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

Insight into sbmask()

Bitmask is a widely used technique to validate authority, often using the bitwise AND operation for fast operations. A well-known example is the subnet mask, which operates on IP addresses in a network and yields the routing prefix. In the context of bonded atoms in LAMMPS, sbmask() uses the same mechanism to identify whether a particle is linked by a special bond.

In order to analyze bitmask operations in the LAMMPS source code, we now return to the example LAMMPS script (test.in) and pair_lj_cut.cpp implemented as pair style lj/cut. As described in Chapter 4, Accessing Information by Variables, Arrays, and Methods, the ilist array represents a collection of central atoms to loop over, and the jlist array represents the corresponding neighbors of each member of ilist. Recall that in our example LAMMPS script, the cutoff radius is 5.5 units, so the first atom (i=0) has five pairwise atoms (j) interacting with it.

A short simulation run is performed and using...