In this paper we consider a 2D hexagonal crystal lattice model first proposed by Marin, Eilbeck and Russell in 1998. We perform a detailed numerical study of nonlinear propagating localized modes, that is, propagating discrete breathers and kinks. The original model is extended to allow for arbitrary atomic interactions, and to allow atoms to travel out of the unit cell. A new on-site potential is considered with a periodic smooth function with hexagonal symmetry. We are able to confirm the existence of long-lived propagating discrete breathers. Our simulations show that, as they evolve, breathers appear to localize in frequency space, i.e. the energy moves from sidebands to a main frequency band. Our numerical findings contribute to the open question of whether exact moving breather solutions exist in 2D hexagonal layers in physical crystal lattices.Comment: Both this paper and arXiv 1408.6853 discuss similar models with the same on-site potential. This paper has a Lennard-Jones interparticle potential, 1408.6853 has a piecewise polynomial function. The latter favours the existence of long-lived kinks, and much of 1408.6853 is given to a study of these. Both models support long-lived breathers, and the present paper concentrates on such solution
Thermal bath coupling mechanisms as utilized in molecular dynamics are applied to partial differential equation models. Working from a semi-discrete (Fourier mode) formulation for the Burgers or KdV equation, we introduce auxiliary variables and stochastic perturbations in order to drive the system to sample a target ensemble which may be a Gibbs state or, more generally, any smooth distribution defined on a constraint manifold. We examine the ergodicity of approaches based on coupling of the heat bath to the high wave numbers, with the goal of controlling the ensemble through the fast modes. We also examine different thermostat methods in the extent to which dynamical properties are corrupted in order to accurately compute the average of a desired observable with respect to the invariant distribution. The principal observation of this paper is that convergence to the invariant distribution can be achieved by thermostatting just the highest wave number, while the evolution of the slowest modes is little affected by such a thermostat.
Abstract. A broad array of canonical sampling methods are available for molecular simulation based on stochastic-dynamical perturbation of Newtonian dynamics, including Langevin dynamics, Stochastic Velocity Rescaling, and methods that combine Nos茅-Hoover dynamics with stochastic perturbation. In this article we discuss several stochasticdynamical thermostats in the setting of simulating systems with holonomic constraints. The approaches described are easily implemented and facilitate the recovery of correct canonical averages with minimal disturbance of the underlying dynamics. For the purpose of illustrating our results, we examine the numerical application of these methods to a simple atomic chain, where a Fixman term is required to correct the thermodynamic ensemble.
We consider the approximation of the phase-space flow of a dynamical system on a triangulated surface using an approach known as Discrete Flow Mapping. Such flows are of interest throughout statistical mechanics, but the focus here is on flows arising from ray tracing approximations of linear wave equations. An orthogonal polynomial basis approximation of the phase-space density is applied in both the position and direction coordinates, in contrast with previous studies where piecewise constant functions have typically been applied for the spatial approximation. In order to improve the tractability of an orthogonal polynomial approximation in both phase-space coordinates, we propose a careful strategy for computing the propagation operator. For the favourable case of a Legendre polynomial basis we show that the integrals in the definition of the propagation operator may be evaluated analytically with respect to position and via a spectrally convergent quadrature rule for the direction coordinate. A generally applicable spectral quadrature scheme for integration with respect to both coordinates is also detailed for completeness. Finally, we provide numerical results that motivate the use of p-refinement in the orthogonal polynomial basis.
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