refactor collimator computation

We modify the collimator inputs as follows:

• beta_x and beta_y are read directly from the twiss file
• only one between half-gap and number of sigmas is specified (if number of sigmas the half gap is computed...)

Moreover we add a new class Collimator which extends Element by adding some fields related to collimators and a method which allows adding a contribution to the collimator impedance (e.g. add the geometric impedance to a purely resistive collimator) and a method to compute the one sigma half-gap from the beam parameters.

Many redundant or hard-coded parameters are removed, and also materials redundant with PyWIT. In general a large refactoring has taken place, to make the code simpler and cleaner).

This solves issues #7 (closed) , #15 (closed) , #16 (closed) , #18 (closed) , #20 (closed) , and #23 (closed) .