Related papers: ls1 mardyn: The massively parallel molecular dynam…
This article describes algorithms for the hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-range forces. The parallelization method combines domain decomposition with a thread-based parallelization…
Molecular simulations in an open environment, involving ion exchange, are necessary to study various systems, from biosystems to confined electrolytes. However, grand-canonical simulations are often computationally demanding in condensed…
Molecular Dynamics (MD) codes predict the fundamental properties of matter by following the trajectories of a collection of interacting model particles. To exploit diverse modern manycore hardware, efficient codes must use all available…
In this work, we have developed a multiscale computational algorithm to couple finite element method with an open source molecular dynamics code --- the Large scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) --- to perform…
Recent advances in random-walk particle-tracking have enabled direct simulation of mixing and reactions on particles by allowing the particles to interact with each other using a multi-point mass transfer scheme. The mass transfer scheme…
A second-order accurate divergence-conserving hybrid particle-in-cell code Maximus has been developed for microscopic modeling of collisionless plasmas. The main specifics of the code include a constrained transport algorithm for exact…
Molecular dynamics (MD) simulations are used in biochemistry, physics, and other fields to study the motions, thermodynamic properties, and the interactions between molecules. Computational limitations and the complexity of these problems,…
Developers of Molecular Dynamics (MD) codes face significant challenges when adapting existing simulation packages to new hardware. In a continuously diversifying hardware landscape it becomes increasingly difficult for scientists to be…
A parallel implementation of coupled spin-lattice dynamics in the LAMMPS molecular dynamics package is presented. The equations of motion for both spin only and coupled spin-lattice dynamics are first reviewed, including a detailed account…
Molecular dynamics (MD) simulation has long been the principal computational tool for exploring protein conformational landscapes and dynamics, but its application is limited by high computational cost. We present ProTDyn, a foundation…
The simulation of large ensembles of particles is usually parallelized by partitioning the domain spatially and using message passing to communicate between the processes handling neighboring subdomains. The particles are represented as…
In this talk I discuss the general question of the portability of Molecular Dynamics codes for diffusive systems on parallel computers of the APE family. The intrinsic single precision arithmetics of the today available APE platforms does…
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…
We compare a newly developed hybrid simulation method which combines classical molecular dynamics (MD) and computational fluid dynamics (CFD) to a simulation consisting only of molecular dynamics. The hybrid code is composed of three…
Recent developments in many-body potential energy representation via deep learning have brought new hopes to addressing the accuracy-versus-efficiency dilemma in molecular simulations. Here we describe DeePMD-kit, a package written in…
Modelling has become a third distinct line of scientific enquiry, alongside experiments and theory. Molecular dynamics (MD) simulations serve to interpret, predict and guide experiments and to test and develop theories. A major limiting…
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…
Molecular dynamics simulations, an indispensable research tool in computational chemistry and materials science, consume a significant portion of the supercomputing cycles around the world. We focus on multi-body potentials and aim at…
We present a plane-wave ultrasoft pseudopotential implementation of first-principle molecular dynamics, which is well suited to model large molecular systems containing transition metal centers. We describe an efficient strategy for…
Computer simulation is an important tool for scientific progress, especially when lab experiments are either extremely costly and difficult or lack the required resolution. However, all of the simulation methods come with limitations. In…