I'll ask those more clearly:
Q: Would it be for the current model only, or for all models?
Q: How would we decide that? Perhaps by previously selecting the atoms it
would apply to?
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.
>
Q: What do you mean, "and you want to get out" only a portion. Get out in
what way? What does that have to do with the unit cell?
Q: Are you saying that the way the calculation is set up, you have to create
an imaginary unit cell that has nothing to do with the actual unit cell, and
that now you want to go back to that original unit cell?
It would be good to have a sample to work with.
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
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