Some questions about the equilibrium

Hello, everybody!
The workpiece start to shake when i use lammps to equilibrate the system. Why dose the workpiece shake? Is the wrong potentials or something else that causes this phenomenon? Or is this just a normal phenomenon? What steps can I take to avoid this phenomenon?
Thank you! Hoping for your help.

There is very little one can say from your scant post. If I understand it correctly, the video shows a surface of some sort jiggling. I believe that all matter above 0 K displays this behaviour, so nothing to worry about here!
You may well discuss your findings with a senior colleague or supervisor.

Thanks for your reply!
I am sorry for the length of post(it is too big). And I upload a new post now. This is the link:
I find that the jiggling will persist in the cutting process. And I think that the jiggling may be the cause of the subsequent violent diffusion of amorphous atoms and seriously affect the subsequent cutting process. Is that right?

The “jiggling” is due to phonons in your system due to how you have initialized and set up your system.
This can happen, if you use a lattice constant that is not consistent with the potential you are using. It should be possible to reduce this by a) running a minimization on your workpiece only (immobilize all other atoms in the system with fix setforce 0 0 0) before starting an MD and/or by using a dissipative thermostat like fix langevin to dissipate and dampen all large scale motions in your system.

No. These are independent effects. The “violent” reaction of your workpiece to your tool looks more like an effect of using inadequate settings in your simulation, e.g. a too large time step or a too high cutting speed or a combination of those.

That gives me a lot of inspiration. Thanks!!!