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

Incorporating new data types

When a certain data type does not exist in the standard C++ repository, it can be created and incorporated in the LAMMPS source code by defining it appropriately in lmptype.h. For example, the tagint data type described earlier in tagint **bond_atom = atom->bond_atom is a variation of the int data type. This tagint data type has been defined in lmptype.h, as shown in the following screenshot:

Figure 4.12 – Code snippet from lmptype.h showing the declaration of the tagint and bigint data types

As you can see, the built-in typedef function in C++ can be used to declare new data types with custom properties in lmptype.h, and these data types can be accessed in the rest of the source code.

Generally, int is a 4-byte (32-bit) data type by default, which means it can accommodate a 10-digit number up to . Sometimes, if a simulation system has to accommodate a larger number, we can use typedef to alias the int (32 bit) and...