note that these are the values used for autobonding.
On Thu, Feb 4, 2010 at 11:07 AM, Robert Hanson <[email protected]> wrote:
> OK, Alan.
>
> load nacl.cif {1 1 1}
> {_Na}.formalcharge = 1
> {_Cl}.formalcharge = -1
>
> {_Na and formalcharge = 1}.ionicRadius = 0.600
> {_Cl and formalcharge = -1}.ionicRadius = 1.2
>
> spacefill ionic
>
>
> now works. This is the general way to set all atom properties. Files should
> finish uploading in a few minutes.
>
> Bob
>
>
>
>
>
> On Thu, Feb 4, 2010 at 10:59 AM, Alan Hewat
> <[email protected]>wrote:
>
>> You mean something like:
>> { _Ti and formalcharge = 2}.ionic = 0.94
>> { _Ti and formalcharge = 3}.ionic = 0.76
>> { _Ti and formalcharge = 4}.ionic = 0.68
>> etc...
>>
>> Yes, that would be fine. Alan.
>>
>> On 4 February 2010 17:40, Robert Hanson <[email protected]> wrote:
>> > How about if I allow you to set .ionic?
>> >
>> >
>> > On Thu, Feb 4, 2010 at 10:35 AM, Alan Hewat <
>> [email protected]>
>> > wrote:
>> >>
>> >> Well yes I do care :-) I want a custom table of *ionic radii* with
>> >> different values for different ionisation states like you have hard
>> >> coded into Jmol. Is there a way to input that as a script in the way
>> >> you have suggested for van der Waals radii ?
>> >>
>> >> Alan.
>> >>
>> >> On 4 February 2010 17:24, Robert Hanson <[email protected]> wrote:
>> >> > I don't think you need me to do this. Just:
>> >> >
>> >> > create a list that looks like this:
>> >> >
>> >> > {Na and formalcharge = 1}.vdw = 1.3
>> >> > {Cl and formalcharge = -1}.vdw = 2.4
>> >> >
>> >> > etc.
>> >> >
>> >> > then run it as a default script. True, it's van der waals, but you
>> >> > probably
>> >> > don't care. Right?
>> >> >
>> >> > Bob
>> >> >
>> >> >
>> >> >
>> >> > On Thu, Feb 4, 2010 at 9:18 AM, Alan Hewat <[email protected]> wrote:
>> >> >>
>> >> >> Alan Hewat wrote Sept 2006:
>> >> >>
>> >> >> > Can we eventually use our own table of radii ?
>> >> >> >...
>> >> >> > David Brown tells me that the best values for ionic radii are
>> still
>> >> >> > those of Shannon and Prewitt 1969, Acta Cryst. B25, 925-946 (for
>> >> >> > oxides)
>> >> >> > and Shannon 1976 Acta Cryst. A32, 751-767 (for halides)
>> >> >>
>> >> >> Bob and others tidied up Jmol's ionic radii since I wrote that, and
>> the
>> >> >> radii for different ionic states are included as tables in the Jmol
>> >> >> source
>> >> >> code. I understand these values are taken from the CRC Handbook of
>> >> >> Chemistry and Physics (1996-97) with some mods to make them work for
>> >> >> organic compounds.
>> >> >>
>> >> >> But I would still like to be able to input my own table of ionic
>> radii
>> >> >> :-)
>> >> >>
>> >> >> The reason is that to my mind ionic radii have been determined by
>> >> >> Brown-Shannon-Prewitt from bond lengths and strengths in simple
>> >> >> inorganic
>> >> >> compounds, and are really only valid for that class of material. For
>> >> >> the
>> >> >> Inorganic Crystal Structure Database (ICSD) we would prefer
>> therefore
>> >> >> to
>> >> >> use ionic radii based only on simple inorganic materials.
>> >> >>
>> >> >> It would be great if we could load our own table of radii when Jmol
>> is
>> >> >> launched. Bob? :-)
>> >> >>
>> >> >> Alan (now retired and working on other things as well)
>> >> >> ______________________________________________
>> >> >> Dr Alan Hewat, NeutronOptics, Grenoble, FRANCE
>> >> >> <[email protected]> +33.476.98.41.68
>> >> >> http://www.NeutronOptics.com/hewat
>> >> >> ______________________________________________
>> >> >>
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> > Robert M. Hanson
>> >> > Professor of Chemistry
>> >> > St. Olaf College
>> >> > 1520 St. Olaf Ave.
>> >> > Northfield, MN 55057
>> >> > http://www.stolaf.edu/people/hansonr
>> >> > phone: 507-786-3107
>> >> >
>> >> >
>> >> > 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
>> >> >
>> >>
>> >>
>> >>
>> >> --
>> >> ______________________________________________
>> >> Dr Alan Hewat, NeutronOptics, Grenoble, FRANCE
>> >> <[email protected]> +33.476.98.41.68
>> >> http://www.NeutronOptics.com/hewat
>> >> ______________________________________________
>> >
>> >
>> >
>> > --
>> > Robert M. Hanson
>> > Professor of Chemistry
>> > St. Olaf College
>> > 1520 St. Olaf Ave.
>> > Northfield, MN 55057
>> > http://www.stolaf.edu/people/hansonr
>> > phone: 507-786-3107
>> >
>> >
>> > 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
>> >
>>
>>
>>
>> --
>> ______________________________________________
>> Dr Alan Hewat, NeutronOptics, Grenoble, FRANCE
>> <[email protected]> +33.476.98.41.68
>> http://www.NeutronOptics.com/hewat
>> ______________________________________________
>>
>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> 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
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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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