Before you start¶
LAMMPS tutorials is made of seven tutorials that are ordered by increasing difficulty. The first tutorial, Lennard-Jones fluid, is meant for LAMMPS absolute beginners. The complexity of the simulations is then progressively increased for Pulling on a carbon nanotube, Polymer in water, Nanosheared electrolyte, and Reactive silicon dioxide. Finally, in Water adsorption in silica and Free energy calculation, some more advanced simulation methods are used, namely grand canonical Monte Carlo simulations and a free energy method named umbrella sampling.
Required software¶
The 2Aug2023 version of LAMMPS is required to follow the tutorials [1].
LAMMPS (2Aug2023)¶
Download and install the 2Aug2023 version of LAMMPS by following the instructions of the LAMMPS website. Depending on your operative system (i.e. Linux, macOS, or Windows), the procedure may differ.
LAMMPS must be compiled with the following packages:
MANYBODY
MOLECULE
KSPACE
RIGID
REAXFF
EXTRA-DUMP
If you decide to use another LAMMPS version, certain commands may not work and LAMMPS will throw an error message.
VMD (optional)¶
In order to visualize the simulation, the version 1.9.3 of VMD will be used [2]. Some basic instructions for VMD are given here in the VMD tutorial. If you prefer, feel free to use an alternative visualization software like Ovito.
Python (optional)¶
To perform post-mortem analysis of the data during the MDAnalysis tutorials, the version 2.6.1 of MDAnalysis is used together with the version 3.11.4 of Python [3, 4, 5].
To plot the results from the simulations, the version 3.5.2 of Matplotlib Pyplot is used in combination with lammps logfile, a library allowing one to read the log file produced by LAMMPS [6, 7].
Text editing software¶
Find the input scripts¶
You can access the input scripts and data files that are used in these tutorials from this Github repository. This repository also contains the full solutions to the exercises.
Recommended reading¶
To better understand molecular dynamics simulations, I recommend the reading of Understanding molecular simulation by Daan Frenkel and Berend Smit [8], as well as Computer simulation of liquids by Michael Allen and Dominic Tildesley [9]. To understand the basic concepts of fluid and Soft Matter systems, I recommend reading Basic concepts for simple and complex liquids by Jean-Louis Barrat and Jean-Pierre Hansen [10], as well as Theory of simple liquids: with applications to soft matter by Jean-Pierre Hansen and Ian Ranald McDonald [11].