Re: [Spglib-users] symmetrizing positions/cell vectors without altering cell?

[Noam B. <noa...@nr...>]

> On Sep 25, 2017, at 9:54 AM, Atsushi Togo <atz...@gm...> wrote:
> 
> Good!

> 
> Togo
> 
> On Mon, Sep 25, 2017 at 10:49 PM, Noam Bernstein
> <noa...@nr...> wrote:
>> On Sep 25, 2017, at 9:15 AM, Atsushi Togo <atz...@gm...> wrote:
>> 
>> If the distortion is not that much, then the approach by
>> Grosse-Kunstleve and Adams should work. If you write a python script,
>> I think I can comment to it. The C-code is about here,
>> https://github.com/atztogo/spglib/blob/master/src/site_symmetry.c#L244
>> 
>> 
>> 
>> Hmm.  I tried something like this initially, and it wasn't working at all,
>> but I must have had a bug, since I redid it cleanly (so I could show the
>> code), and the new version's apparently working.  Maybe because I was coding
>> for an audience I was more careful.  In any case, while I think it would be
>> useful to have a version of standardize_cell() that only moved atoms,
>> without touching the cell vectors, I think my problem is solved for now
>> (especially if I can recode it without a tight loop in python).  It should
>> probably be redone without so many tight loops in explicit python, but here
>> it is, in case it’s useful for anyone else:



Hi Togo - hopefully you remember this discussion.  Thanks to your help, I was able to code up in pure python the symmetrization of the atomic positions, based on your C code in site_symmetry.c.   Now I’m wondering if there is an equivalent algorithm for the symmetrized cell vectors.  Can you just apply the same algorithm to fake atoms placed at the cell vector endpoints?

									thanks,
									Noam


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