Dear Qusay,
You thesis looks crowded. Lots of topic to cover. Anyway, you may download 30-days OptiSystem software free trial from Optiwave’s website. OptiSystem addresses most of your research topics. You may use it for optimization as well. The best start is to go through the Example Library of OptiSystem, which is part of the installation. The examples will give you guidance on the different projects. You may contact me directly at ahmad.atieh@optiwave.com to discuss further.
Regards,
Ahmad