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

Analyzing the Fix Wall and Fix Wall/LJ126 classes

In molecular dynamics, a wall serves as a boundary condition that exerts a force on an atom that approaches its interaction range. Unlike forces exerted by typical atoms, the wall force is not radially symmetric and is usually perpendicular to the wall. The Fix Wall class creates such planar walls that are perpendicular to the x, y, or z axis and can exert forces according to pre-defined potential functions in its child classes.

In a LAMMPS input script, the corresponding syntax for implementing a wall is as follows:

fix  FIX_ID  GROUP_ID  WALL_STYLE  FACE  COORDS  …

The parameters described in the manual (https://lammps.sandia.gov/doc/fix_wall.html) include WALL_STYLE, which is the type of potential between the wall and an atom, such as Lennard-Jones (LJ), Morse, and Harmonic; FACE, which is the direction that the wall is facing in, and can be one of ; and...