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

Introducing MD theory

MD is based on simulating individual particle trajectories over a desired time period to analyze the time evolution of an entire system of particles in a solid, liquid, or gaseous state. Each particle (usually an atom) is allowed to traverse in space as determined by Newton's laws of classical dynamics, where the atomic positions, velocities, and accelerations at one point in time are used to calculate the corresponding kinematics quantities at a different point in time. This process is repeated over a sufficiently long-time interval for every atom in a system, and the final configuration of the atoms indicates the time evolution of the system over the said time interval.

Typical MD simulations are limited to the study of atomistic systems consisting of atoms in the range of to , occupying a simulation box with a length in the order of nanometers, over a regular timescale of nanoseconds. MD simulations of such microscopic systems are relevant when the systems are able to represent the time evolution of corresponding macroscopic systems.

The theory behind MD is described briefly in the following sections. For a more detailed understanding, you are advised to refer to the dedicated literature on MD theory (Computer Simulation of Liquids by Michael P. Allen and Dominic J. Tildesley, and Understanding Molecular Simulation by Daan Frenkel and Berend Smit).