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