Book Image

Extending and Modifying LAMMPS Writing Your Own Source Code

By : Dr. Shafat Mubin, Jichen Li
Book Image

Extending and Modifying LAMMPS Writing Your Own Source Code

By: Dr. Shafat Mubin, Jichen Li

Overview of this book

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.
Table of Contents (21 chapters)
1
Section 1: Getting Started with LAMMPS
4
Section 2: Understanding the Source Code Structure
11
Section 3: Modifying the Source Code

Reviewing the general structure of pair styles

As described in Chapter 3, Source Code Structure and Stages of Execution, each individual pair style inherits from pair.cpp and pair.h, including the init() method.

In this section, we briefly cover the methods commonly used in the child pair style classes that are inherited from the pair.cpp and pair.h classes.

The parent classes take care of validating pair coefficient assignments, mixing parameters, determining cutoff, requesting neighbor lists, and setting up computations. Some of the methods and variables are also inherited from pair.h. Hybrid styles are accommodated by the pair_hybrid.cpp and pair_hybrid_overlay.cpp classes.

The child pair style classes commonly contain the following methods:

  • allocate() allocates memory to arrays used to calculate pair interaction forces.
  • settings() reads and processes global pair potential parameters entered after the pair_style command in the LAMMPS input script.
  • coeff...