Coherent manipulation of atomic states is a key concept in high-precision spectroscopy and used in atomic fountain clocks and a number of optical frequency standards. Operation of these standards can involve a number of cyclic switching processes, wh
ich may induce cycle synchronous phase excursions of the interrogation signal and thus lead to shifts in the output of the frequency standard. We have built a FPGA-based phase analyzer to investigate these effects and conducted measurements on two frequency standards. For the caesium fountain PTB-CSF2 we were able to exclude phase variations of the microwave source at the level of a few $mu$rad, corresponding to relative frequency shifts of less than 10$^{-16}$. In the optical domain, we investigated phase variations in PTBs Yb$^+$ optical frequency standard and made detailed measurements of AOM chirps and their scaling with duty cycle and driving power. We ascertained that cycle-synchronous as well as long-term phase excursion do not cause frequency shifts larger than 10$^{-18}$.
We evaluate the frequency error from distributed cavity phase in the caesium fountain clock PTB-CSF2 at the Physikalisch-Technische Bundesanstalt with a combination of frequency measurements and ab initio calculations. The associated uncertainty is 1
.3E-16, with a frequency bias of 0.4E-16. The agreement between the measurements and calculations explains the previously observed frequency shifts at elevated microwave amplitude. We also evaluate the frequency bias and uncertainty due to the microwave lensing of the atomic wavepackets. We report a total PTB-CSF2 systematic uncertainty of 4.1E-16.
