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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

Exploring the Variable class

In this section, we will outline the Variable class and its source code in the variable.cpp and variable.h files. This class can assign variables in order to store constants or calculate atom and group properties, among other functionalities (see https://lammps.sandia.gov/doc/variable.html).

A variable can return scalar values or arrays of values that are useful for conveying information from one part of the script to another during a simulation run. An equal style variable sets the variable to a provided constant value or to a formula that performs a mathematical calculation or extracts a group, atom, region, compute, fix property, and more. The following screenshot from the set() method shows the relevant code:

Figure 8.5 – Code snippet from the Variable::set() method showing the equal style variables

As you can see, upon detecting the equal keyword (line 401), the find() method is used to locate the name of the variable...

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