[ase-users] atomic numbers outside the physical range

[Gaël Donval]

On Fri, 2017-03-24 at 10:09 +0100, Jens Jørgen Mortensen wrote:
> On 03/22/2017 03:33 PM, Gaël Donval wrote:
> > > 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/la
> > > > > bels.
> > > > > 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.
> 
> I've updated the proposal:
> 
>      https://wiki.fysik.dtu.dk/ase/development/proposals/labels.html
>      https://gitlab.com/ase/ase/commit/57a7b73c6a
> 
> Jens Jørgen

Should we really include the mass in this? (mass is an Atom property
and if we put it in, we should put the magnetic moment and charges in
there too)

Now I am wondering whether the tag is still useful as this whole `Kind`
object does represent what the tag used to be. What would it be used
for?

Gaël


> 
> > 
> > > > -----
> > > > 
> > > > 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 (`@class
> > > > meth
> > > > 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
> > > > 
> > > > 
> > > > _______________________________________________
> > > > ase-users mailing list
> > > > ase-users at listserv.fysik.dtu.dk
> > > > https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
> 
> 
-------------- next part --------------
A non-text attachment was scrubbed...
Name: smime.p7s
Type: application/x-pkcs7-signature
Size: 3199 bytes
Desc: not available
URL: <http://listserv.fysik.dtu.dk/pipermail/ase-users/attachments/20170324/aaac722c/attachment-0001.bin>