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Extending and Modifying LAMMPS Writing Your Own Source Code

You're reading from Extending and Modifying LAMMPS Writing Your Own Source Code A pragmatic guide to extending LAMMPS as per custom simulation requirements

Product type Paperback

Published in Feb 2021

Publisher Packt

ISBN-13 9781800562264

Length 394 pages

Edition 1st Edition

Languages

C++

Tools

GitHub

Concepts

Programming Language

Authors (2):

Jichen Li

Dr. Shafat Mubin

View More author details

Table of Contents (21) Chapters

Preface

1. Section 1: Getting Started with LAMMPS

2. Chapter 1: MD Theory and Simulation Practices FREE CHAPTER

3. Chapter 2: LAMMPS Syntax and Source Code Hierarchy

4. Section 2: Understanding the Source Code Structure

5. Chapter 3: Source Code Structure and Stages of Execution

6. Chapter 4: Accessing Information by Variables, Arrays, and Methods

7. Chapter 5: Understanding Pair Styles

8. Chapter 6: Understanding Computes

9. Chapter 7: Understanding Fixes

10. Chapter 8: Exploring Supporting Classes

11. Section 3: Modifying the Source Code

12. Chapter 9: Modifying Pair Potentials

13. Chapter 10: Modifying Force Applications

14. Chapter 11: Modifying Thermostats

15. Assessments

16. Other Books You May Enjoy

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Appendix A: Building LAMMPS with CMake

1. Appendix B: Debugging Programs

2. Appendix C: Getting Familiar with MPI

3. Appendix D: Compatibility with Version 29Oct20

Technical requirements

To execute the instructions in this chapter, you need a text editor (for example, Notepad++ or Gedit) and a platform to compile LAMMPS (for example, a Linux Terminal). The LAMMPS version 29Oct20 can be accessed from https://github.com/lammps/lammps/tree/stable_29Oct2020, or downloaded from https://lammps.sandia.gov/download.html.

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Authors (2)

Dr. Shafat Mubin

Dr. Shafat Mubin

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.

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Li

Li

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.

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