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.
Assessments, contains the answers to all the questions from this book.
