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 9: Modifying Pair Potentials

In the previous chapters, we discussed various classes that implement MD features and LAMMPS tools, such as pair styles, fixes, computes, variables, and groups. From this chapter onward, we will write custom features into LAMMPS, starting with custom pair potentials.

In this chapter, we will construct custom pair potentials to describe the process of writing and incorporating them in a LAMMPS input script. In the process, we will use the content covered in the previous chapters to program LAMMPS according to our requirements.

We will cover the following pair potentials in this chapter:

  • Writing a harmonic potential
  • Writing a height-dependent pair potential
  • Writing a tangential friction-based pair style for spherical atoms

By the end of this chapter, you will have learned how to write your own pair styles and how to connect information from previous chapters to custom pair styles.