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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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Concepts
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Authors (2):
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Jichen Li Jichen Li
Author Profile Icon Jichen Li
Jichen Li
Jichen Li (graduated from Qingdao University of Science and Technology) is now studying for his master's degree at the University of Science and Technology of China. He used LAMMPS to conduct many molecular simulations to explore the relationship between polymer microstructure and macro mechanical and rheological properties. He developed several modeling and post-processing frameworks for LAMMPS and had a certain understanding of its program architecture. He dedicated to the community construction and wrote many columns and tutorials for LAMMPS starters. At present, he is working on the trans-scale simulation and the combination of deep learning and simulation.
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Dr. Shafat Mubin Dr. Shafat Mubin
Author Profile Icon Dr. Shafat Mubin
Dr. Shafat Mubin
Dr. Shafat Mubin (PhD, Physics, Penn State) is an assistant professor of physics at Valdosta State University. Since his graduate student days, he has worked with molecular simulations using primarily LAMMPS and has investigated a variety of simulation systems employing a wide array of techniques. He possesses extensive experience in writing custom routines and extending the LAMMPS source code, and hosts his own website to instruct and demonstrate the same to other users. At present, he is engaged in computational physics research including molecular simulations, and endeavours to train undergraduate students in computational techniques to help them better prepare for careers in physics.
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Toc

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

Section 3: Modifying the Source Code

You have understood the LAMMPS source code and the programming logic, which is encoded. Now it is time to make your own modifications to it and to implement custom features in your simulations.

In this section, you will learn how to modify and extend the LAMMPS source code by writing and implementing custom features in the source code. Examples are provided to illustrate the process of adding modifications according to desired simulation goals.

This section comprises the following chapters:

  • Chapter 09, Modifying Pair Potentials
  • Chapter 10, Modifying Force Applications
  • Chapter 11, Modifying Thermostats
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Authors (2)

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Profile icon Dr. Shafat Mubin
Dr. Shafat Mubin
Dr. Shafat Mubin (PhD, Physics, Penn State) is an assistant professor of physics at Valdosta State University. Since his graduate student days, he has worked with molecular simulations using primarily LAMMPS and has investigated a variety of simulation systems employing a wide array of techniques. He possesses extensive experience in writing custom routines and extending the LAMMPS source code, and hosts his own website to instruct and demonstrate the same to other users. At present, he is engaged in computational physics research including molecular simulations, and endeavours to train undergraduate students in computational techniques to help them better prepare for careers in physics.
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See other products by Dr. Shafat Mubin
Profile icon Li
Li
Sherry Li is an Analytic Consultant who works for a major financial organization with responsibilities in implementing data warehousing, Business Intelligence, and business reporting solutions. She specializes in automation and optimization of data gathering, storing, analyzing and providing data access for business to gain data-driven insights. She especially enjoys sharing her experience and knowledge in data ETL process, database design, dimensional modeling, and reporting in T-SQL and MDX. She has co-authored two books, the MDX with SSAS 2012 Cookbook and MDX with Microsoft SQL Server 2016 Analysis Services Cookbook, which have helped many data professionals advanced their MDX skill in a very short time.
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