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We present a new molecular-dynamics algorithm for integrating the equations of motion for a system of particles interacting with mixed continuous/impulsive forces. This method, which we call Impulsive Verlet, is constructed using operator…
Most approaches in Lagrangian fluid dynamics simulations proceed from the definition of particle volumes, from which discrete versions of the spatial differential operators are derived. Recently, Gallou\"et and M\'erigot [1] simultaneously…
In this work, a methodology is proposed for formulating general dynamical equations in mechanics under the umbrella of the principle of energy conservation. It is shown that Lagrange's equation, Hamilton's canonical equations, and…
We construct a discrete model of fluid particles according to the GENERIC formalism. The model has the form of Smoothed Particle Hydrodynamics including correct thermal fluctuations. A slight variation of the model reproduces the…
We present a new and improved method for simultaneous control of temperature and pressure in molecular dynamics simulations with periodic boundary conditions. The thermostat-barostat equations are build on our previously developed…
Molecular simulations of many particles which move rather according to a brownian than a newtonian type of dynamics, nevertheless, can be performed by means of a "velocity-Verlet-like" algorithm. The derivation of this algorithm requires…
In this paper we will study some interesting properties of modifications of the Euler-Poincar\'e equations when we add a special type of dissipative force, so that the equations of motion can be described using the metriplectic formalism.…
We show that for any liquid or solid with strong correlation between its $NVT$ virial and potential-energy equilibrium fluctuations, the temperature is a product of a function of excess entropy per particle and a function of density,…
We expand on the previously published Gr{\o}nbech-Jensen Farago (GJF) thermostat, which is a thermodynamically sound variation on the St{\o}rmer-Verlet algorithm for simulating discrete-time Langevin equations. The GJF method has been…
We propose a variational formulation for the nonequilibrium thermodynamics of discrete open systems, i.e., discrete systems which can exchange mass and heat with the exterior. Our approach is based on a general variational formulation for…
We derive a formulation of the nonhydrostatic equations in spherical geometry with a Lorenz staggered vertical discretization. The combination conserves a discrete energy in exact time integration when coupled with a mimetic horizontal…
A set of algorithms is presented for efficient numerical calculation of the time evolution of classical dynamical systems. Starting with a first approximation for solving the differential equations that has a "reversible" character, we show…
Variational time integrators are derived in the context of discrete mechanical systems. In this area, the governing equations for the motion of the mechanical system are built following two steps: (a) Postulating a discrete action; (b)…
We present an algorithm for the simulation of the exact real-time dynamics of classical many-body systems with discrete energy levels. In the same spirit of kinetic Monte Carlo methods, a stochastic solution of the master equation is found,…
We present a novel approach to investigate the long-time stochastic dynamics of multi-dimensional classical systems, in contact with a heat-bath. When the potential energy landscape is rugged, the kinetics displays a decoupling of short and…
We present a simulation scheme for discrete-velocity gases based on {\em local thermodynamic equilibrium}. Exploiting the kinetic nature of discrete-velocity gases, in that context, results in a natural splitting of fluxes, and the…
We present a super-polynomial improvement in the precision scaling of quantum simulations for coupled classical-quantum systems in this paper. Such systems are found, for example, in molecular dynamics simulations within the…
A robust, simple and fast procedure for the calculation of uncertainties in relative static dielectric permittivity ($\varepsilon_s$) computed via molecular dynamics (MD) is proposed. It arises as a direct application of well founded…
The Stoermer-Verlet-leapfrog group of integrators commonly used in molecular dynamics simulations has long become a textbook subject and seems to have been studied exhaustively. There are, however, a few striking effects in performance of…
Discrete mechanics is presented as an alternative to the equations of fluid mechanics, in particular to the Navier-Stokes equation. The derivation of the discrete equation of motion is built from the intuitions of Galileo, the principles of…