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Question: How do I wire the serial port of the controller to the DB-9 connector on my computer?

Your DB-9 should be wired:

DB-9     U10       function
-----    ---       --------
pin 2    pin 5     data: controller to PC
pin 5    ground    ground return

The above is all you need if you just want to monitor the controller output
as discussed in the QST article (footnote 10).

You can also make a cable arrangement that will permit you to communicate 
between your PC and your GPS receiver.  You can then use the TAC32 
software to initialize "position hold" mode in your receiver and 
monitor its operation.  If you are using a Motorola OnCore UT+ or VP model the 
following description may be helpful.
To set up the UT+ (or VP) using a PC program, you can make a separate
DB-9 connector that uses the spare sections of the MAX233 as inverter
and level shifter to change the (inverted) TTL signals from the
UT+ into real RS-232.  This provides functionality similar to
the TAC-2 board from TAPR.  You will need to make 2 harnesses.  One
connects the controller board to the PC, the other connects the
controller board to the UT+.  The wiring is as follows:

DB-9    U10    UT+ 2x5 header       function
----    ---    --------------       --------
.                    1                ext. BBRAM battery backup (+3.6v)
.                    2                +5v supply to UT+ (can come from controller)
.                    3                gnd (ditto)
.                    4                n.c.
.                    5                n.c.
1                    6                1 pps output (TTL)
.                    7                gnd
.         1          8                TX data to PC (inverted TTL)
2         18                          TX data to PC (RS-232)
3         4                           RX data from PC (RS-232)
.         3          9                RX data from PC (inverted TTL)
5         gnd       10                serial port ground return
Note that the RX and TX signals are true RS-232 since they are converted by
the MAX-233 chip.  The 1 PPS pulse to the DCD input pin of the PC serial
is TTL, however this works fine for most PCs and, in any case, TAC32 will 
work even without the 1 PPS input. 
                           

The pin layout on the UT+ 2x5 header as viewed from the top
side of the board (pins 1 and 2 are at the end nearest to the
edge of the UT+ board).  

__________
| 1    2 |
| 3    4 |
| 5    6 |
| 7    8 |
| 9   10 |
----------

As noted above, the +5 v supply for the UT+ can come from the
regulated 5 v supply bus on the controller.  The A&A PC board
provides a header to make this connection to the UT+ header. 
To monitor the operation of the controller attach the simple DB-9 
cable described at the top of this note to your PC.  To set up the GPS 
receiver attach the DB-9 from the dual-harness arrangement 
to your PC.  If you want to be fancier make a single cable with a 
switch that combines both functions. 
Question: What can I do with the serial port
data?
The first thing to do is capture the data into a file.  There are
many programs that will do this and almost any program that is designed
to make your computer act like a terminal for connection to a modem
should work. The baud rate of the serial port is 9600 and the parity, 
etc are 8N1.
With a data file in hand you can start by making a plot, either
of the phase difference or the DAC voltage. A PC program for parsing the
serial port data and converting it to tab-delimited format for input
to a spreadsheet has been written by Gary Sanders. It can be downloaded
from this website.
I have usually used Mathematica to analyze data.  In addition
to plotting, I can readily compute the rms jitter, fit average 
aging and day/night variation parameters, perform additional smoothing
to see the effect of long-term filtering, etc.  Most of these operations
can be done using the build-in functions and packages that are
standard in Mathematica.  Sometimes a few tricks need to be used
to let Mathematica efficiently handle the very data sets that the
controller can generate after a few days of data collection. 
I also have some routines for computing Allan variances from the 
data. The Mathematica code to perform these operations is available 
for those who are interested.
Question: I just bought a truckload of Quartztown
model 17YZR-4P2-S crystal oscillators on eBay. 
Can I use these with the controller?
Probably not. The controller was designed to produce a frequency 
standard that would compare in accuracy with the GPS atomic clocks 
themselves.  The stability of the VCXO is important in achieving this 
goal since we must rely heavily on it to provide short term accuracy.  
This generally means that the VCXO must reside in a temperature-regulated 
oven and that the quartz crystal unit be fabricated with stability, not 
low cost, in mind. If you are going to the effort of building this 
frequency standard it is reasonable to try to find a good quality 
VCXO.  A surplus ovenized oscillator module (e.g. the HP 10811) is a
good choice. The surplus HP 5328A counter with the high stability option
contains an HP 10811 module (check to make sure it has not been removed) 
and these are often available for about $100. 
Question: I have just bought a carton of Super 
Skyrider model 17YZR-4P2-S GPS receivers on eBay.  
Can I use these with the controller?
Probably not. Unless a GPS receiver is especially designed otherwise,
the 1 pps timing pulse is likely to have a large time jitter due to 
quantization inherent in the receiver CPU clock.  A jitter of 1 microsecond 
in not uncommon. If you are going to the effort of building this 
frequency standard it is reasonable to get a GPS receiver designed for 
timing applications such as the Motorola VP or UT+ which have a timing 
jitter of the order of 10 nanoseconds (when averaged over 30 seconds).
See "Construction and Setup Notes" for information on getting the UT+.