The main method to calibrate fluxes in MBE is the RHEED oscillation technique: Article Dynamics of film growth of GaAs by MBE from RHEED observations
,
Article Damped oscillations in reflection high energy electron diffr...
. It is also possible to estimate the atomic fluxes using the pressure controller, but it is more complicated:
Article Beam equivalent pressure measurements in chemical beam epitaxy
.
And also, in MBE chamber the quartz crystal resonator can be introduced. Measuring the change in the frequency the mass per unit area and, therefore, the growth rate can be monitored.