Rotation with periodic boundary conditions

I added a rotate option to the displace_atoms command, so that you
can rotate a group of atoms to a desired configuration before a simulation
begins. Fix move, by contrast, rotates them slowly while a simulation
is running. I doubt this will fix any of the problems you are having
with your model and periodic BC, but you can give it a try.

See the 30Nov patch.

Steve

Thank you Barry.
And do you know how I can find the proper size for my new box without pbc?

Meysam