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 group/group class

In this section, we will analyze a more elaborate compute that employs a larger number of methods.

The interaction energy and the forces between two groups of atoms can be obtained using compute group/group and are implemented by the compute_group_group.cpp and compute_group_group.h classes. The LAMMPS input script command to implement this compute is as follows:

compute  COMPUTE_ID  G1  group/group  G2   

The COMPUTE_ID parameter is the unique ID of the compute, while the G1 and G2 parameters are the IDs of the groups of atoms that the compute acts on (see manual: https://lammps.sandia.gov/doc/compute_group_group.html). The optional parameter keywords listed in the manual can be entered after these parameters to specify other options, such as the interaction type (pair potential or electrostatic) and molecule ID (same or different). The constructor method accommodates these optional...