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Re: Strange behavior of periodic cell


> I'm trying to do some simulations using periodic cell. In one case, I prescribed some extension of the periodic cell, but the particles in the simulation behave really strange - the dispacement of particles si continuously increasing.
> So if someone ran the attached script and said what is wrong in it, I would be very grateful :-)
You make one dimension shorter and that creates a rather big overlap
between two consecutive planes of spheres. That, in turn, creates big
repulsive force, so they go apart, then going back. There is nothing
wrong with that.

That said, I observe that the two planes of spheres somehow go through
each other after a while, which it clearly should not. I will try to
find out tomorrow about what is going on and I let you know. 

PS you can replace those ugly loops by something like


and also see
http://docs.python.org/library/itertools.html#itertools.product where
you could write (not tested)

  for i,j,k in itertools.product(range(3),repeat=3): ...

to replace those loops

Cheers, Vaclav