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 NH class

In this section, we'll discuss the role of the Fix NH class, which is implemented by fix_nh.cpp and fix_nh.h. The Fix NVT, Fix NPT, and Fix NPH classes inherit from this class when employing thermostats and barostats.

In this section, we will only focus on the thermostat functionalities of Fix NH for the sake of conciseness. Fix NH applies the Nose-Hoover thermostat, which introduces a virtual heat bath tethered to the simulated system. This heat bath can contain a 1D chain of virtual particles where the particle has mass , position , and momentum , which gives us the following velocity:

The time derivative of the velocity, , of an atom, i, being thermostatted is given by the following formula:

For a virtual particle, k, the is calculated by the following formula:

Here, is the difference between double the neighboring virtual particle's kinetic energy and its targeted kinetic energy, which is determined by its thermal energy...