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

Reviewing the compute KE class

In this section, we'll study the methods implemented in the compute KE class, which calculates kinetic energy of a group of atoms.

The kinetic energy (KE) of an atom of mass m and linear velocity is calculated using the following equation:

The compute_ke.cpp class can be used to calculate the kinetic energy of a specified group of atoms. In a LAMMPS input script, the corresponding syntax is as follows:

compute  COMPUTE_ID  GROUP_ID  ke

As you can see, the COMPUTE_ID parameter is the unique ID of the compute defined, while the GROUP_ID parameter is the ID of the group of atoms that the compute acts on. This is described in detail in the LAMMPS manual (https://lammps.sandia.gov/doc/compute_ke.html). First, we will look at the constructor method, ComputeKE::ComputeKE(), of this class.

ComputeKE::ComputeKE()

This constructor method inherits from the Compute parent class (line 26) and checks the number...