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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
Author Profile Icon Jichen Li
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

Data exchange between owned atoms and ghost atoms

LAMMPS is able to run on a distributed-memory machine, requiring the communication among processors to be carried out by MPI. This is implemented by the Comm class and its two child classes that implement specific functionalities:

  • One of the child classes is CommBrick, described by comm_brick.h and comm_brick.cpp. In this Comm style, the simulation box is considered as a 3D grid where each block in the grid is assigned to a processor, which is responsible for communicating with its six neighboring blocks in the (x, y, z) directions to exchange information about neighboring atoms. This decomposition is especially suitable for uniform particle density, where every block can be expected to contain the same number of particles.
  • The other child class is CommTiled, described in comm_tiled.h and comm_tiled.cpp, which can adjust the processor domains dynamically and is more effective when the system particle density is non-uniform...
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