Multi-scale computer simulations combine the computationally efficient classical algorithms with more expensive but also more accurate ab-initio quantum mechanical algorithms. This work describes one implementation of multi-scale computations using the Atomistic Simulation Environment (ASE). This implementation can mix classical codes like LAMMPS and the Density Functional Theory-based GPAW. An...

The Green’s function molecular dynamics method, which enables one to study the elastic response of a three-dimensional solid to an external stress field by taking into consideration only the surface atoms, was implemented as an extension to an open source classical molecular dynamics simulation code LAMMPS. This was done in the style of fixes. The first fix, FixGFC, measures the elastic stiffne...

Description: This project will work toward the simulation of a cell membrane using a type of molecular dynamics known as Dissipative Particle Dynamics (DPD). In the first week, we will implement a basic molecular dynamics simulator in C++, probably in 2D, to learn about the inner workings of particle-based simulators. In the second week, we will learn about the DPD method and how to implement i...

Scientific software is as important to scientific studies as raw data. Yet, attention to this genre of research data is limited in studies on data reuse, citation, and metadata standards. This paper presents results from an exploratory study that examined how scientific software’s reuse information is presented in the current citation practice and natural language descriptions in research paper...

Adaptively Restrained Molecular Dynamics (ARMD) is a recently introduced particles simulation method that switches positional degrees of freedom on and off during simulation in order to speed up calculations. In the NVE ensemble, ARMD allows users to trade between precision and speed while, in the NVT ensemble, it makes it possible to compute statistical averages faster. Despite the conceptual ...

Abstract We present a package to simulate long-term diffusive mass transport in systems with atomic scale resolution. The implemented framework is based on non-equilibrium statistical thermo-chemo-mechanical formulation of where effective rates are computed using kinematic diffusion law. Our implementation built as an add-on the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS)...

The first version of this code (Mackay et al., 2013) [10] implemented long-range hydrodynamic interactions into the open-source molecular dynamics package LAMMPS. This was done through creation a fix, lb/fluid which subsequently included as user-package in main LAMMPS distribution. Here we substantially update by making improvements to its accuracy, adding significant new features, and simplify...

Abstract Dense suspensions are widespread in nature, manufacturing and process engineering. Particle-based simulations have proven to be an invaluable complement experimental rheological characterisation, serving as a virtual rheometer that enables rapid exploration of parameter space detailed scrutiny microscopic dynamics. To maximise the utility such simulations, it can advantageous exploit p...