Bob,
Thanks for you reply.
Well, lets hope we find someone. This is certainly beyond by capabilities. Of
course, the concept of tilings is not limited to zeolites or silicates.
I am not directly involved in the calculation of these tilings, but you got me
interested. I understand that they use a program called 3dt
(http://gavrog.org/) that is also written in Java and uses the open-source
visualization library jReality (http://www3.math.tu-berlin.de/jreality/) which
is being developed at the Technische Universität Berlin. This uses OpenGL
(jogl) as interactive backend.
Now my question: As far as you can judge, would there be a simple way of adding
this software to Jmol (I guess without the OpenGl backend)? Or would it be just
easier to use this software in a separate window by itself? At the moment I am
only concerned about the 3d display, I will have the programs and input files
required to generate the tilings.
Thanks for your help
Christian
On 23. Sep, 2014, at 12:44, Robert Hanson <hans...@stolaf.edu> wrote:
> There's a project for someone. I think the main problem with something like
> SiO2 in quartz is that there is no specific subset of atoms that is unique to
> that formula. I think a more likely alternative would be for Jmol to be able
> to tell you the empirical formula of a crystal. At least for full-occupancy
> structures, that might be possible.
>
> FYI:
>
> Error: I cannot find CIF file cif/.cif for the structure of !
>
> On Tue, Sep 23, 2014 at 4:17 AM, Christian Baerlocher
> <ch.baerloc...@mat.ethz.ch> wrote:
> Dear Bob,
>
> You are of course quite right, there is no SiO2 molecule, because quartz and
> all its polymorphs are „periodic nets“. You have to select a „cluster“ and to
> make it neutral you would have to add terminal OH groups.
>
> This is a problem we face also in zeollite chemistry (many of them are
> polymorphs of SiO2) and a number of attempts had been made to define suitable
> clusters that describe a structure. So far the best approach for periodic
> nets seems to be that of "natural tilings“, defined and described by V. A.
> Blatov, O. Delgado-Friedrichs, M. O'Keeffe & D. M. Proserpio, Acta
> Crystallogr. A 63, 418-425 (2007). These natural tilings are further
> discussed by N. Anurova, V. A. Blatov, G. D. Ilyushin and D. M. Proserpio, J.
> Phys. Chem. C 114, 10160-10170 (2010).
>
> You can see examples of such tilings on our zeolite website. For example, for
> the natural zeolite faujasite in
> http://izasc.ethz.ch/fmi/xsl/IZA-SC/Tilings/FAU.pdf
>
> Its framework of faujasite can be viewed with JSmol on
> http://izasc.ethz.ch/fmi/xsl/IZA-SC/ftc_3d_JSmol.php
>
> These natural tilings have been done for all zeolites.
>
> I am not sure, if this is what Hans Horn was looking for, but it would
> certainly be nice if Jmol could display such drawings ;-)
>
> Thanks and best wishes
>
> Christian
>
>
>
> On 20 Sep 2014, at 04:24, Robert Hanson <hans...@stolaf.edu> wrote:
>
>> Well, I think it is an interesting request. Help me define what the idea is
>> a bit more, and I can see what I can do. Given a few choice examples, how
>> would you define your request exactly?
>>
>> For example, we have quartz (SiO2):
>> http://chemapps.stolaf.edu/jmol/simple2.htm?load%20jsmol/data/quartz.cif%20{1%201%201}
>>
>> In this unit cell we have
>>
>> Si 1 + 4(1/2) = 3 atoms
>> O 6 atoms
>>
>> But which three atoms would you choose to represent the model for "SiO2"? Is
>> it always possible to identify such a subset? Some cases probably involve
>> multiple options, and they are not equivalent. For example, in this case,
>> there is not a perfect tetrahedron around that Si atom. So picking different
>> O atoms would give different structures for the formula unit. Which one
>> would be the correct one to load? Sounds very challenging to me.
>>
>> Bob
>>
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> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Department of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
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