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

Writing a fix to print output at evaporation

Here is a list of changes made to the source code:

  • These are the new files created: fix_printEvaporate.cpp and fix_printEvaporate.h
  • These are the existing files that have been modified: fix_print.cpp and fix_print.h
  • These are the methods that have been modified: constructor, destructor, init(), end_of_step()
  • These are the parameters used: iregion, idregion
  • LAMMPS syntax: fix FIX_NAME GROUP printEvaporate N STRING region R (we'll look at this syntax later in this section)

In this section, we will modify Fix Print to print out specified quantities when an atom enters into a particular region, as might be useful when simulating desorption.

Theory – Evaporation region

When studying the desorption of particles that are adsorbed on a surface, it is assumed that a particle has desorbed when it crosses a certain threshold or enters a certain region, usually located far from the surface where the interaction...