", one could
set id=-1 where there is no particle. If the fill value [1] of "id"
is set to -1, this is achieved at no cost for empty slots and it
would also not impose any specific memory arrangement for the empty

Counting the number of >=0 items in "id" would give the number of
particles at a given time.

[1] http://www.hdfgroup.org/HDF5/doc/UG/10_Datasets.html#Allocation

Just thinking out loud :-)

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