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
Rewrote the calculation of the number of DOFs.

It was broken for the combination of PIMD, centroid freezing and ghost
atoms present in the system. This fixes it.
Use the right number of DOFs to estimate pressure
Fixed normal modes code:

* Use FFT wrapper, rather than platform libraries for normal modes.
* Clean up unused variables.
* Some readability and style changes.
Style, readability, unused variables, if-else structure.
Put serial debug code back in.
Put example of parallel debug code back in.
Reorder as in implementations.
Merge pull request #10 from OndrejMarsalek/normal-modes

Fixed normal modes transformation
Merge pull request #12 from OndrejMarsalek/n_DOF

Rewrote the calculation of the number of DOFs.
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
Add a code section timer mechanism

Define TIMER in make_head.h to activate - add "-DTIMER" to DEFINE.