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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 message

MPI message includes two parts—envelope and data. The envelope consists of identifying information including the source/destination, tag, and communicator, while data is the content to be delivered. The envelope and data include three parts, which can be represented by a ternary array:

  • Envelope: Source/destination, ID, communication domain
  • Data: Start address, count, datatype

The following screenshot illustrates this structure:

Figure 14.1 – Structure of the envelope and data

In addition to the source and destination, there are tags in the message envelope to allow the receiver to distinguish between two or more messages of the same type sent from the same sender to the same receiver, as shown in the following screenshot:

Figure 14.2 – The role of envelope tags in distinguishing between simultaneous messages

In the preceding figure, Message 2 with tag2 arrives without a matching receive...

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