Question #695558 on Yade changed:
https://answers.launchpad.net/yade/+question/695558

    Status: Open => Answered

Bruno Chareyre proposed the following answer:
Ah... the clumping step is using positions+mass to deduce total mass and
center of mass while "position" of the cylinder is one of its end nodes
IIRC (not the middle point as one would expect) .  Hence some randomness
depending on the ordering of nodes and cylinders.

It would explain why setting those masses to zero helped. So,  setting 
cylinders mass to zero sounds like a good idea. It should only happen after 
assigning half of its actual mass to each of the nodes though.
The facets should do the same to avoid the "change mass by clumping" problem: 
compute self mass, then split in three and assign to the nodes, and finally set 
facet mass to zero.

If you check what's behind functions like cylinderConnection()  or
pFacetCreator1() you should quickly reach where such things happen and
change behavior. If you are able to do that feel free to contribute it
to trunk. Else maybe we should open a bug to not forget.

Bruno

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