Recently, a novel type of multiscale simulation, called Relative Resolution (RelRes), was introduced. In single system, molecules switch their resolution in terms relative separation, with near neighbors interacting via fine-grained potentials yet far coarse-grained potentials; notably, these two are analytically parameterized by multipole approximation. This approach is consequently able to co...

Polymeric materials modelling has the potential to rapidly accelerate discovery of new due comparative ease simulations compared laboratory testing campaigns. High quality molecular dynamics simulation software, such as LAMMPS, are able facilitate transition from empirical digitised chemistry. However, in order fully benefit speed simulations, tools need be developed automate preprocessing stag...

An elastic rod model for semi-flexible polymers is presented. Theory for a continuum rod is reviewed, and it is shown that a popular discretised model used in numerical simulations gives the correct continuum limit. Correlation functions relating to both bending and twisting of the rod are derived for both continuous and discrete cases, and results are compared with numerical simulations. Final...

We investigate two mechanisms of crystallographic slip in graphene, corresponding to glide and shuffle generalized stacking faults (GSF), and compute their -curves using Sandia National Laboratories Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS). We find evidence of metastable partial dislocations for the glide GSF only. The computed values of the stable and unstable stackin...

We implement two recently developed fast Coulomb solvers, HSMA3D (Zhao et al. (2018) [49]) and HSMA2D (Liang (2020) [50]), into a new user package HSMA for the molecular dynamics simulation engine LAMMPS. The is designed efficient accurate modeling of electrostatic interactions in 3D 2D periodic systems with dielectric effects at O(N) cost. implementation hybrid MPI OpenMP parallelized compatib...

W e introduce a software package integrated with the molecular dynamics software LAMMPS for fluctuating hydrodynamics simulations of fluid-structure interactions subject to thermal fluctuations. The package is motivated to provide dynamic thermostats to extend implicit-solvent coarse-grained (IS-CG) models by incorporating kinetic contributions from the solvent to facilitate their use in a wide...

We present a guide to compute the phase-boundaries of classical systems using dynamic Clausius–Clapeyron integration (dCCI) method within LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) code. The advantage dCCI is because it provides coexistence curves spanning wide range thermodynamic states relatively short single non-equilibrium simulations. describe state-of-the-art free-...

While machine learning approaches have been successfully used to represent interatomic potentials, their speed has typically lagged behind conventional formalisms. This is often due the complexity of structural fingerprints describe local atomic environment and large cutoff radii neighbor lists in calculation these fingerprints. Even recent learned methods are at least 10 times slower than trad...

With the growth of available computational resource, CFD–DEM (computational fluid dynamics–discrete element method) becomes an increasingly promising and feasible approach for the study of sediment transport. Several existing CFD–DEM solvers are applied in chemical engineering and mining industry. However, a robust CFD–DEM solver for the simulation of sediment transport is still desirable. In t...

Summary The molecular dynamics simulation software, LAMMPS, utilizes the Kokkos acceleration library to port computation a diverse set of architectures including those based on GPU accelerators. In addition Kokkos, LAMMPS contains vast code base that leverages CUDA application programming interface using functions such as cuFFT , CUDA's fast‐fourier transform (FFT) library, and, more recently, ...