Thanks Vaclav and Vincent!  I'm updating the questions, since some have been 
answered.

Q1. I've looked at eigen-tuxfamily library.  It doesn't seem to require linkage 
and I just need to include the following header?
   #include <Eigen/Core> 
   USING_PART_OF_NAMESPACE_EIGEN

Q2. Why are we using the approximated rotations in updating Shear, and not 
quaternions.  It has been commented out in many files.  Is there sth that I'm 
not aware of?

Q3. I've been searching for the command TRVAR3 in ElasticContactLaw for quite 
long.  But couldn't find where it is defined.  The function is not explained in 
doxygen
TRVAR3(currentContactGeometry->penetrationDepth,de1->se3.position,de2->se3.position);



Yours sincerely,
CWBoon

Vicent's answer below:

>I cannot answer all your questions, but only give an opinion.>I
think you're right. This may be critical point only for "viscous"
damping. I think that something like the Beeman's algorithm should be a
better candidate than leap-frog or velocity Verlet when viscous damping
(with >high velocities) is "activated". With quasistatic simulations, it
seems not to be critical since viscous damping is a kind of
"regularizator". With Cundall Damping, no problem since velocities are
not required if the >force-laws.
                                          
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