Related papers: Cell List Algorithms for Nonequilibrium Molecular …
The linked cell list algorithm is an essential part of molecular simulation software, both molecular dynamics and Monte Carlo. Though it scales linearly with the number of particles, there has been a constant interest in increasing its…
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…
Many applications of computational fluid dynamics require multiple simulations of a flow under different input conditions. In this paper, a numerical algorithm is developed to efficiently determine a set of such simulations in which the…
To simulate plasma phenomena, large-scale computational resources have been employed in developing high-precision and high-resolution plasma simulations. One of the main obstacles in plasma simulations is the requirement of computational…
A cell lists method based on doubly linked lists and with complexity O(N) is developed for particle deletion and insertion in reaction ensemble Monte Carlo simulation. Because the random move in Metropolis algorithm can be reduced to…
In the first part of a series of two papers, we present in considerable detail a collision-driven molecular dynamics algorithm for a system of nonspherical particles, within a parallelepiped simulation domain, under both periodic or…
Numerous algorithms and parallelisations have been developed for short-range particle simulations; however, none are optimally performant for all scenarios. Such a concept led to the prior development of the particle simulation library…
Active gel theory has recently been very successful in describing biologically active materials such as actin filaments or moving bacteria in temporally fixed and simple geometries such as cubes or spheres. Here we develop a computational…
We use a novel non-equilibrium algorithm to simulate steady-state fluid transport through a two-dimensional (2D) membrane due to a concentration gradient by molecular dynamics (MD) for the first time. We confirm that, as required by the…
For accurate simulations of rarefied gas flows around moving obstacles, we propose a cut cell method on Cartesian grids: it allows exact conservation and accurate treatment of boundary conditions. Our approach is designed to treat Cartesian…
In this paper I present a first attempt for a possible description of fluids dynamics by mean of a cellular automata technique. With the use of simple and elementary rules, based on random behaviour either, the model permits to obtain the…
Event-driven molecular dynamics is a valuable tool in condensed and soft matter physics when particles can be modeled as hard objects or more generally if their interaction potential can be modeled in a stepwise fashion. Hard spheres model…
In this paper we investigate how standard nonlinear programming algorithms can be used to solve constrained optimization problems in a distributed manner. The optimization setup consists of a set of agents interacting through a…
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…
In simulations of crystals, unlike liquids or gases, it may happen that the properties of the studied system depend not only on the volume of the simulation cell but also on its shape. For such cases it is desirable to change the shape of…
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 particles…
Complex quantum simulation workflows are often hindered by incompatible wavefunction representations adopted across different algorithmic frameworks. In particular, the mismatch between the first- and second-quantization formalisms prevents…
We introduce density dependence of the cell size in cellular-automaton models for traffic flow, which allows a more precise correspondence between real-world phenomena and what observed in simulation. Also, we give an explicit calibration…
We propose a fast method for the calculation of short-range interactions in molecular dynamics simulations. The so-called random-batch list method is a stochastic version of the classical neighbor-list method to avoid the construction of a…
A simple and efficient algorithm of the molecular-dynamics simulation of the hard disk system based on the Event-Driven method is developed. From the analysis of algorithm, the complexity is O(log N) per 1 event, and the constant…