I'm writing a master thesis and want to use software on BSD License to carry out my calculations. As I understand, I can use it freely since it's not even a commercial use. Just need somebody to confirm it. Also, should I disclose information about the license in my thesis?
Yes, BSD-licensed code is free for anyone to use for any purpose. You don't need to disclose the license in your thesis.
As @MadHatter pointed out, if you were to include the source of the program in your thesis, say as an appendix, you would need to include the license in that.
You should of course give credit as you would for any resource that you use, but that's an academic issue not a licensing issue.