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

MPI message

MPI message includes two parts—envelope and data. The envelope consists of identifying information including the source/destination, tag, and communicator, while data is the content to be delivered. The envelope and data include three parts, which can be represented by a ternary array:

  • Envelope: Source/destination, ID, communication domain
  • Data: Start address, count, datatype

The following screenshot illustrates this structure:

Figure 14.1 – Structure of the envelope and data

In addition to the source and destination, there are tags in the message envelope to allow the receiver to distinguish between two or more messages of the same type sent from the same sender to the same receiver, as shown in the following screenshot:

Figure 14.2 – The role of envelope tags in distinguishing between simultaneous messages

In the preceding figure, Message 2 with tag2 arrives without a matching receive...