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

Summary

This chapter demonstrated how to modify thermostats in LAMMPS to implement custom features, such as random velocity assignments and non-linear temperature increments. In addition, a short example of writing a fix to control the printing of quantities is provided.

Combined with the examples in the previous chapters, the content in this chapter has provided you with a platform to analyze your simulation requirements and determine an effective strategy of choosing an appropriate fix to modify or extend and implement your custom features with the proper tools and commands.

Overall, this book starts by introducing the LAMMPS source code and gradually builds up to the final chapter where custom fixes are created to apply custom thermostats to the simulated system. Using the concepts discussed in the earlier chapters, a robust framework is developed for users to refer to when writing their own modifications to the LAMMPS source code. The current version of LAMMPS includes a...