Related papers: ls1 mardyn: The massively parallel molecular dynam…
We describe a parallelised version of the MOLDY molecular dynamics program. This Fortran code is aimed at systems which may be described by short-range potentials and specifically those which may be addressed with the embedded atom method.…
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…
We develop an algorithm suitable for parallel molecular dynamics simulations in $d$ spatial dimensions and describe its implementation in C++. All routines work in arbitrary $d$; the maximum simulated $d$ is limited only by available…
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 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…
The objective of this article is to report the parallel implementation of the 3D molecular dynamic simulation code for laser-cluster interactions. The benchmarking of the code has been done by comparing the simulation results with some of…
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…
Machine learning potentials have emerged as a means to enhance the accuracy of biomolecular simulations. However, their application is constrained by the significant computational cost arising from the vast number of parameters compared to…
This article introduces a highly parallel algorithm for molecular dynamics simulations with short-range forces on single node multi- and many-core systems. The algorithm is designed to achieve high parallel speedups for strongly…
Machine learning potentials have achieved great success in accelerating atomistic simulations. Many of them relying on atom-centered local descriptors are natural for parallelization. More recent message passing neural network (MPNN) models…
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…
We report scaling results on the world's largest supercomputer of our recently developed Billions-Body Molecular Dynamics (BBMD) package, which was especially designed for massively parallel simulations of the atomic dynamics in structural…
Parallel code design is a challenging task especially when addressing petascale systems for massive parallel processing (MPP), i.e. parallel computations on several hundreds of thousands of cores. An in-house computational fluid dynamics…
Parallelism of tight-binding molecular dynamics simulations is presented by means of the order-N electronic structure theory with the Wannier states, recently developed (J. Phys. Soc. Jpn. 69,3773 (2000)). An application is tested for…
Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a…
High precision atomic data is indispensable for experiments involving studies of fundamental interactions, astrophysics, atomic clocks, plasma science, and others. We develop new parallel atomic structure codes and explore the difficulties…
Modern graphics processing units (GPUs) provide impressive computing resources, which can be accessed conveniently through the CUDA programming interface. We describe how GPUs can be used to considerably speed up molecular dynamics (MD)…
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…
Furthering our understanding of many of today's interesting problems in plasma physics---including plasma based acceleration and magnetic reconnection with pair production due to quantum electrodynamic effects---requires large-scale kinetic…
Extended Lagrangian molecular dynamics (XLMD) is a general method for performing molecular dynamics simulations using quantum and classical many-body potentials. Recently several new XLMD schemes have been proposed and tested on several…