Hi @Akhil,

The orientation of the electric or magnetic field also depends on your chosen Polarization Reference Method. The X Axis Reference is set by default since many systems use the Z-Axis as the direction of propagation. However, in your case, the rays propagate along the X-Axis so using a Y- or Z- Axis Reference would be a better choice. 

When you define Jx and Jy (Jones vector components), OpticStudio uses the following definitions to compute the appropriate E fields, where Jx is along S and Jy is along P:

1. X Axis Reference: The P vector is determined from K cross X, and S = P cross K.
2. Y Axis Reference: The S vector is determined from Y cross K, and P = K cross S.
3. Z Axis Reference: The S vector is determined from K cross Z, and P = K cross S.

Therefore, if we choose Y Axis Reference and we set Jx = 1 / Jy = 0, then you will have a TE polarization for each ray hitting the structure.

For more detailed information about defining polarization, please see the Help File: The Setup Tab > System Group (the Setup Tab) > System Explorer > Polarization (System Explorer) > Defining the Initial Polarization. 

Best,
Ethan