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I cannot really answer for specifics of OptiFDTD 10, but the general idea is as following:
-setup your geometry and materials
-setup a pulsed (GMCW) input plane with enough bandwidth to cover the phenomenon of interest (let’s say you set it up between 500-900 nm FWHM)
-draw a observation area (3D) or observation line (2D) to capture light transmitted through the structure
-In the simulation parameters, setup the DFT option so that enough points are calculated for the bandwidth of interest (for example 101 points between 500-900 nm).
After running the simulation, you can observe the field pattern of your observation area/line. There is an option to calculate the power spectrum. These spectra can be normalized with regards to the input plane, enabling a |E|/|E0| calculation.
From next update of OptiFDTD (12.1), it will be possible to directly export the total field intensity at specific wavelengths using scripts. It might be useful in complement to what you described.