Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
many changes to keep track of particle potentials for both bonded and non-bonded interactions
Inversion fixes and amber mostly working
A few formatting changes to prettify the code
Adding single precision capabilities to c++ side
xemacs has been drafted to perform our indentation services
more memory leak are fixed
merging new_design branch into OOPSE-2.0
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