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

Writing a height-dependent pair potential

In this section, we will create a pair style that represents a potential between two atoms, which decays as the height increases from a reference level, so that both the distance between the atoms and the heights of the atoms above the reference determine the potential between them.

A height-dependent potential is relevant when simulating the interaction between atoms that are adsorbed on a substrate, where forces mediated by the substrate vary with the height. As a result, along with the usual inter-molecular interactions, two adsorbed atoms on the substrate experience additional interaction by virtue of their proximity to the substrate. At a certain threshold above the substrate, the interaction decays to zero. An example of such an interaction is the McLachlan interaction (https://doi.org/10.1016/0039-6028(94)91259-9) based on repulsion between dipoles of adsorbed atoms and the substrate.

A model is established where represents the...