The use of the term “code” in this way is universal among the US national laboratories and adjacent scientific computing fields.

It refers to a complete software package. So, a “hydrodynamics code” is a hydrodynamics simulation, like Gerris.

It seems peculiar but they’ve been using the term this way since the 1960’s and probably long before. Given how much of modern computer science arose from the US government scientific complex I’d say they’ve earned the right to define their own usage.