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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

Product type Paperback

Published in Feb 2021

Publisher Packt

ISBN-13 9781800562264

Length 394 pages

Edition 1st Edition

Languages

C++

Tools

GitHub

Concepts

Programming Language

Authors (2):

Jichen Li

Dr. Shafat Mubin

View More author details

Table of Contents (21) Chapters

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

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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

Chapter 11: Modifying Thermostats

In this chapter, we will provide examples of writing custom fixes to modify the thermostat controlling the system temperature, along with an example of modifying Fix Print to aid in custom simulation designs. We will create new fixes that are able to thermostat the system by adjusting atom velocities and temperature increments per iteration.

We will cover the following topics in this chapter:

Writing a fix to apply the Andersen thermostat
Writing a fix to apply a non-linear temperature increment
Writing a fix to print the output at evaporation

By the end of this chapter, you will learn to modify the source code relating to the thermostatting of a system. It will enable you to design systems that require non-conventional thermostats or related features not available in a standard LAMMPS download.

The rest of the chapter is locked

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Authors (2)

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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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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