Yeah, the problem is that you’re letting your teenage daughter hang out with a teenage boy. Girls do absolutely insane things for the affection of boys, and that is especially true at that age.
You can’t ground your daughter for being an atheist. It should first of all be said that she very likely isn’t an atheist at all, but is rather seeking to assert her own unique identity apart from the family. That’s normal, and she is turning to the atheist boy who she may admire very much to fill that identity. Give her a little space and more than anything let her know that you will love her absolutely passionately no matter what she believes or does.
I have a good friend who is a very, very serious Catholic–seven kids, daily Mass, etc.–who has a teenage daughter who informed him that she has no problem with having relations with boys and that she has, in fact, already done as much. You can tell them what to do, but you can’t tell them what to believe.
I was doing voodoo and Wicca at her age in defiance of my nominally Protestant family. My parents never told me what to believe, although they did tell me that I couldn’t do any voodoo or Wicca rituals, so I became Jewish and, eventually, Catholic. And here I am.
It is important to give your daughter enough intellectual space to figure these things out, without actually enabling atheist or Wicca or whatever it might be. It is perfectly acceptable to demand her attendance at Mass. It is fine to require her obedience in moral issues. You can and should tell he what you believe, what the Church teaches, why, and then show her Christ’s love very tangibly in your marriage and in your relationship with your daughter. And pray a lot, right?
And certainly I would discern very carefully and courageously about this atheist boy. I am not sure what to advise in that matter, but it does seem like something must be done that disrupts the status quo a bit.