Extending and Modifying LAMMPS-Writing Your Own Source Code

A pragmatic guide to extending LAMMPS as per custom simulation requirements

Dr. Shafat Mubin , Jichen Li 지음

Packt(GCO Science) 2021년 02월 19일 출간

작품소개

책소개

Understand the LAMMPS source code and modify it to meet your research needs, and run simulations for bespoke applications involving forces, thermostats, pair potentials and more with ease

▶Book Description
LAMMPS is one of the most widely used tools for running simulations for research in molecular dynamics. While the tool itself is fairly easy to use, more often than not you'll need to customize it to meet your specific simulation requirements. Extending and Modifying LAMMPS bridges this learning gap and helps you achieve this by writing custom code to add new features to LAMMPS source code. Written by ardent supporters of LAMMPS, this practical guide will enable you to extend the capabilities of LAMMPS with the help of step-by-step explanations of essential concepts, practical examples, and self-assessment questions.

This LAMMPS book provides a hands-on approach to implementing associated methodologies that will get you up and running and productive in no time. You'll begin with a short introduction to the internal mechanisms of LAMMPS, and gradually transition to an overview of the source code along with a tutorial on modifying it. As you advance, you'll understand the structure, syntax, and organization of LAMMPS source code, and be able to write your own source code extensions to LAMMPS that implement features beyond the ones available in standard downloadable versions.

By the end of this book, you'll have learned how to add your own extensions and modifications to the LAMMPS source code that can implement features that suit your simulation requirements.

▶What You Will Learn
-Identify how LAMMPS input script commands are parsed within the source code
-Understand the architecture of the source code
-Relate source code elements to simulated quantities
-Learn how stored quantities are accessed within the source code
-Explore the mechanisms controlling pair styles, computes, and fixes
-Modify the source code to implement custom features in LAMMPS

▶Key Features
-Understand the structure of the LAMMPS source code
-Implement custom features in the LAMMPS source code to meet your research needs
-Run example simulations involving forces, thermostats, and pair potentials based on implemented features

▶Who This Book Is For
This book is for students, faculty members, and researchers who are currently using LAMMPS or considering switching to LAMMPS, have a basic knowledge of how to use LAMMPS, and are looking to extend LAMMPS source code for research purposes. This book is not a tutorial on using LAMMPS or writing LAMMPS scripts, and it is assumed that the reader is comfortable with the basic LAMMPS syntax. The book is geared toward users with little to no experience in source code editing. Familiarity with C++ programming is helpful but not necessary.

목차

▶TABLE of CONTENTS
▷Section 1: Getting Started with LAMMPS
-Chapter 1: MD Theory and Simulation Practices
-Chapter 2: LAMMPS Syntax and Source Code Hierarchy

▷Section 2: Understanding the Source Code Structure
-Chapter 3: Source Code Structure and Stages of Execution
-Chapter 4: Accessing Information by Variables, Arrays, and Methods
-Chapter 5: Understanding Pair Styles
-Chapter 6: Understanding Computes
-Chapter 7: Understanding Fixes
-Chapter 8: Exploring Supporting Classes

▷Section 3: Modifying the Source Code
-Chapter 9: Modifying Pair Potentials
-Chapter 10: Modifying Force Applications
-Chapter 11: Modifying Thermostats

-Appendix A: Building LAMMPS with CMake
-Appendix B: Debugging Programs
-Appendix C: Getting Familiar with MPI
-Appendix D: Compatibility with Version 29Oct20

책 속으로

▶What this book covers
- Chapter 1, MD Theory and Simulation Practices, briefly introduces fundamental concepts of molecular dynamics, common techniques, and features that will be addressed later in the book to provide a link between theory and simulation.

- Chapter 2, LAMMPS Syntax and Source Code Repository, introduces LAMMPS input script and the execution of MD simulation features through LAMMPS commands and an introduction to the repository of standard LAMMPS code.

- Chapter 3, Source Code Structure and Stages of Execution, introduces the LAMMPS source code format and the sequence of execution followed in a LAMMPS script.

- Chapter 4, Accessing Information by Variables, Arrays, and Methods, describes the elements that store information and perform calculations during a simulation run.

- Chapter 5, Understanding Pair Styles, describes and dissects selected pair styles.

- Chapter 6, Understanding Computes, describes and dissects selected computes.

- Chapter 7, Understanding Fixes, describes and dissects selected fixes.

- Chapter 8, Exploring Supporting Classes, describes and dissects other additional LAMMPS features.

- Chapter 9, Modifying Pair Potentials, discusses the implementation of custom pair styles.

- Chapter 10, Modifying Force Applications, discusses the implementation of custom fix styles to apply forces based on pre-defined criteria.

- Chapter 11, Modifying Thermostats, discusses the implementation of custom fix styles associated with temperature control.

- Appendix A, Building LAMMPS with CMake, introduces LAMMPS compilation using CMake in Linux and Windows.

- Appendix B, Debugging with GDB and Visual Studio Code, introduces debugging tools with applications on understanding bit operations.

- Appendix C, Getting Familiar with MPI, introduces MPI parallel processing.

- Appendix D, Compatibility with Version 29Oct20, discusses source code differences between stable versions 3Mar20 and 29Oct20.

출판사 서평

▶ Preface
LAMMPS is one of the most widely used tools for running simulations for research in molecular dynamics. While the tool itself is fairly easy to use, more often than not, you'll need to customize it to meet your specific simulation requirements.

Extending and Modifying LAMMPS bridges this learning gap and helps you achieve this by writing custom code to add new features to LAMMPS source code. Written by ardent supporters of LAMMPS, this practical guide will enable you to extend the capabilities of LAMMPS with the help of step-by-step explanations of essential concepts, practical examples, and self-assessment questions.

Filled with real-world examples, this book teaches you how to find your way around the LAMMPS source code and shows you, in a pragmatic and easily digestible way, how to modify the code to achieve custom simulations for your work.

This LAMMPS book provides a hands-on approach to implementing associated methodologies that will get you up and running and productive in no time. You'll begin with a short introduction to the internal mechanisms of LAMMPS and gradually transition to an overview of the source code along with a tutorial on modifying it.

You'll also learn how to identify how LAMMPS input script commands are executed within the source code and understand the architecture of the source code. You'll learn how to modify the source code to implement custom features in LAMMPS, relate source code elements to simulated quantities, and explore pair styles and computes within LAMMPS. You'll also learn how to create various custom fixes to control your simulation using pre-defined criteria.

As you advance, you'll learn about the structure, syntax, and organization of LAMMPS source code, and will be able to write your own source code extensions to LAMMPS that implement features beyond the ones available in standard downloadable versions. You'll understand how to work with custom solutions for applications on force, thermostats, and pair potentials.

By the end of this source code book, you'll have learned how to how to add your own extensions and modifications to the LAMMPS source code that can implement features that suit your simulation requirements.

작가정보

저자(글) 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.

저자(글) 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.