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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 an active force

The following is a list of changes that should be made to the source code:

  • The new files that should be created are fix_activeforce.cpp and fix_activeforce.h.
  • The existing files that are modified are fix_addforce.cpp, fix_addforce.h, and compute_bond_local.cpp.
  • The methods that are modified are constructor, post_force().
  • The input parameters are fMagnitude, and direction.
  • The other quantities introduced in this section can be seen in a full list in Figure 10.9 under post_force().
  • The LAMMPS syntax is fix FIX_NAME GROUP activeforce FMAGNITUDE DIRECTION (we'll review the syntax in this section).

In this section, we will create an active force in Fix Activeforce that applies a specified magnitude of force along the direction defined by two bonded atoms.

Theory (active force on bonded atoms)

An active force is generated by an atom and acts on the same atom. In this example, the active force acts on an...

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