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

Reading parameters from the input script

In this section, we will learn about parsing parameters entered by a user in the LAMMPS input script. In Chapter 3, Source Code Structure and Stages of Execution, the role of input.cpp in parsing the first words of input script commands was discussed. In this section, we will discuss the methods responsible for parsing user-entered quantities associated with various commands.

User-entered parameters associated with various styles, such as numeric pair coefficient values in pair styles and force values in fixes, are parsed from the LAMMPS input script by the corresponding classes or their parent classes.

Important Note:

These methods are located in force.cpp in the LAMMPS stable version, 3Mar20, whereas they have been moved to utils.cpp in the stable version, 29Oct20. Please refer to Appendix D for more information about version compatibility.

The parsing of these quantities is performed by the force.cpp class through several methods...