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Sridarshini,
You did not understand my original response as your new design has effectively all the same issues as the first in terms of testing for an amplitude of 1 from your input plane.
1) You cannot check the amplitude of the signal at an observation point on the output of a photonic crystal and expect it to be the same as the input, therefore you are not testing to see if the input plane has an amplitude of 1. Photonic crystals have loss, they can also focus a beam (one of the possible reasons you are getting an amplitude greater than one). The best way to check is to delete your photonic crystal, create an Observation Area and see the amplitude, see ObservationAreaNotParaxial.png. See point 2 why you are seeing 1.08 in that figure.
2) You did not correct the issue with the Gaussian source. As stated previously the Gaussian source operates under the paraxial approximation which requires that the width of the Gaussian distribution be much greater than your source. Your source is 1.55um and your width is set to 1.44um, this does not satisfy that condition which results in an amplitude higher than one, see ObservationAReaNotParaxial.png.
3) You are not running with a high enough resolution. While your spatial mesh is acceptable for your wavelength in the material, you did not take into consideration the sizes of your features. Your rods have a radius of 0.1um but your resolution is 0.044um, this means that some of your rods will only be defined by 4, maybe 5 grid points. In designer take a look at your 2D Refr_Idx-Re(y) tab and see how irregular your rods are, see attachment discretizedStructure.png. With higher resolutions the rods are better defined and the values you are looking at drop off.
Scott
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