Dear Bob,
Q: Would it be for the current model only, or for all models? How would we
decide that? Perhaps by previously selecting the atoms it would apply to?
A: No you want all the atom to be affected. You literally want to rebuild
the cell around.
Q: We would not necessarily have to remove all the space group info. Of
course, doing this might wreck that. Symmetry is not an aspect of the unit
cell, per se, but of the model itself. Is there some reason you feel we
would have to remove symmetry operators?
A: I got your point, I always thought that symmetry is linked to atomic
positions. So that atom in special potion are related with their replication
across space by simple matrix transformation according with the space group.
Q: It seems to me the only benefit of this is that you get to use different
fractional coordinates. Do you see anything else that would be beneficial?
A: The answer lies to this
It would be interesting especially if you want to to run cluster type
> systems within PWs codes.
I have no idea what that means, sorry!
Or if you want to extract a cluster from a periodic system.
When you would like to simulate molecule within a plane wave basis sets
approximation, you must build a cell around the molecule, to sizing the PW
problem. To do that you take a molecule and you bild around a sufficient
large cell avoiding electrostatic interactions with their replica across
space. Another case is when you have a periodic system and you want to get
out only a portion from that (namely a cluster). In this case you end up
having a sort of molecule which has to be included in a bigger cell.
Now you probably see why you should loose the symmetry.
Conclusion, In the case of a cluster you want to increase for certain the
cell parameters.
All the best,Piero
On Thu, Nov 11, 2010 at 6:48 PM, P.Canepa <pc...@kent.ac.uk> wrote:
>
> -------------------------------------------
> From: Robert Hanson[SMTP:hans...@stolaf.edu <smtp%3ahans...@stolaf.edu>]
> Sent: Thursday, November 11, 2010 6:47:54 PM
> To: jmol-users@lists.sourceforge.net
> Subject: Re: [Jmol-users] FW: FW: change cell parameters
> Auto forwarded by a Rule
>
> On Thu, Nov 11, 2010 at 9:30 AM, pieremanuele canepa <pc...@kent.ac.uk>wrote:
>
>> Yes you leave the atoms in their positions rebuilding the cell around. Of
>> course the symmetry is lost. This is the price the user has to pay.
>>
>>
> So, you mean, just giving them different fractional coordinates. They are
> stored as Cartesian coordinates anyway, so this should not be a particular
> problem.
>
> Q: Would it be for the current model only, or for all models? How would we
> decide that? Perhaps by previously selecting the atoms it would apply to?
>
> Q: We would not necessarily have to remove all the space group info. Of
> course, doing this might wreck that. Symmetry is not an aspect of the unit
> cell, per se, but of the model itself. Is there some reason you feel we
> would have to remove symmetry operators?
>
> Q: It seems to me the only benefit of this is that you get to use different
> fractional coordinates. Do you see anything else that would be beneficial?
>
>
>
>> It would be interesting especially if you want to to run cluster type
>> systems within PWs codes.
>
>
> I have no idea what that means, sorry!
>
>
>> Or if you want to extract a cluster from a periodic system.
>>
>>
> What's extracting anything from the model have to do with it? Can't you do
> that already?
>
> Bob
>
> --
> 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
>
--
*Please consider the environment before printing this e-mail.*
**
Pieremanuele Canepa
Room 104
Functional Material Group
School of Physical Sciences, Ingram Building,
University of Kent, Canterbury, Kent,
CT2 7NH
United Kingdom
e-mail: pc...@kent.ac.uk
mobile: +44 (0) 7772-9756456
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