Question #536811 on Yade changed:
https://answers.launchpad.net/yade/+question/536811

    Status: Open => Answered

Christian Jakob proposed the following answer:
hi,

using O.bodies.replaceByClumps() within a loop is not a good idea.

to solve your problem i see two ways:

1.) you generate particles with radius < 0.01 first, then you run
replaceByClumps() and generate the rest of the particles afterwards

2.) you can modify replaceByClumps() function in c++ [1], so that you
can exclude particles with an excludeList like in
updateClumpProperties() [2].

[1] https://github.com/yade/trunk/blob/master/py/wrapper/yadeWrapper.cpp#L210
[2] 
https://yade-dem.org/doc/yade.wrapper.html?highlight=updateclump#yade.wrapper.BodyContainer.updateClumpProperties

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