Related papers: A molecular-dynamics algorithm for mixed hard-core…
The hybrid method combining particle-in-cell and magnetohydrodynamics can be used to study the interaction between energetic particles and global plasma modes. In this paper we introduce the M3D-C1-K code, which is developed based on the…
We present, in a unifying way, the main components of three asynchronous event-driven algorithms for simulating physical systems of interacting particles. The first example, hard-particle molecular dynamics, is well-known. We also present a…
We propose a novel solid-fluid interaction method for coupling elastic solids with impulse flow maps. Our key idea is to unify the representation of fluid and solid components as particle flow maps with different lengths and dynamics. The…
We report on a lattice based algorithm, completely vectorized for molecular dynamics simulations. Its algorithmic complexity is of the order $O(N)$, where $N$ is the number of particles. The algorithm works very effectively when the…
The emergence and understanding of new design paradigms that exploit flow induced mechanical instabilities for propulsion or energy harvesting demands robust and accurate flow structure interaction numerical models. In this context, we…
A new scheme for numerical integration of the 1D2V relativistic Vlasov-Maxwell system is proposed. Assuming that all particles in a cell of the phase space move with the same velocity as that of the particle located at the center of the…
In this paper, we present a new framework for addressing the nonlinear Landau collision operator in terms of particle-in-cell methods. We employ the underlying metriplectic structure of the collision operator and, using a macro particle…
Although event-driven algorithms have been shown to be far more efficient than time-driven methods such as conventional molecular dynamics, they have not become as popular. The main obstacle seems to be the difficulty of parallelizing…
An improved neighbor list algorithm is proposed to reduce unnecessary interatomic distance calculations in molecular simulations. It combines the advantages of Verlet table and cell linked list algorithms by using cell decomposition…
The Boris algorithm, a closely related variational integrator and a newly proposed filtered variational integrator are studied when they are used to numerically integrate the equations of motion of a charged particle in a non-uniform strong…
This is the final paper in a series that introduces geodesic molecular dynamics at constant potential energy. This dynamics is entitled NVU dynamics in analogy to standard energy-conserving Newtonian NVE dynamics. In the first two papers…
Molecular Dynamics method is based on solution of Newtonian differential equations of motion. A new very accurate and efficient time-reversible explicit integrator was derived on the basis of second order Tailor expansion of force. There is…
An extended Hamiltonian approach to conduct isothermal-isobaric molecular dynamics simulations with full cell flexibility is presented. The components of the metric tensor are used as the fictitious degrees of freedom for the cell, thus…
We propose a new mixed finite element method for the three-dimensional steady magnetohydrodynamic (MHD) kinematics equations for which the velocity of the fluid is given. Although prescribing the velocity field leads to a simpler model than…
Simulations of nano- to micro-meter scale fluidic systems under thermal gradients require consistent mesoscopic methods accounting for both hydrodynamic interactions and proper transport of energy. One such method is dissipative particle…
Multibody dynamics simulators are an important tool in many fields, including learning and control for robotics. However, many existing dynamics simulators suffer from inaccuracies when dealing with constrained mechanical systems due to…
We address the formulation and analysis of energy and momentum conserving time integration schemes in the context of particle dynamics, and in particular atomic systems. The article identifies three critical aspects of these models that…
The dynamics of dissipative soft-sphere gases obeys Newton's equation of motion which are commonly solved numerically by (force-based) Molecular Dynamics schemes. With the assumption of instantaneous, pairwise collisions, the simulation can…
We introduce a variational algorithm to estimate the likelihood of a rare event within a nonequilibrium molecular dynamics simulation through the evaluation of an optimal control force. Optimization of a control force within a chosen basis…
In this work we assess the quality and performance of several novel dissipative particle dynamics integration schemes that have not previously been tested independently. Based on a thorough comparison we identify the respective methods of…