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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 bond-boost potential

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

  • The new files that are created are fix_addboost.cpp and fix_addboost.h.
  • The existing files that have been modified at fix_addforce.cpp, fix_addforce.h, and fix_orient_fcc.cpp.
  • The methods that have been modified are constructor, destructor, init(), and post_force().
  • The new method that is added is init_list().
  • The input parameters are jgroup, potentialType, atomID, param1, param2, param3, and cutoff.
  • The other quantities that are introduced can be seen in a full list in Figure 10.19 in the header file.
  • The LAMMPS syntax is fix FIX_NAME GROUP addboost GROUP2 ATOMID POTENTIAL P1 P2 P3 CUTOFF (we will reviews this syntax in this section).

In this section, we will create a fix that applies a boost potential and boost force to the atom located farthest from a surface along the z direction, while ensuring that the neighboring atoms that interact...

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