Initially you have to designate the parameters such as the refractive indices and the non-linearity issues ( such as kerr non-linearity) and other second order effects before going for further steps. Also you have to designate the radius and other parameters of the PhC rods which you'll be using. The axis also needs to be specified in 2D simulations parameters before running the 2D simulation. You also need to calculate the bandgap of your structure prior to assigning the wavelength of operation.
I made all what you told, but what is the other adjustment like the location of the source, number of PML layer, reflectance, and the characteristic of the input signal.
You are welcome, well as for the location of the source you've to place it in the respective inputs and for the PML part you have to check with the properties. The characteristic of the input signal can be specified when you select the input signal and check its properties and specify the parameters according to your need. If you face any problem you can always feel free to ask me or drop an email at [email protected]