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

Role of pointers class

The pointers.h file facilitated information transfer between classes by creating pointers to all important quantities listed in lammps.h. All classes inherit from pointers.h and are able to access these variables. The following screenshot illustrates the pointers created:

Figure 3.15 - Code snippets from pointers.h showing (left) pointers to classes and (right) pointers to pointers in lammps.h

The pointers to different classes are created, as well as pointers to pointers listed in lammps.h, indicated by *& at the front. This way, variables from lammps.h can be accessed from other classes directly by declaring proper pointers, as will be explained in later chapters.

In the next section of this chapter, we will describe how input script commands are parsed using a pre-defined list of permitted commands in input.cpp.