Question #678426 on Yade changed:
https://answers.launchpad.net/yade/+question/678426

    Status: Open => Answered

Chao Yuan proposed the following answer:
hi,
the timestep you are using for preparing the sample is too large, leading to 
some grains out of the box. Change it to:
O.dt=.1*PWaveTimeStep()
O.dynDt=False
it should work. 

cheers,
chao

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