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

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

Dear Keith,

Thanks for your comment. I will merge this to master branch and will
be released soon.

Togo

On Mon, Oct 31, 2016 at 5:53 PM, Keith Refson <kr...@gm...> wrote:
> Dear Togo,
>
> This branch certainly works for my test case.  Given the widespread
> occurrence of site disorder in the ICSD, this capability to analyse systems
> with mixed sites will surely find many uses.
>
> Keith Refson
>
>
> On 29/10/16 02:30, Atsushi Togo wrote:
>>
>> 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...