Re: [Spglib-users] Partial site occupancy supported?

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

Hi Keith,

You are correct.

'cel_any_overlap_with_same_type' itself allows to distinguish atomic
types, but not for many other general routines, i.e., I didn't
consider something like partial occupancy.

I felt that the change required to make it is not a lot. So I worked
for it. I first made the function below in cell.c.

int cel_is_overlap_with_same_type(const double a[3],
 const double b[3],
 const int type_a,
 const int type_b,
 SPGCONST double lattice[3][3],
 const double symprec);

and replaced the calls of the function 'cel_is_overlap' by this
function in case required. This modification is pushed to the
'overlap_atoms' branch on github. If you are interested in it, you can
pull it and try.

This change didn't induce any failure of the tests, so I will consider
this change to be merged to the main branch.

Togo

On Fri, Oct 28, 2016 at 9:07 PM, Keith Refson <kr...@gm...> wrote:
> Dear list,
>
> I read the contents of the changelog for 1.9.5
>
>         To check overlap of atoms, 'cel_any_overlap' and
>         'cel_any_overlap_with_same_type' were implemented. The former
>         doesn't check atomic type but the later does. Currently this check
>         is done before symmetry search and the later is used for
>         it. Therefore overlap of different types of atoms is allowed.
>
> to mean that analysis of a cell containing mixed sites with partial
> occupancy is supported.  But my test - attached - fails in
> "ssm_get_exact_positions"  as this fails to allow for multiple atoms on the
> same site.  Specifically the test at line 108 in cite_symmetry.c detects a
> mismatch.
>
> Have I misunderstood the intention, or is this a bug?
>
> Keith Refson
>
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-- 
Atsushi Togo
Elements Strategy Initiative for Structural Materials, Kyoto university
E-mail: atz...@gm...