Emittance calculation

Hello, There are a few changes that need to be verified. I've changed the way emittance is computed. For nonzero dispersion, it gives the correct results. When dispersion is included, I think the difference is minimal for realistic values. But I am not sure.

• Calculation of emittances and CS invariants for nonzero dispersion (based on PyHEADTAIL "cobra" functions)
• Different ion species data in impedance.ions

mbtrack2/tracking/particles.py

@@ -288,7 +288,7 @@ class Bunch:
         cov_y = np.cov(self['y'], self['yp'])        
         cov_z = np.cov(self['tau'], self['delta'])
         
-        if (self.ring.optics.local_dispersion[0:1] != 0):
+        if (self.ring.optics.local_dispersion != [0, 0, 0, 0]):
             cov_xdelta = np.cov(self['x'], self['delta'])
             cov_xpdelta = np.cov(self['xp'], self['delta'])
             cov_ydelta = np.cov(self['y'], self['delta'])        
@@ -317,7 +317,7 @@ class Bunch:
 
         """
         xb = self['x'] - self['delta'] * self.ring.optics.local_dispersion[0]
-        yy = self['y'] - self['delta'] * self.ring.optics.local_dispersion[2]
+        yb = self['y'] - self['delta'] * self.ring.optics.local_dispersion[2]
         xpb = self['xp'] - self['delta'] * self.ring.optics.local_dispersion[1]
         ypb = self['yp'] - self['delta'] * self.ring.optics.local_dispersion[3]
         Jx = (self.ring.optics.local_gamma[0] * xb**2) + \