Scope

This set of tutorials consists of eight tutorials arranged in order of increasing difficulty. The novelties associated with each tutorial are briefly described below.

In Lennard-Jones fluid, the structure of LAMMPS input files is illustrated through the creation of a simple atomic Lennard-Jones fluid system. Basic LAMMPS commands are used to set up interactions between atoms, perform an energy minimization, and finally run a simple MD simulation in the microcanonical (NVE) and canonical (NVT) ensembles.

In Pulling on a carbon nanotube, a more complex system is introduced in which atoms are connected by bonds: a small carbon nanotube. The use of both classical and reactive force fields (here, OPLS-AA [1] and AIREBO [2], respectively) is illustrated. An external deformation is applied to the CNT, and its deformation is measured. This tutorial also demonstrates the use of an external tool to visualize breaking bonds, and show the possibility to import LAMMPS-generated YAML log files into Python.

In Polymer in water, two componentstextemdash liquid water (flexible three-point model) and a polymer moleculetextemdash are merged and equilibrated. A long-range solver is used to handle the electrostatic interactions accurately, and the system is equilibrated in the isothermal-isobaric (NPT) ensemble; then, a stretching force is applied to the polymer. Through this relatively complex solvated polymer system, the tutorial demonstrates how to use type labels to make molecule files more generic and easier to manage [3].

In Nanosheared electrolyte, an electrolyte is confined between two walls, illustrating the specifics of simulating systems with fluid-solid interfaces. With the rigid four-point TIP4P/2005 [4] water model, this tutorial uses a more complex water model than Polymer in water. A non-equilibrium MD is performed by imposing shear on the fluid through moving the walls, and the fluid velocity profile is extracted.

In Reactive silicon dioxide, the ReaxFF reactive force field is used, specifically designed to simulate chemical reactions by dynamically adjusting atomic interactions [5]. ReaxFF includes charge equilibration (QEq), a method that allows the partial charges of atoms to adjust according to their local environment.

In Water adsorption in silica, a Monte Carlo simulation in the grand canonical ensemble is implemented to demonstrate how LAMMPS can be used to simulate an open system that exchanges particles with a reservoir.

In Free energy calculation, an advanced free energy method called umbrella sampling is implemented. By calculating an energy barrier, this tutorial describes a protocol for addressing energy landscapes that are difficult to sample using classical MD or MC methods.

In Reactive Molecular Dynamics, a CNT embedded in nylon-6,6 polymer melt is simulated. The REACTER protocol is used to model the polymerization of nylon, and the formation of water molecules is tracked over time~cite{gissinger2020reacter}.