Question #691548 on Yade changed:
https://answers.launchpad.net/yade/+question/691548

    Status: Open => Answered

Jan Stránský proposed the following answer:
> how can I modify the size of periodic cell?

O.cell.setBox(x,y,z) # [1]

but the cell size has no effect on this "4 pieces problem" if the center of 
cylinder is at (0,0,0).
My suggestion was to let the cell as it is, just "shift" the simulation: 
increase all x and y coordinates by a number to shift the cylinder "in the 
middle".

> In addition, It also have the same observation as you are after
O.step(). Is that normal?

no, it is not... I have no idea about the reason, especially as the first 
iteration is OK.. I have checked b.state.pos, vel, angVel and everything looks 
OK..
(sometimes I have this issue if my simulation is unstable and the particle fly 
away to "infinity", but it is not this case)

cheers
Jan

[1] https://yade-dem.org/doc/yade.wrapper.html#yade.wrapper.Cell.setBox

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