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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 Memory class

In this section, we will demonstrate how the Memory class (memory.cpp and memory.h) in LAMMPS allocates and deallocates memory blocks as requested.

The Memory class is widely used in the LAMMPS source code, and it is often encountered in relation to data structure creation. Its three main methods – create(), grow(), and destroy() – provide handles to create, extend/shrink, and release primitive data structures, respectively. By using template overrides, these methods can accommodate 1D, 2D, and 3D arrays that serve the same function.

In memory.h, various template functions are defined for the create(), grow(), and destroy() methods in different dimensions. The following screenshot shows these template functions in 1D:

Figure 8.12 – The create(), grow(), and destroy() methods for 1D arrays (from memory.h)

As you can see, in the create() method, TYPE (line 44) is initially an undefined data type that is automatically...

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