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 RDF class

In this section, we will look at the source code for the compute_rdf.cpp and compute_rdf.h classes, which govern the compute RDF class.

The compute RDF class calculates the radial distribution function (RDF) of a group of atoms and returns the normalized numbers of neighbors, sorted into bins that have a uniform radial width () and that extend from zero to a specified cutoff distance. The output is returned as a 1D array that can be used to plot an RDF histogram. For each atom, the value of its RDF (g(r)) at a distance, r, is calculated by taking the ratio of the number of its neighboring atoms (N), which are located in the distance range (r, ) from the atom, to the number of atoms that would have been located in the same range if the atom distribution were uniform.

To derive this function, we must divide the periphery space of a central atom into shells of width dr that each occupy a volume of :

From the preceding equation, dn(r) represents...