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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
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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

Writing a fix to apply a custom wall force

Here is a list of changes that are made to the source code:

  • The existing files that have been modified are fix_wall_region.cpp and fix_wall_region.h.
  • The methods that have been modified are constructor, init(), and post_force().
  • The new method added is lj126Expanded().
  • The new input parameter introduced is deltaLJ.
  • The LAMMPS syntax is fix FIX_NAME GROUP wall/region REGION lj126Expanded EPSILON SIGMA DELTALJ CUTOFF (we'll review this syntax in this section).

In this section, we will add a custom wall potential to the inventory of existing ones in the Fix Wall/Region class.

Theory (expanded Lennard–Jones wall force)

The Fix Wall/Region class (https://lammps.sandia.gov/doc/fix_wall_region.html) defines the surface of a region as a wall that can apply forces to an atom that interacts with it. This force of interaction can be defined in terms of a potential function (for example, Lennard–...

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