At the end of the FDTD simulation of a periodic structure with plane wave excitation, the reflection and transmission coefficients of the structure are calculated and saved into two complex data files with '''.CPX''' file extensions. These coefficients behave like the S<sub>11</sub> and S<sub>21</sub> parameters of a two-port network. You can think of the upper half-space as Port 1 and the lower half-space as Port 2 of this network. The reflection and transmission (R/T) coefficients can be plotted on 2D graphs in '''EM.Grid '''similar to the scattering parameters. You can plot them from the Navigation Tree. To do so, right click on the '''Periodic Characteristics''' item in the '''Observables''' section of the Navigation Tree and select '''Plot Reflection Coefficients''' or '''Plot Transmission Coefficients'''. The complex data files are also listed in EM.Cube's data manager. To open data manager, click the '''Data Manager''' [[Image:data_manager_icon.png]] button of the '''Simulate Toolbar''' or select '''Simulate > Data Manager''' from the menu bar or right click on the '''Data Manager''' item of the Navigation Tree and select Open Data Manager... from the contextual menu or use the keyboard shortcut '''Ctrl+D'''. Select any data file by selecting its row in the table and then click the '''Plot''' button to plot the graph in EM.Grid.
<font color="red"><u>'''{{Note|It is very important to keep in mind that only in the case of normal incidence does EM.Cube compute the reflection and transmission coefficients over the entire specified bandwidth of the project.'''</u></font> At oblique incidences when θ > 0, the computed R/T coefficients after the discrete Fourier transformation are valid only at the center frequency of the project for the given value of the incident θ<sub>0</sub> angle. In other words, the computed R/T coefficients at all the other frequencies away from the center frequency correspond to different values of the incident θ angle. As a result, EM.Cube only saves the reflection and transmission coefficients at the center frequency into the output data files "reflection_coefficient.CPX" and "transmission_coefficient.CPX".}}
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