Add Ncav parameter and Rs_per_cavity attribute to remove ambiguity about what should be used
Add attributes and methods to compute Pc, Pb and Pr.
Add method to set optimal coupling value.

Check that the bunch is not empty before binning in Mpi.share_distributions. If it is then the beam filling pattern is updated and empty array are sent.
In CavityResonator.track, the tracking without mpi is modified to take into account the case with an empty bunch. Mpi case is fine as the beam filling pattern is updated in the call for Mpi.share_distributions.
In WakePotential.track, if the bunch is empty tracking does nothing.

Beam.mpi_share_distributions is now moved to mpi.share_distribution
Now mpi4py is only needed for the multi-bunch tracking and not for single bunch

bunch_index returns the array with the positions (index) of the non-empty bunches, to be used with Beam.not_empty iterator.
bunch_mean, bunch_std and bunch_emit now iterate only over non empty bunches.

CavityResonator.init_phasor is now CavityResonator.init_phasor_track
New CavityResonator.init_phasor uses analytic formula
Fix phase slipping factor for initialization case (rf frame should be delta = (self.wr - self.m*self.ring.omega1))

fix init

Fix mpi_share_distributions

CavityResonator.init_phasor is now CavityResonator.init_phasor_track
New CavityResonator.init_phasor uses analytic formula
Fix phase slipping factor for initialization case (rf frame should be delta = (self.wr - self.m*self.ring.omega1))

fix init

Wrong data shared in Beam.mpi_share_distributions
Old names in CavityResonator.track corrected

Add a dict_dtype optional parameter to Monitor.monitor_init to allow to choose the dtype to use to save the data.
Improve CavityMonitor to allow for saving beam and cavity phasor for all bunches
Add a plot_cavitydata function
Fix a bug on CavityResonator.track -> nturn += 1 at correct time
Change CavityResonator.track to allow for monitoring the cavity/beam phasor at each bunch

Add comments.
Remove usage of bins, use only center.

Not needed any more due the SynchrotronRadiation change.

Correct time decay !
Now ok versus for loop (decay then beam loading)

In track method of cavity resonator, there was an additional phasor decay of bin length.
To avoid that the good boundaries are set bins[0] instead of center[0].
For now the bins are also shared in Beam.mpi_share_distributions

Add single core tracking for CavityResonator
Correct missing ref_frame is CavityResonator.track
Change phase of generator voltage to be the bin phase
Correct generator phase for non integer m
Change init_phasor track time to 10 times
Change phasor_evolution k to change order of steps

Add phasor initialization (on the "rf" reference)
Change beam phasor evolution to allow for "beam" or "rf" reference

Correct case when where is no mp in the bin
Remove useless test

Add tracking to CavityResonator based on the mbtrack implementation but using a analytic formula for speed-up
Add method to Beam to share longitudinal distributions
Add methods to Mpi to look for next and previous bunches
Add start of a CavityMonitor, to improve to deal with multi-cores

Add CavityResonator class
Add BeamLoadingVlasov class, to do tested and developped further.
From BeamLoadingVlasov, only the beam_equilibrium method is well tested and benchmarked.
The cannonical_transform and solveB methods have to be tested and benchmarked further.

Remove tools.py to avoid circular import problem with wakefield.py -> merged into wakefield.py
Remove machines folder to save machine data in a seperate git instance
Rework import so the code can be used as independant module mbtrack2

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

To be PEP8 complient:
Lowercase folders
Extended docstrings
Rename and divide some files