Simplified utility.hpp and utility.cpp
Renamed utility to safe_counter
Removed redundant using namespace std;
Replaced \n by endl
Renamed t1,t2 to t0,t1
Shuffled a few lines, and added const siZe_t s = eng() before io.post
Moved xs related functions from atom.hpp to scoring_function.cpp
Moved xs_vdw_radii from atom.hpp to scoring_function.cpp
Rewrote atom class
Added atom.cpp
Removed the assign function in vec3.hpp