status: Accepted in H5MD 1.1
This proposal aims at defining the storage of the charge associated with each particle.
Charge data is missing from H5MD 1.0. It is, at the very least, useful for atomic-level simulations. The interpretation of the value depends however on the situation.
See the original request and the subsequent discussion http://thread.gmane.org/gmane.science.simulation.h5md.user/685
This proposal does not list explicitly all use cases but clarifies the most common interpretations.
PDB stores integer atomic charge http://www.wwpdb.org/documentation/format33/sect9.html#ATOM.
Currently, no other file format clarifies the meaning of the
An element that contains the charge associated to each particle as a
charge has the optional attribute
type of fixed-length string
datatype and of scalar dataspace, possible values are
formal. In the case
effective, the charge is part of an
effective description of the interactions with the precise meaning
depending on the underlying empirical force fields or coarse-grained
In the case
formal, the charge is the so-called “formal charge”
assigned to an atom (see http://en.wikipedia.org/wiki/Formal_charge)
and must be of
Integer type. This case corresponds to the entries
in PDB files (see definition in the PDBx/mmCIF dictionary
If none of
formal describes the data properly,
type may be omitted.