The Allen deviation is used to describe the performance of  a stable
  clock. Measuring the performance of a good clock requires  a counter
  with resolution  down  to picosecond levels. As  Dr  Griffith points
  out, some  modern counters may have internal signal  processing that
  makes them unsuitable for this task.

  Another thread  discussed using a mixer to  generate  the difference
  frequency between  two oscillators, then measuring the  stability of
  the resulting beat note:

  http://www.febo.com/pipermail/time-nuts/2005-July/019006.html

  The basic  principle  is sound. If the oscillators  were  running at
  10MHz, and  the  frequency difference was 1 Hz, then  the  beat note
  would be 1 Hz.

  This represents  one  part in 10 million, or  1e-7  of  the original
  frequency. If  the  beat   note   is   measured  with  1 microsecond
  resolution, the  overall resolution is 1e-7 / 1e-6 = 1e-13.  This is
  beyond the capability of most commercial counters.

  The difficulty  with this approach is the output of a mixer is  at a
  fairly low  level, perhaps 50 millivolts or so. The  frequency would
  also be very low, perhaps 1 Hz. This means the counter would have to
  trigger accurately on a very slow-rising, low amplitude signal.

  This is  a very difficult measurement problem. The accuracy  will be
  degraded by  noise,  such  as the 60Hz  AC  line  frequency  and its
  harmonics, switching noise from the pc power supplies  and monitors,
  radiation from nearby fluorescent lighting, plus thermal  noise from
  the mixer and input stage of the amplifiers.

  This low-level noise is very difficult to eliminate, especially when
  coax cables are needed to transfer the desired signal from one place
  to another.  The result is the measurement system is not as  good as
  it could be.

  There is a solution to this problem. Another kind of mixer  called a
  "digital mixer"  is ideally suited for this application.  It  uses a
  d-flop, with one signal going to the clock pin, and one going to the
  "D" input.  The resulting signal on the "Q' output is  the frequency
  difference between the two signals.

  The output signal is a full logic level swing, perhaps 5 Volts, with
  a risetime  of a couple of nanoseconds. This is an  ideal  signal to
  pass on  a terminated coax cable to the counter.  The  schematic and
  waveforms are shown in the attached GIF.

  The output  of  the  first d-flop is passed to  a  second  d-flop to
  eliminate glitches due to metastability in the first stage. This can
  occur when  the signal on the "D" input is exactly on  the switching
  threshold when the clock transition occurs. The resulting glitch can
  severely disrupt the following logic stages.

  In practice, it might be difficult to offset two  stable oscillators
  by 1  Hz.  In this case, the frequencies can be  multiplied  to some
  higher value. For example, the frequencies could be multiplied  by a
  factor of 10 to 100MHz, and offset by 1 Hz.

  There may be some jitter in the leading edge of the beat  note since
  the d-flop  may  or may not catch the transition as  it  crosses the
  threshold on  the  "D" input. Instead of the  standard  +/-  1 clock
  ambiguity in  digital circuits, the output could  be  several clocks
  late. However,  if the counter had a resolution  of  100 nanoseconds
  (10MHz clock),  the  extra  delay  is  much  less  than  the counter
  resolution and should have no effect.

  The overall resolution in this example would be 1e-8 / 1e-7 = 1e-15.

  This is  achieved in one second, which is an impossible  task  for a
  counter. This means the Allen deviation can be measured  much faster
  than before, and with much higher accuracy.

  A simple LTspice analysis is included in the attached ZIP.

  Best Regards,

  Mike Monett