Question #678525 on Yade changed:
https://answers.launchpad.net/yade/+question/678525

    Status: Open => Answered

Jan Stránský proposed the following answer:
> but the particles shown are the initial, uncompressed cloud.

well, you saved "the initial, uncompressed cloud", so this is expected behavior 
:-)
Add some compression before saving and Yade will save the compressed state.
cheers
Jan

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