Your thesis advisor’s role it to guide you to the pearly gates of enlightened rationalism by giving you advice on how to make progress on whatever irrelevant topic you may be overspecializing in. So when you are stuck on something, you ask them, and they fill you in on the stuff that no one ever told you, but you are expected to know. You then say, “Aha, I see. Thank you so much for sharing your wisdom with me.” And your problem is solved and research continues. At least that’s how it works in theory. And as a theoretician I can tell you that theory does NOT always work. Just try applying Redfield theory to nuclear dynamics when electronic coherences are involved. As another example I give you my conversation with big boss man last week:

BBM: So how are things going?
Me: OK. I’ve almost got my eigenfunctions and eigenvalues determined, but I’m having a some normalization issues.
BBM: Hmm.
Me: Yeah..
BBM: Well all that I can tell you about normalization issues is, don’t have them.
Me: OK, thanks.

I’ve since gotten all of my wavefunctions normalized to the same value. It’s not 1, but whatever. It’s 0.313314 to be exact, which who knows where the heck that came from, but I’m going with it.