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

Stages of executing the simulation

A LAMMPS simulation is executed by iterating over timesteps (for example, velocity Verlet integration) or through algorithms that do not perform timestepping (for example, minimization). Next, we will describe the Verlet integration scheme as implemented in verlet.cpp and then briefly outline the minimization scheme implemented in min.cpp.

verlet.cpp

The verlet.cpp class implements timestepping through a series of methods that are executed in a pre-defined order. At the beginning of a timestep, the following methods in verlet.cpp are called:

  • init(): This method checks whether fixes are defined in the input script and sets up flags for arrays, shown as follows:

Figure 3.10 – Code snippet from verlet.ccp showing the init() method

  • force_clear(): This method clears forces on all atoms to store combined forces during the course of the timestep:

Figure 3.11 - Code snippet...