Stochastic Isokinetic Classical MD

NOTE: Isokinetic thermostats are coupled to each degree of freedom.
Cleanup: Removed some debug tests and aligned text
Deleted files for compilation on Curie
Removed local binary file
removed unnecessary include files
Update main.c

Removed blank line.
Updated permissions
Merge branch 'isokinetic' of github.com:dmargul/PINY into isokinetic
Deleted Plumed file
Merge pull request #11 from dmargul/isokinetic

Stochastic Isokinetic Classical MD