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

Parsing input script commands by input.cpp

In this section, the parsing of input script commands is described as handled by the execute_command() method in input.cpp, along with the steps followed after each command.

The execute_command() method in input.cpp is responsible for parsing the first word of each line of the input script. This method contains a list of permitted commands that are compared with the first word of each line. An error is returned if there is no match, and pre-defined methods in input.cpp are called for each match. This method is called within the file() method and the one() method in input.cpp to facilitate parsing and execution.

The following screenshot shows the execute_command() method:

Figure 3.16 – The execute_command() method in input.cpp containing a list of permitted input script commands

As you can see, in the preceding screenshot, the command variable represents the first word of the line being parsed, and it is...