The supercell code is available under the GPLv2 license. That means there is no restriction on using the program “as is” for your research — academic, commercial or private — for free. I’d appreciate it if you cite the supercell paper in your work. License restrictions apply when you use the program in general, or its code (in full or in part), in your project. Please consult the license carefully 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 behavior.