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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

MPI in LAMMPS

In this section, we will explore how LAMMPS uses the MPI in main.cpp to execute the input script code in the correct order. The initialization is performed by MPI_Init on line 36, as shown in the following screenshot:

Figure 14.3 – Screenshot showing MPI_Init in main.cpp

Next, a predefined communication domain descriptor, MPI_COMM_WORLD, can be used (line 64), as shown in the following screenshot:

Figure 14.4 – Screenshot showing MPI calls in main.cpp

The MPI communication domain consists of two parts: process group and communication context. The process group is the collection of all the processes participating in the communication. If n processes participate in the communication, the number is 0-n-1. The communication context provides a relatively independent communication area. Different messages are delivered in different contexts, and messages in different contexts do not interfere with each other. The...

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