The supercell code is available by GPLv2 license. That means no restriction for using the program “as is” for your reseach: academic, commercial or private for free. I’ll appriciate if you cite supercell paper in your work. Licence restrictions appear in case of using the program in general or its code (full or partially) in your project. Please consult carefully the license in such cases. For example, I won’t be happy if you take my program, rename it and start selling it to users. The license protects the program from such behaviour.