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There are several issues in your scripted simulation file:
1: the substrate should be included for a small portion, like a fraction of wavelength (when no SPP). Currently you are simulating the substratge suspended in air, which forms a cavity;
2: the distance from source to the up surface is too long. A fraction of wavelength is good.
3: you used periodic boundary conditions but the substrate is not large enough to be outside of the periodic BCs. FDTD is a discrete method that ExEyEz and HxHyHz are not collocated:
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Therefore you will need to extend the substrate to outside of the PBC.
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You current settings and PEC material use much less memory, but the long distance and THz simulation needs longer simulation time to have the pulse propagate to the bottom.
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