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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

Summary

This chapter outlined some of the supporting classes that complement the fixes, computes, and pair potentials that control simulation dynamics. In this chapter, we discussed groups, variables, errors, memory, and angle styles, all of which will help you understand their supporting roles in the simulation execution and enable you to implement them in your own custom LAMMPS code.

This was also the last chapter that focuses on explicating existing LAMMPS features in terms of their source code. In the next chapter, we will write custom features into LAMMPS, starting with custom pair potentials, to provide you with some hands-on practice of modifying and extending the LAMMPS source code.

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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

Sherry Li is an Analytic Consultant who works for a major financial organization with responsibilities in implementing data warehousing, Business Intelligence, and business reporting solutions. She specializes in automation and optimization of data gathering, storing, analyzing and providing data access for business to gain data-driven insights. She especially enjoys sharing her experience and knowledge in data ETL process, database design, dimensional modeling, and reporting in T-SQL and MDX. She has co-authored two books, the MDX with SSAS 2012 Cookbook and MDX with Microsoft SQL Server 2016 Analysis Services Cookbook, which have helped many data professionals advanced their MDX skill in a very short time.

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