Extending and Modifying LAMMPS Writing Your Own Source Code: A pragmatic guide to extending LAMMPS as per custom simulation requirements

by Shafat Mubin, Jichen Li

Overview

Understand the LAMMPS source code and modify it to meet your research needs, and run simulations for bespoke applications involving forces, thermostats, pair potentials and more with ease

Key Features

Understand the structure of the LAMMPS source code

Implement custom features in the LAMMPS source code to meet your research needs

Run example simulations involving forces, thermostats, and pair potentials based on implemented features

Book Description

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.

What You Will Learn

Identify how LAMMPS input script commands are parsed within the source code

Understand the architecture of the source code

Relate source code elements to simulated quantities

Learn how stored quantities are accessed within the source code

Explore the mechanisms controlling pair styles, computes, and fixes

Modify the source code to implement custom features in LAMMPS

Who this book is for

This book is for students, faculty members, and researchers who are currently using LAMMPS or considering switching to LAMMPS, have a basic knowledge of how to use LAMMPS, and are looking to extend LAMMPS source code for research purposes. This book is not a tutorial on using LAMMPS or writing LAMMPS scripts, and it is assumed that the reader is comfortable with the basic LAMMPS syntax. The book is geared toward users with little to no experience in source code editing. Familiarity with C++ programming is helpful but not necessary.

Product Details

ISBN-13:	9781800562264
Publisher:	Packt Publishing
Publication date:	02/19/2021
Pages:	394
Product dimensions:	7.50(w) x 9.25(h) x 0.81(d)

About the Author

Dr. Shafat Mubin (PhD, Physics, Penn State) is an assistant professor of physics at Valdosta State University. Since his graduate student days, he has worked with molecular simulations using primarily LAMMPS and has investigated a variety of simulation systems employing a wide array of techniques. He possesses extensive experience in writing custom routines and extending the LAMMPS source code, and hosts his own website to instruct and demonstrate the same to other users. At present, he is engaged in computational physics research including molecular simulations, and endeavours to train undergraduate students in computational techniques to help them better prepare for careers in physics.

Jichen Li (graduated from Qingdao University of Science and Technology) is now studying for his master's degree at the University of Science and Technology of China. He used LAMMPS to conduct many molecular simulations to explore the relationship between polymer microstructure and macro mechanical and rheological properties. He developed several modeling and post-processing frameworks for LAMMPS and had a certain understanding of its program architecture. He dedicated to the community construction and wrote many columns and tutorials for LAMMPS starters. At present, he is working on the trans-scale simulation and the combination of deep learning and simulation.

Table of Contents

1. MD Theory and Simulation Practices
2. LAMMPS Syntax and Source Code Repository
3. Source Code Structure and Stages of Execution
4. Accessing Information by Variables, Arrays, and Methods
5. Understanding Pair Styles
6. Understanding Computes
7. Understanding Fixes
8. Exploring Supporting Classes
9. Modifying Pair Potentials
10. Modifying Force Applications
11. Modifying Thermostats
12. Appendix A: Building LAMMPS with CMake
13. Appendix B: Debugging Programs
14. Appendix C: Getting Familiar with MPI
15. Appendix D: Compatibility with Version 29Oct20