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 10: Modifying Force Applications

In this chapter, we will write custom fixes that are able to apply non-pairwise forces on selected groups of atoms during a simulation run. Starting with existing fixes, we will make modifications that produce new fixes to exert custom forces to the atoms in the system. These forces generally represent agents that are not adequately incorporated into the MD simulation by atoms or potentials, such as self-propelling active forces.

We will cover the following topics in this chapter:

  • Writing a fix to apply a 2D spring force
  • Writing a fix to apply an active force in a molecular chain
  • Writing a fix to apply a custom wall force
  • Writing a fix to apply a bond-boost potential

By the end of this chapter, you will have learned how to write your own fix that can manipulate your MD simulation by modifying forces as programmed in the source code.