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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

Reviewing the Fix Orient/FCC class

In this section, we will discuss how the orientations of two adjoining grains are compared to determine forces that generate grain boundary migration.

This fix applies a force to atoms located at the interface of two planar grains, that is, the grain boundary, to account for a range of potential energies that may be added to these atoms based on their neighboring atom positions. It is assumed that the two grains are face-centered cubic (FCC) crystals with different orientations, with their orientation vectors defined in two separate files. Altogether, this force results in atoms being migrated from one grain to the other.

The Fix Orient/FCC source code files, fix_orient_fcc.cpp and fix_orient_fcc.h, are located inside the MISC folder and need to be compiled as a separate package. The syntax for implementing this fix in a LAMMPS input script involves several input parameters:

fix  FIX_ID  GROUP_ID  orient/fcc...
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