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

What is debugging?

There are two types of errors in a program—syntax errors and logical errors. A syntax error is an error in code grammar or composition that can be detected by the compiler, and therefore can usually be corrected relatively easily.

A logical error refers to an error in code design in terms of its intended purpose versus actual outcome. The quintessential symptom of a logical error in the program is successful compilation followed by an erroneous output upon execution. These errors have to be detected and corrected manually.

The debugging process involves letting the code execute step by step and tracking the program's process of execution. Generally, the most efficient way to detect logical errors is to debug the program with designated debugging tools that allow the tracking of execution steps.

For example, you can make the program stop at a certain step to view the contents of variables or data in memory. You can also make the program execute...