Question #466297 on Yade changed:
https://answers.launchpad.net/yade/+question/466297

    Status: Open => Answered

Bruno Chareyre proposed the following answer:
Hello,
Some settings of PeriodicFlowEngine are apparently missing.
You need to tell explicitely which bodies are used as walls:
flow.wallIds=[-1,-1,1,0,-1,-1]
and there is an internal variable of the periodic triangulation that could be 
increased to help generating a correct triangulation:
flow.duplicateThreshold=0.5 (the default 0.06 is ok only for large numbers of 
particles)

However, I tried both in your script without success. I suspect that the 
regular packing of the top layer could be the problem. The periodic mesh is not 
built robustly in this case because the triangulation is not unique. You could 
first try to remove this layer. 
If it solves the problem then you could reintroduce it by adding a noise on 
positions of the regular packing. A limited disorder is usually enough to avoid 
the degenerate cases.

Bruno

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