[TCOD] What structures do we accept to TCOD?

[Linas Vilciauskas]

Dear Saulius,


On Tue, Jul 22, 2014 at 3:02 PM, Saulius Gražulis <grazulis at ibt.lt> wrote:

> 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/)
>
>
But would it not becoming, reaction and not crystallographic database?
Having a phonon spectrum, even if there are imaginary modes is probably
very useful, some materials only become stable due to anharmonicity, so
their phonon spectra always contain some imaginary modes. But storing
transition state structures would be an enormous overhead... Moreover, if
one wants to store TS one should also store the reactant and product states
as well. Then all the definitions of the method on how that TS was
obtained...  Would one store all the intermediate NEB images then?

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).
>

That's is kind of correct.


>
> 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.
>

This schism results from the fact that there are two main approaches to the
basis sets used to expand the wave-functions in electronic structure codes.
Plane-wave are very popular in the solid-state community and due to their
inherent periodicity are very suitable for dealing with periodic systems
(solids > surfaces > infinite wires). Atomic basis sets such as
Gaussian-type orbitals are very popular in the molecule calculations or
non-periodic systems. PW are rarely used for doing molecule calculations,
since you need a big box so that the molecules would not interact, or you
have to decouple them, by e.g. setting the potential to zero at the cell
boundaries and self-consistently solving that problem.


>
> 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?
>

We should be only interested in periodic structures. Or I would be even
more strict - 3D periodic (crystals). We should not worry about the
molecules or clusters... or leave it to others :-) We just should not have
any limitation on the supercell size of the structure, but in general it
should be strictly 3D periodic for this database. That would make life much
easier and give the database some shape on what we are trying to
systematize.


>
> Regards,
> Saulius
>

Best regards,

Linas

>
> --
> Saulius Gražulis
>
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-- 
Linas Vilciauskas
Postdoctoral Research Fellow
Dept. of Chemistry
New York University
100 Washington Square East / 830BB
New York, NY 10003
linas.vilciauskas at nyu.edu
Phone:  +1-347-614-6831
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