Just don't mention it. If it comes up in conversation at some point (whether he/she asks about your beliefs or finds out you are an atheist), just say "I don't like talking about my private beliefs.", or "My religious views are personal, and I don't like talking about them."
You could always say that you respect people of all beliefs, as long as they don't try to preach or convert you over to their side. You'd much rather prefer to live in a diverse but peaceful society.
Basically, if you don't make an issue of it, and strive to be as open and welcoming as possible, then there is no reason for your supervisor to bring it up or try to harass you over it. Remember though, that if he does start doing that, you should speak to the head of department and try to get your supervisor changed. It isn't worth embarking on a PhD with a supervisor who you can't get along with, especially if you've made the effort.
You could always say that you respect people of all beliefs, as long as they don't try to preach or convert you over to their side. You'd much rather prefer to live in a diverse but peaceful society.
Basically, if you don't make an issue of it, and strive to be as open and welcoming as possible, then there is no reason for your supervisor to bring it up or try to harass you over it. Remember though, that if he does start doing that, you should speak to the head of department and try to get your supervisor changed. It isn't worth embarking on a PhD with a supervisor who you can't get along with, especially if you've made the effort.