[TCOD] What structures do we accept to TCOD?

[Saulius Gražulis]

On 2014-07-31 10:46, Armel le Bail wrote:
> More ideally, I think that the whole DFT instruction file should
> be provided inside of the CIF. As you know, IUCr is now asking
> for such refinement instruction details in the following way with
> a tag :
> 
> _iucr_refine_instructions_details
> ;
>    insert here the SHELX .ins or .res file
>    or etc (Rietveld entry file for powders)
> ;

Absolutely. This is suggested for the Level 2 description.

What the tag names and semantics is open for discussion, but once we
decide on them here we put the TCOD CIF dictionaries and we can reuse them.

As was mentioned on this list several times by DFT experts, some codes
might require more complicated computation flow for complete
reproducibility; e.g. relaxation might be done using different program
than was used for DFT optimisation. Still, such work flow can still be
accommodated in the same way, by providing a shell script or .bat file
as an input to /bin/sh or cmd.exe, and providing contents, or stable web
references, of all additional input files as well.

> We could have some specific TCOD tag :
> 
> _tcod_optimization_instructions_details
> ;
>   insert here the VASP/WIEN2K/CASTEP/... entry file
> ;

Since there may be more than one file needed for a DFT computation,
we'll probably need a loop (see the attached CIF file).

This would be a level-2 description.

> Of course the software name and the version should be given.

Tags are already here for this:

_tcod_software_package
_tcod_software_package_version

(http://www.crystallography.net/tcod/cif/dictionaries/cif_tcod.dic)

Maybe we should be more specific to mention the *code* version (as
versioned by the developers of the code) and a *package* version (e.g.
Debian package version used for installation and computation).

> This would allow for some reproducibility test and for example
> test files. The fact that cell parameters are optimized or not
> (and other details) will appear there.

Indeed. There are concerns that full description will be too large, or
too soon obsolete to be useful; I would say however that TCOD should
provide uniform mechanisms to describe the necessary information; if
people want, they use it; if they don't -- not a big deal, a lot of CIF
tags are used only once in a while. But we definitely do not want a
situation where people would like to provide information but TCOD has no
means to capture it :)

Regards,
Saulius

-- 
Dr. Saulius Gražulis
Vilnius University Institute of Biotechnology, Graiciuno 8
LT-02241 Vilnius, Lietuva (Lithuania)
fax: (+370-5)-2602116 / phone (office): (+370-5)-2602556
mobile: (+370-684)-49802, (+370-614)-36366
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