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 Fix NVE class

In this section, we will study the Fix NVE class, which time-integrates a system using the velocity Verlet algorithm we described in Chapter 1, MD Theory and Simulation Practices.

The first half of the algorithm updates the velocity over a half-timestep and the position over a full-timestep. How the velocity and position components are updated is shown in the following equations.

The velocity update for the x component is given as follows:

The position update for the x coordinate is given as follows:

The y and z coordinates are updated similarly. The second half of the algorithm updates the three components of the velocity over the second half of the timestep.

We get the x component as follows:

The y and z components are updated in a similar fashion.

The source code for this class is provided in the fix_nve.cpp and fix_nve.h files. In a LAMMPS input script, the corresponding syntax is as follows:

fix  FIX_ID...