Question #644244 on Yade changed:
https://answers.launchpad.net/yade/+question/644244

Jérôme Duriez proposed the following answer:
About lines 64-66, yes you've got it. 
Except that the newly created interactions will still be of JCFpmPhys type 
(nothing "less expensive"). It will indeed be of a non-cohesive variant, most 
probably (depends on Ip2_JCFpmMat_JCFpmMat_JCFpmPhys.cohesiveTresholdIteration).

For my previous 3rd paragraph, the point is this "D =
geom->penetrationDepth - phys->initD;" was surely introduced having in
mind the distant interaction case: in order to allow non-touching
particles to still interact, including the instance of repulsive
(compressive) interaction forces.

How the model behaves with initially overlapping particles (what we're 
discussing right now) is just a side effect which (I think) has never been 
considered as detrimental.
What I meant was to give an example of model generation for which the model 
still behaves very classically with respect to these initially overlapping 
particles.

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