Question #678583 on Yade changed:
https://answers.launchpad.net/yade/+question/678583

    Status: Open => Answered

Jan Stránský proposed the following answer:
Hello,

> O.run(11200)
> O.save('init_config.yade.gz')

I would suggest O.run(11200,True), otherwise O.save saves immediately.
Maybe it is also related to the problem of running 11200 iterations in
the second script..

> i can't add harmonic motion

see my previous comment, there is no Cylinder defined in the second script. You 
can try 
print Cylinder # will print something like yade.wrapper.Cylinder

Do you really need two scripts?
Would saving the packing instead of O.save be sufficient?

cheers
Jan

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