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[Václav Šmilauer <eu@xxxxxxxx>]

I was thinking about this a bit and I think the bug is not valid.

The Cell.homoDeform==1 updates positions and does not touch velocities
at all. Hence incident velocity (computed from difference of velocities)
will always correspond to the fluctuation velocity, regardless of
positions in absolute space -- the meanfield velocity only acts at
positions, and does not affect velocities.

If you look at Cell.bodyFluctuationVel, it simply returns state->vel in
cases homoDeform∈{0,1}.

Yes, meaning of the number is shifted, but if you assign the old
parameter to NewtonIntegrator, it will shift it before assigning to
Cell.homoDeform (and gives a very clear warning about that). The
ordering is according to the increasing smoothness of the adjustment
(none, positions, velocities, velocities+convection).

-- 
homoDeform=1 does not handle the periodic case correctly.
https://bugs.launchpad.net/bugs/674000
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Status in Yet Another Dynamic Engine: New

Bug description:
Currently, in the periodic case, if homoDeform=1 (alias Cundall way) we do not adjust the values of the relative velocities as according to the velocity gradient. This should be done, since, in such a case, we only update particle positions and not particle velocities.