Forcing the simulaion to completion before it reaches the auto shutoff level might result in inaccuracy. For calculating the Fourier transform the fields must decay sufficiently enough and an auto shutoff of 1e-05 works for most cases. I would recommend you to check how the auto shutoff level changes over the duration. If the simulation diverges just before reaching the auto shutoff, for ex. it decays to 5e-05 and then starts growing exponentially, you may try to end the simulation earlier. But if it starts diverging pretty soon then there is no point doing this.
Do you have a script that you are using to produce the entire simulation setup? In that case you can send the script here and I can run some tests as well. Thank you!
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