Related papers: The MOLDY short-range molecular dynamics package
Writing efficient hybrid parallel code is tedious, error-prone, and requires good knowledge of both parallel programming and multithreading such as MPI and OpenMP, resp. Therefore, we present a framework which is based on a job model that…
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…
Molecular dynamics simulations provide a mechanistic description of molecules by relying on empirical potentials. The quality and transferability of such potentials can be improved leveraging data-driven models derived with machine learning…
Massively-parallel, distributed-memory algorithms for the Lagrangian particle hydrodynamic method [R. Samulyak, X. Wang, H.-C. Chen, Lagrangian particle method for compressible fluid dynamics, J. Comput. Phys., 362 (2018), 1-19] have been…
Programming for distributed memory machines has always been a tedious task, but necessary because compilers have not been sufficiently able to optimize for such machines themselves. Molly is an extension to the LLVM compiler toolchain that…
We provided a concise and self-contained introduction to molecular dynamics (MD) simulation, which involves a body of fundamentals needed for all MD users. The associated computer code, simulating a gas of classical particles interacting…
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…
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…
With multi-core processors a ubiquitous building block of modern supercomputers, it is now past time to enable applications to embrace these developments in processor design. To achieve exascale performance, applications will need ways of…
Particle tracking has several important applications for solute transport studies in aquifer systems. Travel time distribution at observation points, particle coordinates in time and streamlines are some practical results providing…
Numerical investigation of compressible flows faces two main challenges. In order to accurately describe the flow characteristics, high-resolution nonlinear numerical schemes are needed to capture discontinuities and resolve wide…
Lattice Boltzmann methods are a popular mesoscopic alternative to macroscopic computational fluid dynamics solvers. Many variants have been developed that vary in complexity, accuracy, and computational cost. Extensions are available to…
Constant potential methods (CPM) enable computationally efficient simulations of the solid-liquid interface at conducting electrodes in molecular dynamics (MD). They have been successfully used, for example, to realistically model the…
A high-performance gas kinetic solver using multi-level parallelization is developed to enable pore-scale simulations of rarefied flows in porous media. The Boltzmann model equation is solved by the discrete velocity method with an…
Molecular dynamics is widely used to study various phenomena, such as diffusion, shock wave propagation, and plasma dynamics. A wide range of software packages supports the expanding scope of molecular dynamics applications. However, the…
MDMP is a new parallel programming approach that aims to provide users with an easy way to add parallelism to programs, optimise the message passing costs of traditional scientific simulation algorithms, and enable existing MPI-based…
Regions of nested loops are a common feature of High Performance Computing (HPC) codes. In shared memory programming models, such as OpenMP, these structure are the most common source of parallelism. Parallelising these structures requires…
The aim of parallel computing is to increase an application performance by executing the application on multiple processors. OpenMP is an API that supports multi platform shared memory programming model and shared-memory programs are…
A new method for the simulation of evolving multi-domains problems has been introduced in a previous work (RealIMotion), Florez et al. (2020). In this article further developments of the model will be presented. The main focus here is a…
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…