One problem is that we don't have "atomic", only "ionic". It's a bit
inappropriate because it really means "bonding" -- covalent if uncharged,
ionic if charged. The other thing we have is "vanderwaals".
load cyclohexane_movie.xyz
# "ionic" here will just mean "covalent"
print {hydrogen}.ionic
0.23
print {carbon}.ionic
0.68
# These number are then used with bondTolerance to establish the range of
distances for autobonding.
# setting carbon charge to +1:
{atomno=1}.formalcharge = 1
print {atomno=1}.ionic
0.16
# totally separate are van der Waal radii -- these are not charge-dependent:
print {hydrogen}.vdw
1.1
print {atomno=1}.vdw
1.7
So I don't think there is an "atomic" option. I realize that "ionic" is a
misnomer. Just don't know how else to say that. "radius" is reserved for the
current spacefill size.
Bob
On Sun, Feb 28, 2010 at 5:43 PM, Alan Hewat <[email protected]> wrote:
> Yes, I got the syntax wrong; I meant something like:
> connect 0.8 2.5 (~cations) (~anions);
> connect 0.8 1.2 ionic (~cations) (~anions);
> connect 0.8 1.2 atomic (~cations) (~anions);
>
> Alan Hewat said:
> > connect (~cations) (~anions) 0.8 2.5;
> > connect (~cations) (~anions) 0.8 1.2 ionic;
> > connect (~cations) (~anions) 0.8 1.2 atomic;
> ______________________________________________
> Dr Alan Hewat, NeutronOptics, Grenoble, FRANCE
> <[email protected]> +33.476.98.41.68
> http://www.NeutronOptics.com/hewat
> ______________________________________________
>
>
>
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--
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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