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Yes, you can design a project normally using OptiSystem component in the project layout, then using the Script tab in the main layout write a code to process and run the system. You may use loops and save data in excel sheets and graph at the same time. You need to use Scrip/Run in the main toolbar to run your Script code.
There are few examples in OptiSystem Example Library. Two samples (Free Space Link – Earth to Satellite.osd) and (BER_Calculation_RS_FEC_BPSK.osd) located at the following links, respectively.
C:\Users\USER NAME\Documents\OptiSystem 18.0 Samples\Optical wireless\Earth-satellite design
C:\Users\USER NAME\Documents\OptiSystem 18.0 Samples\Advanced modulation systems\Error coding techniques\Reed Solomon FEC
Make sure that you use proper path in the script to run it properly.