I'd like to try and understand how the PPM of the clock is stepped when using the ATOM driver and flag3 is set or unset. If you look at the loopstats file http:/acarver.net/ntpd/loops.20120223 and observe the PPM column, you'll see that it will sit at one value for a while and then step to another value and hold again (say from -77.058 to -77.112). This is with flag3 set (kernel discipline enabled). It never quite settles, it's always adjusting the number.

Now, if I clear flag3, the ATOM driver continues to adjust the clock PPM but it does so in very fine increments of 0.001 and then manages to hold that for a very long time without jumping around. It may drift up and down by +/- 0.005 PPM or so depending on the room temperature but it never really strays from some center value. It also makes the adjustments sooner than with flag3 set. If a temperature change starts to occur while flag3 is clear, the PPM shifts within one or two polling cycles. If flag3 is set, the PPM is held steady for many polling cycles (typically at least 8-10) and then makes the sudden jump instead of a graceful slew.

I don't really understand why flag3 is making a difference in the step size of the adjustment. It seems that flag3 causes a much more coarse correction to the clock which isn't very stable compared to no flag3 which stabilizes the clock fairly well (stable in terms of a very mildly changing PPM offset). I would have expected the adjustments to be the same regardless of mode and try to fine tune the clock. I can't imagine the large steps are keeping things as stable as they could be.
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