Canonical Temperature Control by Molecular Dynamics

"Pedagogical derivations for Nos\'e's dynamics can be developed in two different ways, (i) by starting with a temperature-dependent Hamiltonian in which the variable $s$ scales the time or the mass, or (ii) by requiring that the equations of motion generate the canonical distribution including a Gaussian distribution in the friction coefficient $\zeta$. Nos\'e's papers follow the former approach. Because the latter approach is not only constructive and simple, but also can be generalized to other forms of the equations of motion, we illustrate it here. We begin by considering the probability density $f(q,p,\zeta)$ in an extended phase space which includes $\zeta$ as well as all pairs of phase variables $q$ and $p$. This density $f(q,p,\zeta)$ satisfies the conservation of probability (Liouville's Continuity Equation)" $$(\partial f/\partial t) + \sum (\partial (\dot q f)/\partial q) + \sum (\partial (\dot p f)/\partial p) + \sum (\partial (\dot \zeta f)/\partial \zeta) = 0 \ .$$ The multi-authored ``review''\cite{b1} motivated our quoting the history of Nos\'e and Nos\'e-Hoover mechanics, aptly described on page 31 of Bill's 1986 {\it Molecular Dynamics} book, reproduced above\cite{b2}.