Book Image

Extending and Modifying LAMMPS Writing Your Own Source Code

By : Dr. Shafat Mubin, Jichen Li
Book Image

Extending and Modifying LAMMPS Writing Your Own Source Code

By: Dr. Shafat Mubin, Jichen Li

Overview of this book

LAMMPS is one of the most widely used tools for running simulations for research in molecular dynamics. While the tool itself is fairly easy to use, more often than not you’ll need to customize it to meet your specific simulation requirements. Extending and Modifying LAMMPS bridges this learning gap and helps you achieve this by writing custom code to add new features to LAMMPS source code. Written by ardent supporters of LAMMPS, this practical guide will enable you to extend the capabilities of LAMMPS with the help of step-by-step explanations of essential concepts, practical examples, and self-assessment questions. This LAMMPS book provides a hands-on approach to implementing associated methodologies that will get you up and running and productive in no time. You’ll begin with a short introduction to the internal mechanisms of LAMMPS, and gradually transition to an overview of the source code along with a tutorial on modifying it. As you advance, you’ll understand the structure, syntax, and organization of LAMMPS source code, and be able to write your own source code extensions to LAMMPS that implement features beyond the ones available in standard downloadable versions. By the end of this book, you’ll have learned how to add your own extensions and modifications to the LAMMPS source code that can implement features that suit your simulation requirements.
Table of Contents (21 chapters)
1
Section 1: Getting Started with LAMMPS
4
Section 2: Understanding the Source Code Structure
11
Section 3: Modifying the Source Code

Introducing the LAMMPS input script structure

LAMMPS offers built-in features to construct MD simulations using its own scripting syntax. An inventory of LAMMPS script syntax is available on the LAMMPS website (www.lammps.sandia.gov). The input script is executed line by line from beginning to end. A typical input script consists of the following parts:

  • Initialization Settings
  • System Definitions
  • Simulation Settings
  • Simulation Execution

A sample input script may look like the one shown here:

Figure 2.1 – A sample input script of LAMMPS

An input script such as this sets up an MD simulation by specifying the simulation box size and boundaries, creating atoms, defining the pair potentials between atoms, applying a thermostat, and finally executing the simulation. The command lines starting with pair define pair potentials, and the lines starting with fix perform a multitude of operations on the system, including thermostat and...