Related papers: HSMA: An O(N) electrostatics package implemented i…
We propose a harmonic surface mapping algorithm (HSMA) for electrostatic pairwise sums of an infinite number of image charges. The images are induced by point sources within a box due to a specific boundary condition which can be…
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…
Simulating charged many-body systems has been a computational demanding task due to the long-range nature of electrostatic interaction. For the multi-scale model of electrolytes which combines the strengths of atomistic/continuum…
Due to its flexible architecture, FPGAs support unique, deep hardware pipeline implementations for accelerating HPC applications. However, these devices are quite new in the HPC space, and thus, have been scarcely explored outside some…
We report a novel hybrid method of simultaneous atomistic simulation of solids in critical regions (contacts surfaces, cracks areas, etc.), along with continuum modeling of other parts. The continuum is treated in terms of quasi-atoms of…
The availability of open-source molecular simulation software packages allows scientists and engineers to focus on running and analyzing simulations without having to write, parallelize, and validate their own simulation software. While…
For inhomogeneous systems with interfaces, the inclusion of long-range dispersion interactions is necessary to achieve consistency between molecular simulation calculations and experimental results. For accurate and efficient incorporation…
We present a GPU implementation of LAMMPS, a widely-used parallel molecular dynamics (MD) software package, and show 5x to 13x single node speedups versus the CPU-only version of LAMMPS. This new CUDA package for LAMMPS also enables…
We study parallel particle-in-cell (PIC) methods for low-temperature plasmas (LTPs), which discretize kinetic formulations that capture the time evolution of the probability density function of particles as a function of position and…
Molecular-dynamics algorithms for systems of particles interacting through discrete or "hard" potentials are fundamentally different to the methods for continuous or "soft" potential systems. Although many software packages have been…
The local approach to computing electrostatic interactions proposed by Maggs and adapted by Pasichnyk for molecular dynamics simulations is extended to situations where the dielectric background medium is inhomogeneous. We furthermore…
Molecular Dynamics is an important tool for computational biologists, chemists, and materials scientists, consuming a sizable amount of supercomputing resources. Many of the investigated systems contain charged particles, which can only be…
Quasi-2D Coulomb systems are of fundamental importance and have attracted much attention in many areas nowadays. Their reduced symmetry gives rise to interesting collective behaviors, but also brings great challenges for particle-based…
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…
Electrification, a key strategy in combating climate change, is transforming industries, and off-highway machines (OHM) will be next to transition from combustion engines and hydraulic actuation to sustainable fully electrified machines.…
LAMMPS is a widely popular classical Molecular Dynamics package. It was designed for materials modeling but it is well prepared for simulations in Soft Matter. The use packages like LAMMPS has advantages and disadvantages. The main…
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…
We have extended the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) to support directional bonds and dynamic bonding. The framework supports stochastic formation of new bonds, breakage of existing bonds, and conversion…
MLMOD is a software package for incorporating machine learning approaches and models into simulations of microscale mechanics and molecular dynamics in LAMMPS. Recent machine learning approaches provide promising data-driven approaches for…
In the first part of a series of two papers, we present in considerable detail a collision-driven molecular dynamics algorithm for a system of nonspherical particles, within a parallelepiped simulation domain, under both periodic or…