Traditionally, electrostatic interactions are modelled using Ewald techniques, which provide a good approximation, but are poorly suited to GPU architectures. We use the GPU versions of the LAMMPS MD package to implement and assess the Wolf summation method. We compute transport and structural properties of pure carbon dioxide and mixtures of carbon dioxide with either methane or difluoromethan...

The interaction between plasma particles and tungsten as plasma facing material is one of the critical issues in successfully using tungsten in Tokamak reactors environment. The deuterium bombardment of monocrystalline tungsten was modeled by molecular dynamics simulation using LAMMPS code and Tersoff type interatomic potential. The deuterium trapping rate, implantation depth, and the stopping ...

Wedescribe a highly optimized implementation ofMPI domain decomposition in aGPU-enabled, generalpurpose molecular dynamics code, HOOMD-blue (Anderson and Glotzer, 2013). Our approach is inspired by a traditional CPU-based code, LAMMPS (Plimpton, 1995), but is implemented within a code that was designed for execution on GPUs from the start (Anderson et al., 2008). The software supports shortrang...

Complex plasmas are low-temperature plasmas that contain micrometer-size particles in addition to the neutral gas particles and the ions and electrons that make up the plasma. The microparticles interact strongly and display a wealth of collective effects. Here we report on linked numerical simulations that reproduce many of the experimental results of complex plasmas. We model a capacitively c...

Hydrogen adsorption has been simulated on carbon nanotubes for optimum hydrogen absorption. Parameters that affect the amount of absorbed have studied, such as effect chirality and temperature absorption in CNTs. The simulation method carbone uses molecular dynamics code LAMMPS, applies Lennard-Jones interatomic potential atom movement using Van Der Waals force with Microcanonical Ensemble. Dat...

We explore the effects of geometry on thermal conductivity (?) silicon and germanium nanowires, with lengths between 10–120 nm diameters up to 5–6 nm. To this end we perform molecular dynamics simulations LAMMPS software, using Tersoff interatomic potentials. consider nanowires polygonal cross section discuss effect transverse conductivity. also tubular (hollow) core/shell combinations Si/Ge Ge...

The final report for a Laboratory Directed Research and Development project entitled, Molecular Simulation of Reacting Systems is presented. It describes efforts to incorporate chemical reaction events into the LAMMPS massively parallel molecular dynamics code. This was accomplished using a scheme in which several classes of reactions are allowed to occur in a probabilistic fashion at specified...

A new Langevin–Verlet thermostat that preserves the fluctuation–dissipation relationship for discrete time steps is applied tomolecularmodeling and tested against several popular suites (AMBER, GROMACS, LAMMPS) using a small molecule as an example that can be easily simulated by all three packages. Contrary to existing methods, the new thermostat exhibits no detectable changes in the sampling s...

We present a simulation–visualization pipeline that uses the LAMMPS Molecular Dynamics Simulator and the Visualization Toolkit to create a visualization and analysis environment for atomistic simulations of plasma–surface interactions. These simulations are used to understand the origin of fuzz-like, microscopic damage to tungsten and other metal surfaces by helium. The proposed pipeline serves...

Abrasive flow polishing plays an important part in modern ultra-precision machining. Ultrafine particles suspended in the medium of abrasive flow removes the material in nanoscale. In this paper, three-dimensional molecular dynamics (MD) simulations are performed to investigate the effect of impacting direction on abrasive cutting process during abrasive flow polishing. The molecular dynamics s...