There are several ways to stop a simulation from within an S-function:
1) For MATLAB file S-functions you can use the command:
set_param(bdroot, 'SimulationCommand', 'stop');
For Simulink 4.0 (R12) and above you can use the following on C-MEX S-functions:
1) You can do a 'mexCallMatlab' with the SET_PARAM command with the same input arguments mentioned above for MATLAB file S-functions.
2) You can use the macro ssSetStopRequested, which will allow you to stop a simulation from within your S-function (you will have to set the simulation flag in this macro to not zero). For more information on this function please see pg. 10-187 of the Writing S-function Guide. The online version of this Guide can be found at:
https://www.mathworks.com/help/simulink/sfg/sssetstoprequested.html
