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

Introducing parent and child classes

As mentioned in Chapter 2, LAMMPS Syntax and Source Code Hierarchy, certain styles are given in the source code that can support child classes. These styles serve as parent classes and their child classes inherit their methods, thereby ensuring a degree of uniformity in the child classes that makes classification and syntax synthesis more streamlined. In this section, we will describe some of these parent classes and some of the inherited methods in their child classes.

fix.cpp and fix.h

These are the parent classes of all fixes used in LAMMPS. Among other purposes, they read the first three arguments common to all fixes (fix ID, group ID, and fix style) and sets up energy or virial computations. The following screenshot shows the code snippet from fix.cpp that invokes an instance of LAMMPS and reads the three common arguments:

Figure 3.1 - Code snippet from fix.cpp

All fixes inherit these three arguments from fix...