Re: [Spglib-users] get_symmetry['equivalent_atoms'] - discriminate between rotation and translation

[Atsushi T. <atz...@gm...>]

Hi,

It is difficult for me where I should start to explain, which depends
on your knowledge on crystallography.
You can have a list of symmetry operations (coset representatives of
space group operations with respect to translation group) as
'rotations' and 'translations' in
https://spglib.github.io/spglib/python-spglib.html#get-symmetry-dataset
The number of symmetry operations to map a site to another site may
not be only one. But this kind of information is found in the
textbooks and not here to explain.

Togo

On Tue, Mar 16, 2021 at 5:52 PM Daniel Reta
<dan...@ma...> wrote:
>
> Dear Togo,
>
> Thank you for your reply.
>
> If I may, I'll rephrase my question to make sure that it cannot be done.
>
> Say one has the following mapping of symmetry-related atoms:
>
> get_symmetry['equivalent_atoms'] = [ 0, 0 ,0, 1, 1, 1 ]
>
> so this is telling me that atoms 0, 1 and 2 are related by symmetry (same for atoms 3, 4, 5). Instead, I would want to know the type of symmetry operation (pure rotation, pure translation or combination) that relates atom 0 with 1, atom 0 with 2, etc.
>
> Thank you.
>
> Dani
>
> -----Original Message-----
> From: Atsushi Togo <atz...@gm...>
> Sent: 16 March 2021 01:27
> To: spglib-users <spg...@li...>
> Subject: Re: [Spglib-users] get_symmetry['equivalent_atoms'] - discriminate between rotation and translation
>
> Hi,
>
> If I understand correctly your question, probably what you want to do is not able to do with spglib.
> Spglib relies on periodicity of crystal lattice in theory. This is the reason why I think so.
>
> Togo
>
> On Tue, Mar 16, 2021 at 2:04 AM Daniel Reta <dan...@ma...> wrote:
> >
> > Dear all,
> >
> >
> >
> > I am writing a script that generates a supercell, extracts individual molecules and calculates charges and dipoles on them. This info is later passed to another program to build some sort of embedded cluster approach.
> >
> >
> >
> > To reduce the number of calculations, I would like to consider only the molecules within the unitcell. For that, is there a way to get `get_symmetry` to return a list where the symmetry operations are broken down into rotations and translations? In the same way the key ‘equivalent_atoms’ gives a mapping table of atoms to symmetrically independent atoms, but now differentiating rotation and translations.
> >
> >
> >
> > Thank you in advance,
> >
> > Dani
> >
> >
> >
> > --
> > Dr. Daniel Reta, MRSC
> > Post-doctoral Research Associate
> > Dept. of Chemistry, The University of Manchester Oxford Road,
> > Manchester, M13 9PL, United Kingdom
> >
> > Email: dan...@ma...
> > --
> >
> >
> >
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>
>
>
> --
> Atsushi Togo
>
>
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-- 
Atsushi Togo