Dear @neamin ,
I’m happy to recommend you the FLUKA beginner’s course which will take place at CERN beginning of December, the registrations should be open until October 13th and it’s the ideal place for someone new to FLUKA to receive an excellent basic training. If you are unable to attend, I would advise you to take a look at the course material of previous FLUKA beginner’s courses, you can find those in the timetable of the indico page. In particular, the “Scoring I & II” and “Hadron Physics” items of the basic course will be of interest for you.
Once you get acquainted with the basics you can continue to your heavy ion problem. There is a heavy ion input template in Flair to get you started. The topic of calculating cross sections using FLUKA is quite involved, there is a lot of information available on this forum. You can start for example with this post on scoring cross section values using USRYIELD or this post about the units of the USRYIELD output. In addition, there are this post about calculating cross sections with a thin target and this or this post that give a bit more details on the output and comparison to experimental data.
Don’t hesitate to ask for further questions in case you run into trouble!
Cheers,
Andreas