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

Exploring the Fix Rigid class

The Fix Rigid class can treat a set of atoms as an independent rigid body. Its dynamics is described in terms of the net force on its center-of-mass (COM) and torque around the COM.

As described in Chapter 1, MD Theory and Simulation Practices, the net force, on a rigid body is calculated by summing up all the forces on all its constituent atoms (N), while the torque, , about its COM is calculated from the sum of the cross products of the displacement vector, , of each atom from the COM with the force, , acting on that atom:

The torque is used to update the rigid-body angular momentum, , through the velocity Verlet algorithm for rotational motion:

Using the moment of inertia tensor, I, the angular velocity, , of the rigid body can be obtained as follows:

The angular velocity and the distance from the COM can be used to find the individual atom linear velocities, , with respect to the COM...