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[Robert Caulk <question685486@xxxxxxxxxxxxxxxxxxxxx>]

Question #685486 on Yade changed:
https://answers.launchpad.net/yade/+question/685486

    Status: Open => Answered

Robert Caulk proposed the following answer:
Yup. If you have a regular packing you will likely have two cells with
centers on top of one another. Of course conductivity depends inversely
on the distance between cell centers, and if that distance is zero, the
conductivity would be infinity. Thus the warning. FlowEngine handles it
by assigning an arbitrarily large value of permeability between these
two cells.

If you want to get rid of the warning, you can add small random
perturbations to the body locations:

for b in O.bodies:
	if isinstance(b.shape, Sphere): 
		rand = np.random.uniform(-1,1) 
		rand = rand*0.001+b.shape.radius
		b.state.pos = (b.state.pos[0]+rand,b.state.pos[1]+rand,b.state.pos[2]+rand)

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