Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
Added new restraint infrastructure Added MolecularRestraints Added ObjectRestraints Added RestraintStamp Updated thermodynamic integration to use ObjectRestraints Added Quaternion mathematics for twist swing decompositions Significantly updated RestWriter and RestReader to use dump-like files Added selections for x, y, and z coordinates of atoms Removed monolithic Restraints class Fixed a few bugs in gradients of Euler angles in DirectionalAtom and RigidBody Added some rotational capabilities to prinicpalAxisCalculator
Adding single precision capabilities to c++ side
xemacs has been drafted to perform our indentation services
fix compilation problem for g++ 3.4
merging new_design branch into OOPSE-2.0
more bugs get fixed at math library
fix some bugs in Quaternion class
math library in progress
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