Re: [h5md-user] Additional properties of particles

[Pierre de Buyl]

Hi,

On Fri, Nov 28, 2014 at 06:20:54PM +0100, Konrad Hinsen wrote:
> Pierre de Buyl writes:
> 
>  > As far as molecular data is concerned, this superficial approach to 
> storing the
>  > charges is just fine, no? At the molecular level, this is all that I would
>  > expect. While it is true that it is less unambiguous (note the double 
> negative)
>  > than the position, for instance, it remains a common quantity that one 
> wants to
>  > store. It can be fixed in time (most FF) or even change (ReaxFF, for 
> instance).
>  > 
>  > The interpretation remains to the final user exactly as for "species" and
>  > "charge" sould be included in my opinion.
> 
> My point is that the interpretation depends on where these charges
> come from, so that information must be storable. That's why I don't like
> the idea of just having a property called "charge", without any provenance
> information. I am not saying that such provenance information should be
> compulsory, but if it exists there should be a clear way to store it.
> 
>  > Is the definition of force fields part of MOSAIC yet?
> 
> Not yet, this is quite hard to do in a way that is both flexible and
> useful with today's scientific software technology. I have a pretty
> clear idea of how I will do it, but I don't believe it works until
> I have a working implementation.
> 
>  > A "module" or an attribute could be used to make the distinction
>  > between charges and partial charges. Are there more subtleties
>  > related to charges?
> 
> Nothing I can think of immediately. I'd say that all subtleties
> can be handled with additional annotation.

I didn't think that we would need a full proposal for charges as it would be
just an additional field. To remove the ambiguity about the kind of charges, I
have put a proposal :-)

It is not yet generated on the official homepage but github renders the markdown
at https://github.com/h5md/h5md/blob/master/proposals/0102_particles_charge.mdwn

Cheers,

Pierre