This is a pretty useful feature to prevent you from spending unnecessarily long simulation time. 1e-5 is rather an arbitrary choice but it should work for most simulations that the autoshutoff will kick in and terminate the simulation. The autoshutoff level shows you the amount of energy remaining in the simulation compared to the initial conditions. To learn more about the auto shutoff option take a look at this KX post. On the other hand, if you make the simulation time too small, then the simulation will be unfinished and the results would be wrong. However, a really large value for simulation time will mean the solver will overestimate the time required to finish the simulation. So even if you use a simulation time much larger than required, the simulation will stop once the light signal has passed through the structure completely. One point to note here is that the solver in FDTD keeps track of the remaining energy in the volume and the simulation automatically stops when the energy becomes 1e-5 of the initial value (default value for auto shutoff). So the initial value of 58 fs gives you as starting point but you may want to add a safety margin and use (say) 100 fs as your simulation time. In such a case, the required simulation time will be larger. Note that often the light with reflect on different surfaces in the structure and the actual travel distance may be much larger than the length of the simulation region.

Fdtd solutions