Can LAMMPS rotate atoms and then minimize?

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1

Hi All,

I have a question regarding rotating a group of atoms incrementally and doing minimization after each incremental rotation.

So I have a, say, 20nm long (z=0 to z=20nm) nanowire and I want to simulate bending by rotating atoms from z=0 to z=1nm counter clockwise and atoms from z=19 to z=20 clockwise (looking at the front view of a nanowire extending from left to right); bottom to top is y direction and front to back (into page) is x direction. Atoms are rotated on yz plane ( bottom to top and left to right plane) so that x position does not change with rotation. Here is my attempt to convey the information thorough pictures!

Nanowire before rotation:

2

Fix move will not work b/c it moves/rotates atoms
during a simulation. You want to do it between
simulations. Displace_atoms is the right way to do
it, but it needs a "rotate" option added to it to do
what you want. For now I suggest you write out
your atoms (e.g. a dump file) after every stage,
perform the rotate operation in an external
script (e.g. Python), turn it into a data file,
and read it back in for the next stage. The
Pizza.py tool could do this pretty easily,
if you just wrote the "rotate" opeation in a few
lines of Python.

Steve