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

Discovering the Group class

In this section, we will discuss the source code in group.cpp that's responsible for controlling groups of atoms via the Group class (see https://lammps.sandia.gov/doc/group.html).

Using groups, a set of atoms can be combined as one collective group, which facilitates uniform treatment of the group members when applying fixes. It also allows mathematical operations to be performed on the group.

Groups can be defined based on criteria such as the type and region of atoms, and atoms are registered to groups using the assign() method. The following code snippet illustrates grouping atoms by region occupied:

Figure 8.1 – Code snippet from the Group:assign() method showing atom selection by region

By looping over all the atoms in the core (line 187), the atoms located in a given region with a region ID, iregion, are selected via bitwise operation (line 189).

The following screenshot shows the union of multiple groups...