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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
Author Profile Icon Dr. Shafat Mubin
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

This chapter demonstrated how to modify thermostats in LAMMPS to implement custom features, such as random velocity assignments and non-linear temperature increments. In addition, a short example of writing a fix to control the printing of quantities is provided.

Combined with the examples in the previous chapters, the content in this chapter has provided you with a platform to analyze your simulation requirements and determine an effective strategy of choosing an appropriate fix to modify or extend and implement your custom features with the proper tools and commands.

Overall, this book starts by introducing the LAMMPS source code and gradually builds up to the final chapter where custom fixes are created to apply custom thermostats to the simulated system. Using the concepts discussed in the earlier chapters, a robust framework is developed for users to refer to when writing their own modifications to the LAMMPS source code. The current version of LAMMPS includes a...

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