Related papers: Molecular dynamics simulations with many-body pote…
Recently, successes have been achieved for the high-order gas-kinetic schemes (HGKS) on unstructured meshes for compressible flows. In this paper, to accelerate the computation, HGKS is implemented with the graphical processing unit (GPU)…
We present teraflop-scale calculations of biomolecular electrostatics enabled by the combination of algorithmic and hardware acceleration. The algorithmic acceleration is achieved with the fast multipole method (FMM) in conjunction with a…
Purpose: Very fast Monte Carlo (MC) simulations of proton transport have been implemented recently on GPUs. However, these usually use simplified models for non-elastic (NE) proton-nucleus interactions. Our primary goal is to build a…
The conductor-like polarization model (C-PCM) with switching/Gaussian smooth discretization is a widely used implicit solvation model in chemical simulations. However, its application in quantum mechanical calculations of large-scale…
The LHC experiments are designed to detect large amount of physics events produced with a very high rate. Considering the future upgrades, the data acquisition rate will become even higher and new computing paradigms must be adopted for…
This paper proposes a special-purpose system to achieve high-accuracy and high-efficiency machine learning (ML) molecular dynamics (MD) calculations. The system consists of field programmable gate array (FPGA) and application specific…
The recent progress of linear-scaling or O(N) methods in the density functional theory (DFT) is remarkable. We expect that first-principles molecular dynamics (FPMD) simulations based on DFT can now treat more realistic and complex systems…
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…
We present a GPU-accelerated implementation of a magnetohydrodynamic (MHD) solver using directive-based programming with OpenMP target offloading. The solver is integrated into the DISPATCH framework, which organises the computational…
As they carry great potential for modeling complex interactions, graph neural network (GNN)-based methods have been widely used to predict quantum mechanical properties of molecules. Most of the existing methods treat molecules as molecular…
In this work we present an efficient implementation of Canonical Monte Carlo simulation for Coulomb many body systems on graphics processing units (GPU). Our method takes advantage of the GPU Single Instruction, Multiple Data (SIMD)…
The gravitational many-body problem is a problem concerning the movement of bodies, which are interacting through gravity. However, solving the gravitational many-body problem with a CPU takes a lot of time due to O(N^2) computational…
Modeling multimetallic systems efficiently enables faster prediction of desirable chemical properties and design of new materials. This work describes an initial implementation for performing multireference wave function method localized…
Molecular simulation technologies have afforded researchers a unique look into the nanoscale interactions driving physical processes. However, a limitation for molecular dynamics (MD) simulations is that they must be performed on…
Computational fluid dynamics and fluid-structure interaction simulations involving moving and deforming bodies is extremely hard. In this work, we present a graphical processing unit (GPU) optimized implementation of the sharp-interface…
Autonomous machines (e.g., vehicles, mobile robots, drones) require sophisticated 3D mapping to perceive the dynamic environment. However, maintaining a real-time 3D map is expensive both in terms of compute and memory requirements,…
Scalable and efficient numerical simulations continue to gain importance, as computation is firmly established as the third pillar of discovery, alongside theory and experiment. Meanwhile, the performance of computing hardware grows through…
Maximizing the performance potential of the modern day GPU architecture requires judicious utilization of available parallel resources. Although dramatic reductions can often be obtained through straightforward mappings, further performance…
We present a new approach for the two-temperature molecular dynamics (MD) model for coupled simulations of electronic and phonon heat conduction in nanoscale systems. The proposed method uses a master equation to perform heat conduction of…
Neural network-based molecular dynamics (NNMD) simulations incorporating long-range electrostatic interactions have significantly extended the applicability to heterogeneous and ionic systems, enabling effective modeling critical physical…