El Capitan: New supercomputer is the fastest

I fail to understand how these nuclear bomb simulations require so much compute power.

Are they trying to model every single atom?

Is this a case where the physicists in charge get away with programming the most inefficient models possible and then the administration simply replies "oh I guess we'll need a bigger supercomputer"

It's because of the way the weapons are designed, which requires a CNWDI clearance to know, so your curiosity is not likely to be sated.