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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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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, some of the existing LAMMPS pair styles have been analyzed to demonstrate the roles played by various methods in performing the required calculations and exchanging information. Other variants of potentials implemented in LAMMPS include the many-body (that is, non-pairwise) Stillinger-Weber (SW) potential and the Pair List option that assigns pair coefficients to individual atom pairs instead of atom type pairs.

Position-dependent potentials are implemented using a functional form in the compute() method or can be implemented in a tabulated form read by the pair style. Non-conservative forces can also be implemented alongside by defining the appropriate force functions.

You can now use the lessons and skills learned from this chapter to modify the appropriate methods in a pair potential to customize it per your simulation requirements.

In the next chapter, we will analyze selected compute styles to illustrate the inner mechanism of the code as it has...

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