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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

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Product type Paperback
Published in Feb 2021
Publisher Packt
ISBN-13 9781800562264
Length 394 pages
Edition 1st Edition
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Authors (2):
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Jichen Li Jichen Li
Author Profile Icon Jichen Li
Jichen Li
Dr. Shafat Mubin Dr. Shafat Mubin
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Dr. Shafat Mubin
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Toc

Table of Contents (21) Chapters Close

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 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

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.

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