Regarding your question, I suppose that you need the results from the simulation at each time instant of your test. So, you can use generic names for each variable inside your Simulink file. Moreover, in your script .m  you can read the variables from your workspace, then save these values and run another time your simulation from your script.

I hope that my answer results helpful.   

1. Make sure you modify your models to take parameters/variables from workspace.

2. Run sim with desired step time, after each run, update output parameters to the variables stored in workspace.

By doing so, you will be able to use output of previous run to the current run. Loop as many times as you want.

Instead of developing code try to use matlab function. Otherwise save mdl and script with same name and in same folder. First run code then model.

for t= 1: 100 % total simulation steps

Sim( 'yourmodel.mdl')

end

# change simulink solver setting to fixed step solver with sample time of 0.5