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 friction-based pair style

In this section, a frictional force is implemented on spherical atoms that depends on the tangential time of contact and the tangential velocity difference of two interacting atoms, via the Cundall-Strack scheme (https://doi.org/10.1007/978-94-017-2653-5_22).

In the Cundall-Strack scheme, also known as Coulomb friction, a tangential frictional force, , acts on two spheres in contact that increases with the relative tangential velocities of the spheres up to an upper bound value. It is assumed that, during prolonged contact between the spheres, an imaginary spring of spring constant is extended by a length owing to the relative tangential velocity () and it exerts an opposing force on the spheres to mimic the frictional force. In addition, a drag force is exerted based on a drag coefficient (A) and that also acts tangentially to impede rotational motion.

The frictional and drag forces are pegged at an upper limit defined by , where is the...