Temperature control in molecular dynamic simulations of non-equilibrium processes

Thermostats are often used in various condensed matter problems, e.g. when a biological molecule undergoes a transformation in a solution, a crystal surface is irradiated with energetic particles, a crack propagates in a solid upon applied stress, two surfaces slide with respect to each other, an excited local phonon dissipates its energy into a crystal bulk, and so on. In all of these problems, as well as in many others, there is an energy transfer between different local parts of the entire system kept at a constant temperature. Very often, when modelling such processes using molecular dynamics simulations, thermostatting is done using strictly equilibrium approaches serving to describe the NV T ensemble. In this paper we critically discuss the applicability of such approaches to non-equilibrium problems, including those mentioned above, and stress that the correct temperature control can only be achieved if the method is based on the generalized Langevin equation (GLE). Specifically, we emphasize that a meaningful compromise between computational efficiency and a physically appropriate implementation of the NV T thermostat can be achieved, at least for solid state and surface problems, if the so-called stochastic boundary conditions (SBC), recently derived from the GLE (Kantorovich and Rompotis 2008 Phys. Rev. B 78 094305), are used. For SBC, the Langevin thermostat is only applied to the outer part of the simulated fragment of the entire system which borders the surrounding environment (not considered explicitly) serving as a heat bath. This point is illustrated by comparing the performance of the SBC and some of the equilibrium thermostats in two problems: (i) irradiation of the Si(001) surface with an energetic CaF2 molecule using an ab initio density functional theory based method, and (ii) the tribology of two amorphous SiO2 surfaces coated with self-assembled monolayers of methyl-terminated hydrocarbon alkoxylsilane molecules using a classical atomistic force field. We discuss the differences in behaviour of these systems due to applied thermostatting, and show that in some cases a qualitatively different physical behaviour of the simulated system can be obtained if an equilibrium thermostat is used

Image calculations with a numerical frequency-modulation atomic force microscope

cited By 6International audienceWe investigated the implementation of a numerical tool able to mimic an experimental noncontact atomic force microscope (nc-AFM). Main parts of an experimental setup are modeled and are implemented inside a computer code. The goal was to build a numerical AFM (n-AFM) as versatile, efficient, and powerful as possible. In particular, the n-AFM can be used in the two working regimes, that is, in attractive and repulsive regimes, with settings for a standard AFM cantilever oscillating with a large amplitude (typically, 10 nm) or for a tuning-fork probe with ultrasmall amplitudes (∼0.01 nm). We present various tests to show the reliability of the n-AFM used as a frequency-modulation AFM (FM-AFM). As an example, we calculated FM-AFM images of adsorbed molecular systems, which range from two-dimensional planar molecules to corrugated systems with a three-dimensional molecule. The submolecular resolution of the FM-AFM is confirmed to originate from repulsive Pauli-like interactions between the tip and the sample. The versatility of the n-AFM is finally discussed in the perspective of new functionalities that will be included in the future