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 general structure of computes

In this section, we will briefly cover some of the methods most commonly used in compute child classes.

Similar to pair styles, individual computes inherit from the parent Compute class described by compute.cpp and compute.h classes. These parent classes read the first three arguments (compute ID, group ID, and compute style) from the LAMMPS input script. The following screenshot shows some of the variables and arrays from compute.h that are inherited:

Figure 6.1 – Code snippet from compute.h

The child compute classes may contain one or more of the following methods:

  • The init() method sets up the class and performs preliminary validation checks.
  • The init_list() method sets up neighbor lists or pointers to neighboring lists.
  • The compute_scalar() method computes a scalar quantity generally used as an output.
  • The compute_vector() method computes a vector quantity generally used as an output...