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

Studying the Error class

In this section, we will analyze the Error class and its source code, which can be found in the error.cpp and error.h files.

Before we begin, we will introduce the concepts of Universe and World with regard to parallel processing – a universe consists of all the tasks in the simulation, whereas a world refers to the number of cores dedicated to each task. Subsequently, the world and universe IDs differ only if the simulation runs on more than one partition via -partition command-line switch (see https://lammps.sandia.gov/doc/Run_options.html). Once a set of cores finish a task, the cores execute the next task immediately after, and each task is considered a universe that is executed by a world of constituent cores.

The Error class is used when we intend to display an error message or print information in order to debug. Several types of error messages are offered:

  • The Error::all() method
  • The Error::one() method
  • The Error::warning...