Question #699779 on Yade changed:
https://answers.launchpad.net/yade/+question/699779

    Status: Open => Answered

Karol Brzezinski proposed the following answer:
Hi Hossein,

1) The walls are pushing your particles together. It makes them collide,
and when the packing becomes dense, collisions turn to vibrations. It
occurs until kinetic energy is dissipated. I expect that energy to
decrease in time (if there is a way it can be dissipated - see point 2).
So, once you reach desired porosity, stop compressing the particles
further (I mean leave the walls in their positions). When simulation
"calms down", proceed with the next steps.

2) There are different options to do this, the simplest is numerical damping 
[7] that you set this line:
> newton=NewtonIntegrator(damping=0)
You could increase it slightly to speed up the dissipation process.

Cheers,
Karol

[7] https://yade-dem.org/doc/formulation.html#numerical-damping

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