[ase-users] atomic numbers outside the physical range

[Gaël Donval]

> Den 21-03-2017 kl. 10:56 skrev Gaël Donval via ase-users:
> > Hi,
> > > On 03/01/2017 04:20 PM, Jens Jørgen Mortensen wrote:
> > > > On 03/01/2017 01:59 PM, Noam Bernstein wrote:
> > > > > > On Mar 1, 2017, at 4:05 AM, Jens Jørgen Mortensen
> > > > > > <jensj at fysik.dtu.dk <mailto:jensj at fysik.dtu.dk>> wrote:
> > > > > > Good question - I don't know.  Can xyz files have atomic
> > > > > > numbers
> > > > > > instead of symbols?  What file formats do you use for your
> > > > > > calculations with Z=300 at the moment?
> > > > > > 
> > > > > 
> > > > > I use extxyz, which can.  Is the use of a the short symbol of
> > > > > a
> > > > > real
> > > > > element for the species in xyz anything other than a
> > > > > convention
> > > > > anyway?
> > > > 
> > > > Yes.
> > > > 
> > > > Thanks for your input.  I'll try to write an "ASE enhancement
> > > > proposal" describing what this could look like.  It will take
> > > > me a
> > > > couple of weeks as vacation is coming up for me.
> > > 
> > > Here is one possible solution:
> > > 
> > >       https://wiki.fysik.dtu.dk/ase/development/proposals/labels.
> > > html
> > > 
> > > Please read it a couple of times and then we can continue the
> > > discussion
> > > to see if we can find a solution that works for all/most of us.
> > > 
> > > Jens Jørgen
> > > 
> > 
> > What would the difference between tag and label be then?
> 
> Tags are integers and labels are strings.  We could also include tag
> in 
> the Kind-thing?

Oh I see... It is a bit redundant then, but I personally don't mind.
Tags seem like a property of a species/kind, so including them in an
object representing such a species/kind seems the least surprising.

> 
> > -----
> > 
> > It is not clear whether or not your different kinds of `kind` are
> > what
> > the user provide and/or how things are represented through all the
> > code.
> > 
> > Assuming a "and" in the sentence above, the only single thing that
> > I
> > don't really like there is the incoherent interface provided by the
> > `kind` as it is defined... I certainly don't want to check each
> > single
> > time which kind of `kind` I am provided with (i.e. a `str` or a
> > `tuple`
> > or a special `str` or a `namedtuple`)...
> > 
> > What I propose instead is to create a `Kind` object (i.e. your last
> > item). That object would contain multiple constructors (`@classmeth
> > od`s
> > ) that would create the object from any of your listed `kind`s.
> > This
> > way, we always provide the exact same interface while retaining the
> > input format flexibility.
> > 
> > As a bonus, unlike with tuples, if we ever want to add something we
> > did
> > not think about, it is trivially easy with the guarantee of
> > breaking
> > nothing (as long as the interface is unchanged).
> 
> Yes, I also think we should drop the tuple, but I still think the
> simple 
> string representation would be quite convenient to have (as input).
I agree.

I suppose we could use the following approach to handle input cleanly:

    https://gitlab.com/snippets/1655556

(I have not run that code, so there are bugs).

There is something I am still not sure about: should we put the masses,
magnetic moments, charges and other things in there as you hinted in
the draft? I personally don't think so as the atom object is already
handling that and this is not really related to what a `Kind` is...

That being said, little plumbing work would be needed to say "Hey ASE,
give all `Atom` of `Kind` X in that `Atoms` a mass of 9.0."... 

Gaël

> 
> Jens Jørgen
> 
> > Overall, I really like it (list-like object, new attributes and
> > interaction with the current code included).
> > 
> > Gaël
> > 
> > 
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> > ase-users at listserv.fysik.dtu.dk
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> 
> 
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