Added AtomIteratorAllPairs, looping through the N(N-1)/2 pair
combinations. Added minimum image convention computation in
LennardJonesPotential. Added systemLength property on potentials because
a typical potential could typically need the system length (for minimum
image convention).
Added uniqueId on Atom class as a real unique id on an atom. Also added
originalUniqueId which is the original unique id on an atom that is
copied or moved (removed and readded through periodic boundary
conditions).
Added getAtomByUniqueId and getAtomByOriginalUniqueId to lookup atoms
using the unique id rather than pointers (they are invalidated when
atomList is altered). Also fixed a cell size bug creating cells smaller
than cutoff radius.
Removed debug flag and debug code in velocityverlet.cpp.
Nothing.
Changed addAtom from m_atoms.resize to m_atoms.push_back(Atom atom).
Added two convenient reset velocity functions. Changed some int to
unsigned long to prevent warnings.
Moved the reset velocity outside the for loop.
Added simple measurements of energy and momentum.
Added removeTotalMomentum function on System. Added setSystemLength
function on System. Added << operator overload on system.
Fixed the bug in copyGhostAtomsWithMPI where the atom list was altered
while looping through. Instead of pointers, we now use the uniqueId.
Stuff.