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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

Translating Fix Widom into the 3Mar20 version

Once you download the current version (29Oct20) of LAMMPS, you need to copy the fix_widom.cpp and fix_widom.h files located in the src/MC folder to a temporary location. Use git reset –hard b3040db1e to revert back to the 3Mar20 version, and copy the fix_widom.cpp and fix_widom.h files back to the src/MC folder of this version, renamed as fix_widom_modified.cpp and fix_widom_modified.h, respectively.

Upon performing regular compilation (see Appendix A, Building LAMMPS with CMake) including the MC package, several errors are produced, some of which are shown in the following screenshot:

Figure 15.1 – A partial list of errors when compiling Fix Widom in the 3Mar20 version

As you can see, the errors can be categorized into the following:

  • Parsing input parameters with the Utils class
  • Identifying molecular systems using the Atom class
  • Additional function signatures in group.cpp
...
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