Dear Howard,
1) You are using GRI-3.0 which, as far as I know, is not validated for ammonia chemistry. It was optimized for natural gas combustion. In fact, as far as I can see, they do not use GRI-3.0 in that paper at all.
2) You are only integrating for 1 ms, which may not be long enough to have an ignition. Furthermore, as best I can tell, the point you are trying to match against has an ignition delay time of 1.113 ms...
3) Why are you using a constant pressure reactor? Most shock tubes are modeled using a constant volume reactor
Best,
Bryan
P.S. It is usually not allowed by the journal for people to post a complete article on public websites, because the journal owns the copyright. Please be aware of that in the future.