Temperature and entropy in molecular system

Abstract

The irreversibility, temperature, and entropy are identified for an atomic system of solid material. Thermodynamics second law is automatically satisfied in the time evolution of molecular dynamics (MD). The irreversibility caused by an atom spontaneously moves from a non-stable equilibrium position to a stable equilibrium position. The process is dynamic in nature associated with the conversion of potential energy to kinetic energy and the dissipation of kinetic energy to the entire system. The forward process is less sensitive to small variation of boundary condition than reverse process, causing the time symmetry to break. Different methods to define temperature in molecular system are revisited with paradox examples. It is seen that the temperature can only be rigorously defined on an atom knowing its time history of velocity vector. The velocity vector of an atom is the summation of the mechanical part and the thermal part, the mechanical velocity is related to the global motion (translation, rotation, acceleration, vibration, etc.), the thermal velocity is related to temperature and is assumed to follow the identical random Gaussian distribution for all of its [Formula: see text], [Formula: see text] and [Formula: see text] component. The [Formula: see text]-velocity (same for [Formula: see text] or [Formula: see text]) versus time obtained from MD simulation is treated as a signal (mechanical motion) corrupted with random Gaussian distribution noise (thermal motion). The noise is separated from signal with wavelet filter and used as the randomness measurement. The temperature is thus defined as the variance of the thermal velocity multiply the atom mass and divided by Boltzmann constant. The new definition is equivalent to the Nose–Hover thermostat for a stationary system. For system with macroscopic acceleration, rotation, vibration, etc., the new definition can predict the same temperature as the stationary system, while Nose–Hover thermostat predicts a much higher temperature. It is seen that the new definition of temperature is not influenced by the global motion, i.e., translation, rotation, acceleration, vibration, etc., of the system. The Gibbs entropy is calculated for each atom by knowing normal distribution as the probability density function. The relationship between entropy and temperature is established for solid material.