The file resonator.zmx is included in the zip archive that may be downloaded from the last page of this article. Note that it has the following system parameters:
System unit to mm (System > General > Units)
Wavelength to 0.5106um and 0.5782um (System > Wavelengths)
Set one field with values X=0 and Y=0 (System > Fields)
Set system aperture as Entrance Pupil Diameter of 0.14 mm (System > General > Aperture)

It is set to the geometry equaling to 2 full passes in sequential mode:

On the surfaces 2, 3, 7, 8, 10, 11, 15, 16 are set circular apertures with semi-diameters 7mm representing the apertures of the active medium.

Surface 17 is a user-defined surface which is supplied with Zemax. It represents a soft edged aperture on the central mirror at output lens. The optical density function is given by D =  0.5D_max (1.0 + cos(πr )), where  r is the radial coordinate normalized to the semi-diamater of the surface.

Surfaces 18 and 19 represent the output coupler and may be omitted. The distance 5e4mm at the19^th surface is used for analysis at far field (actually it is not real far field, but the distance is good for analysis).

Coordinate breaks are inserted to model the primary mirror misalignment. Note that if this mirror is decentered, then the chief ray will miss the center of the output surface (this is usually compensated by adjustment and there is no case when only offset of tilt only is present). So the needed tilt may be found by simple optimization. For modelling of significant offset is must be changed iteratively or also by optimization. Operands of merit function are the following:

      
      Here REAY controls the needed tilt and PMVA must be modified to desired target offset (shown +10mm).