Related papers: Huge-scale Molecular Dynamics Simulation of Multib…
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…
The interaction of condensed phase systems with external electric fields is crucial in myriad processes in nature and technology ranging from the field-directed motion of cells (galvanotaxis), to energy storage and conversion systems…
Physical phenomena such as chemical reactions, bond breaking, and phase transition require molecular dynamics (MD) simulation with ab initio accuracy ranging from milliseconds to microseconds. However, previous state-of-the-art neural…
Molecular dynamics simulations are performed for a finite non-relativistic system of particles with Lennard-Jones potential. We study the effect of liquid-gas mixed phase on particle number fluctuations in coordinate subspace. A metastable…
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…
Particle-in-Cell (PIC) Monte Carlo (MC) simulations are central to plasma physics but face increasing challenges on heterogeneous HPC systems due to excessive data movement, synchronization overheads, and inefficient utilization of multiple…
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…
An efficient parallelization approach to simulate optical properties of ensembles of quantum emitters in realistic electromagnetic environments is considered. It relies on balancing computing load of utilized processors and is built into…
We present results from large-scale molecular dynamics (MD) simulations of homogeneous vapor-to-liquid nucleation. The simulations contain between one and eight billion Lennard-Jones (LJ) atoms, covering up to 1.2 {\mu}s (56 million…
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)…
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…
Large-scale first principles molecular dynamics are crucial for simulating complex processes in chemical, biomedical, and materials sciences. However, the unfavorable time complexity with respect to system sizes leads to prohibitive…
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…
We present an efficient open-source implementation of the multiparticle collision dynamics (MPCD) algorithm that scales to run on hundreds of graphics processing units (GPUs). We especially focus on optimizations for modern GPU…
We present a scalable dissipative particle dynamics simulation code, fully implemented on the Graphics Processing Units (GPUs) using a hybrid CUDA/MPI programming model, which achieves 10-30 times speedup on a single GPU over 16 CPU cores…
Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions…
We report the results of intensive numerical calculations for four atomic H2+H2 energy transfer collision. A parallel computing technique based on LAM/MPI functions is used. In this algorithm, the data is distributed to the processors…
Manufacturers have been developing new graphics processing unit (GPU) nodes with large capacity, high bandwidth memory and very high bandwidth intra-node interconnects. This enables moving large amounts of data between GPUs on the same node…
We present a new scalable algorithm for short-range molecular dynamics simulations on distributed memory MIMD multicomputer based on a message-passing multi-cell approach. We have implemented the algorithm on the Connection Machine 5 (CM-5)…
Molecular Dynamics (MD) simulations play a central role in physics-driven drug discovery. MD applications often use the Particle Mesh Ewald (PME) algorithm to accelerate electrostatic force computations, but efficient parallelization has…