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

Data exchange between owned atoms and ghost atoms

LAMMPS is able to run on a distributed-memory machine, requiring the communication among processors to be carried out by MPI. This is implemented by the Comm class and its two child classes that implement specific functionalities:

  • One of the child classes is CommBrick, described by comm_brick.h and comm_brick.cpp. In this Comm style, the simulation box is considered as a 3D grid where each block in the grid is assigned to a processor, which is responsible for communicating with its six neighboring blocks in the (x, y, z) directions to exchange information about neighboring atoms. This decomposition is especially suitable for uniform particle density, where every block can be expected to contain the same number of particles.
  • The other child class is CommTiled, described in comm_tiled.h and comm_tiled.cpp, which can adjust the processor domains dynamically and is more effective when the system particle density is non-uniform...