[ase-users] Cif files standard

[Andrius Merkys]

Dear Korina,


both CIF files are syntactically correct and valid, thus it's
Xrayutilities bug that it can not correctly parse example.cif. The bug
apparently is connected to data value   '_atom_site_type_symbol' being
the last in _atom_site_* loop. I have worked around the bug by placing
'_atom_site_type_symbol' just after '_atom_site_label' (see attached
file 'example-working.cif'). This work-around could be employed by ASE
for now unless such tag order is a problem for some other CIF reader. I
will file a bug report in Xrayutilities's GitHub repository.


Best wishes,
Andrius


On 25/01/17 15:15, Korina Kuhar wrote:
> Dear Andrius,
>
> Example in in the attachment (example.cif).
> I believe that Xrayutilities has problems with all the cif files ase
> creates (all the ones I tries at least), but if one rearranges the cif
> file to look more like the ones from MP database (just a known working
> example), it works.
> The working one is also in the attachment, mp-14_Se.cif.
>
>
> Best,
> Korina
>
> Korina Kuhar
> PhD student
> DTU Physics
>  
>
> Technical University of Denmark
>
> 	
> Department of Physics
> Fysikvej
> Building 307
> 2800 Kgs. Lyngby
> Denmark
> Direct +45 45253293
> kokuha at fysik.dtu.dk <mailto:kokuha at fysik.dtu.dk>
> www.fysik.dtu.dk <http://www.fysik.dtu.dk>
>
> ------------------------------------------------------------------------
> *From:* ase-users-bounces at listserv.fysik.dtu.dk
> [ase-users-bounces at listserv.fysik.dtu.dk] on behalf of Andrius Merkys
> via ase-users [ase-users at listserv.fysik.dtu.dk]
> *Sent:* Tuesday, January 24, 2017 5:22 PM
> *To:* ase-users at listserv.fysik.dtu.dk
> *Subject:* Re: [ase-users] Cif files standard
>
> Dear Korina,
>
>
> there is a fine documentation of the CIF format hosted at IUCr's
> website with formal grammar of the format [1]. However, from my
> experience, reading CIF is not trivial and many programs misinterpret
> the syntax [2]. Could you attach some examples of ASE-produced CIF
> file, especially the cases, that are failing Xrayutilities, please? I
> would check them for any syntax irregularities.
>
>
> Best wishes,
> Andrius
>
>
> [1] http://www.iucr.org/resources/cif/spec/version1.1/cifsyntax
>
> [2] Merkys et al. Journal of Applied Crystallography, 2016, 49,
> 292-301, doi:10.1107/S1600576715022396
>
>
> On 24/01/17 17:56, Korina Kuhar via ase-users wrote:
>> Dear users,
>>
>> As you know, ase has an option to read and write structures in cif
>> format.
>> Reading seems to be working well, but it writes files in format
>> slightly different than ex. Materials project database.
>>
>> Is anyone aware of some universal standard for the cif format?
>> Has anyone had trouble reading ase-made structures with other software?
>>
>> Ex. Xrayutilities can't.
>>
>> The format can easily be modified if it causes trouble.
>> Please share experience.
>>
>>
>> Best,
>> Korina.
>>
>>
>> Korina Kuhar
>> PhD student
>> DTU Physics
>>  
>>
>> Technical University of Denmark
>>
>> 	
>> Department of Physics
>> Fysikvej
>> Building 307
>> 2800 Kgs. Lyngby
>> Denmark
>> Direct +45 45253293
>> kokuha at fysik.dtu.dk <mailto:kokuha at fysik.dtu.dk>
>> www.fysik.dtu.dk <http://www.fysik.dtu.dk>
>>
>>
>>
>> _______________________________________________
>> ase-users mailing list
>> ase-users at listserv.fysik.dtu.dk
>> https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
>
> -- 
> Andrius Merkys
> PhD student at Vilnius University Institute of Biotechnology, Saulėtekio al. 7
> LT-10257 Vilnius, Lithuania

-- 
Andrius Merkys
PhD student at Vilnius University Institute of Biotechnology, Saulėtekio al. 7
LT-10257 Vilnius, Lithuania

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