Related papers: Simple and efficent algorithm for large scale mole…
A new numerical method is presented to efficiently simulate the inelastic hard sphere (IHS) model for granular media, when fluid and frozen regions coexist in the presence of gravity. The IHS model is extended by allowing particles to…
High-performance computing, together with a neural network model trained from data generated with first-principles methods, has greatly boosted applications of \textit{ab initio} molecular dynamics in terms of spatial and temporal scales on…
In this paper we present the event-chain algorithms, which are fast Markov-chain Monte Carlo methods for hard spheres and related systems. In a single move of these rejection-free methods, an arbitrarily long chain of particles is…
As compute power increases with time, more involved and larger simulations become possible. However, it gets increasingly difficult to efficiently use the provided computational resources. Especially in particle-based simulations with a…
We have developed molecular dynamics codes for a short-range interaction potential that adopt both the flat-MPI and MPI/OpenMP hybrid parallelizations on the basis of a full domain decomposition strategy. Benchmark simulations involving up…
Coulomb interaction, following an inverse-square force-law, quantifies the amount of force between two stationary and electrically charged particles. The long-range nature of Coulomb interactions poses a major challenge to molecular…
Tensor cores, along with tensor processing units, represent a new form of hardware acceleration specifically designed for deep neural network calculations in artificial intelligence applications. Tensor cores provide extraordinary…
In recent years, artificial intelligence (AI) technologies have found industrial applications in various fields. AI systems typically possess complex software and heterogeneous CPU/GPU hardware architecture, making it difficult to answer…
Current trends in parallel processors call for the design of efficient massively parallel algorithms for scientific computing. Parallel algorithms for Monte Carlo simulations of thermodynamic ensembles of particles have received little…
Efficient implementations of the classical molecular dynamics (MD) method for Lennard-Jones particle systems are considered. Not only general algorithms but also techniques that are efficient for some specific CPU architectures are also…
To minimise systematic errors in Monte Carlo simulations of charged particles, long range electrostatic interactions have to be calculated accurately and efficiently. Standard approaches, such as Ewald summation or the naive application of…
In this article we introduce a novel coupled algorithm for massively parallel direct numerical simulations of electrophoresis in microfluidic flows. This multiphysics algorithm employs an Eulerian description of fluid and ions, combined…
Videos of the molecular dynamics simulations of a colliding hard disk reactive medium. A simple event-driven algorithm is used to simulate these colliding hard disks allowing for the study of detonations at the microscopic level. This video…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
We discuss historic pressure computations for the hard-disk model performed since 1953, and compare them to results that we obtain with a powerful event-chain Monte Carlo and a massively parallel Metropolis algorithm. Like other simple…
We propose a computationally efficient method to solve the dynamics of operators of bosonic quantum systems coupled to their environments. The method maps the operator under interest to a set of complex-valued functions, and its adjoint…
A novel Stochastic Event-Driven Molecular Dynamics (SEDMD) algorithm is developed for the simulation of polymer chains suspended in a solvent. The polymers are represented as chains of hard spheres tethered by square wells and interact with…
We present the molecular hyperdynamics algorithm and its implementation to the nonorthogonal tight-binding model NTBM and the corresponding software. Due to its multiscale structure, the proposed approach provides the long time scale…
This article presents new algorithms for massively parallel granular dynamics simulations on distributed memory architectures using a domain partitioning approach. Collisions are modelled with hard contacts in order to hide their…
Design considerations for molecular dynamics algorithms capable of taking advantage of the computational power of a graphics processing unit (GPU) are described. Accommodating the constraints of scalable streaming-multiprocessor hardware…