Classical thermodynamics considers only the macroscopic properties of the system and explain the relationship between those properties. It does not explain how those properties are acquired by the system. Statistical mechanics provides a connection between microscopic and macroscopic behaviour of the system.
Statistical mechanics/ Thermodynamics assumes the existence of atoms and molecules and provides explicit expressions for the macroscopic thermodynamic quantities like Temperature, Pressure, Energy etc. In molecular dynamics, we use these expressions to calculate the quantities of interest.
LAMMPS exactly does this. It calculates various macroscopic properties by solving the equations of statistical mechanic equations and time averaging them. So what LAMMPS does it is, it calculates macroscopic properties of the system by analysing the microscopic behaviour of the system. Today we have many experimental methods to study the macroscopic nature of the system, but the experimental study of microscopic properties are quite difficult. LAMMPS plays a crucial role in the analysis of the microscopic behaviour of the system. And phenomenon like radiational damages happens at a timescale of picoseconds. Their experimental studies are quite complicated, but LAMMPS works at a timescale of femtosecond, so it shouldn't be a problem.
So these are some of the basics of statistical mechanics and advantages of LAMMPS. If you are interested in statistical mechanics, I would recommend you to have a course in it, since it's a huge topic by itself. If you have any doubt or suggestion do mention in the comment section.
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