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

Summary

In this chapter, we saw some examples of custom-written pair styles that illustrate the process of selecting an appropriate pair style and making modifications at the correct sections to generate the required forces and potentials. In addition, the mathematical background behind these pair styles have been provided to help you to see the connection from theory to source code implementation.

In this chapter, you have learned to choose existing pair styles and to create new pair styles by adding proper modifications. Other than modifying input parameters to parse, the force and potential functions usually need to be modified when creating a new pairwise potential. You have also seen examples of non-pairwise potentials being modified to implement location-dependence and frictional forces.

In the next chapter, we will write custom fixes that can perform user-defined maneuvers during a simulation run to suit user requirements.