[TCOD] What structures do we accept to TCOD?

[Saulius Gražulis]

On 2013-09-06 19:02, Stefaan Cottenier wrote:
> (9) Which kind of computed structures will TCOD accept? Ground state
> structures, obviously? Metastable structures probably as well? Also if
> they are not dynamically stable (soft phonon mode)? (that is not
> routinely examined) And what about transition state structures? (never
> observable in experiment, yet very useful to know -- and hard to find --
> in order to understand reactions) If the latter are allowed, then they
> should be tagged as such.

I find this suggestion very good and comprehensive. I have added the 
'_tcode_structure_type' data name to cif_tcod.dic based on this 
suggestion. I would be grateful if you verify that I did not put too 
much nonsense into the definitions, my understanding if the 
metastable/transition/soft phonon structures is so far rather limited... 
The dictionary is in its usual place: 
http://www.crystallography.net/tcod/cif/dictionaries/cif_tcod.dic 
(Subversion repo: svn://cod.ibt.lt/tcod/cif/dictionaries/)

One more related question:

If I understand correctly, from what I recall from the QM lectures, we 
can have in principle two kinds of boundary conditions for localised 
particle wave functions:

a) vanishing at the infinity (modelling single molecule in vacuum), and
b) periodic (modelling an ideal crystal).

 From what I have read in manuals of the QM codes, most implement b), 
and a) is approximated by putting a molecule in a large enough "unit 
cell" so that interactions between molecule images are negligible.

Is this a correct view? Does any code implement (a) as a separate mode 
of computation?

In either case, we should probably have a special tag that distinguishes 
"true" crystal structures from the "convenience" unit cells that are 
non-physical but are set up solely to solve a molecule structure problem 
with the same code that also deals with crystals. Any ideas how to tell 
from the computations which mode was used?

Regards,
Saulius

-- 
Saulius Gražulis

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