Class to store physical parameters
TODO: add up/down and right/left distinction for apperture

Optic functions as arrays
Uses PyAT lattice for import
Adapt other files for the change

The HDF5 is now open only once on all the cores to be able to write in parallel in the same file. The file must be closed at the end of the tracking.
BeamMonitor is used to save global statistics of all bunches
Add docstrings
TODO : Adding a flush() call at some point might be needed !

Add a monitor module to save tracking data based on h5py
Bunch Monitor is used to get statistics from a specific bunch
PhaseSpaceMonitor is used to save the phase space of a specific bunch
For now the .hdf5 file is opened and closed at each write operation, this seems to cause some problems for mpi.

Update machines/__init__.py, machines/soleil.py, tracking/__init__.py, tracking/aperture.py, tracking/element.py, tracking/optics.py, tracking/parallel.py, tracking/particles.py, tracking/rf.py, tracking/synchrotron.py files