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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

Introducing the source code repository

After downloading and unzipping LAMMPS (visit https://lammps.sandia.gov/doc/Install_tarball.html for instructions), the source code can be accessed from the src folder, shown as follows:

Figure 2.2 – A screenshot of the src folder showing .cpp and .h source files in pairs, and a list of packages separated into folders

The source files are mostly arranged in pairs of C++ and header files with the extensions .cpp and .h, respectively, which together are responsible for performing a given role in the simulation.

When a LAMMPS executable is compiled, the source files are built into it, along with any optional package. The folders titled in all uppercase letters in Figure 2.2 contain optional packages that can be built into the LAMMPS executable if specified. Once compiled successfully, the executable is capable of recognizing LAMMPS input script commands and calling the appropriate source code files that have been...

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