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

Chapter 3: Source Code Structure and Stages of Execution

Continuing from the previous chapter, this chapter will further illustrate the source code hierarchy by describing parent and child classes in the source code. The various methods used in some of these classes will also be discussed. To complete the picture, the flow of control from top-level classes to the code termination stage will be explained using the sequence of execution of methods as determined by the integrator.

This chapter is intended to complete your understanding of the source code hierarchy and flow, which will help you to identify code sections that need modifications when implementing custom features.

We will cover the following topics:

  • Parent and child classes in the source code
  • The stages of executing the simulation within each timestep
  • The role played by pointers.h
  • Parsing input script commands by input.cpp