Studying the Fix NH class
In this section, we'll discuss the role of the Fix NH class, which is implemented by fix_nh.cpp and fix_nh.h. The Fix NVT, Fix NPT, and Fix NPH classes inherit from this class when employing thermostats and barostats.
In this section, we will only focus on the thermostat functionalities of Fix NH for the sake of conciseness. Fix NH applies the Nose-Hoover thermostat, which introduces a virtual heat bath tethered to the simulated system. This heat bath can contain a 1D chain of virtual particles where the 
particle has mass 
, position 
, and momentum 
, which gives us the following velocity:
The time derivative of the velocity, 
, of an atom, i, being thermostatted is given by the following formula:
For a virtual particle, k, the 
is calculated by the following formula:
Here, 
is the difference between double the neighboring virtual particle's kinetic energy and its targeted kinetic energy, which is determined by its thermal energy...
