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 apply an active force

The following is a list of changes that should be made to the source code:

  • The new files that should be created are fix_activeforce.cpp and fix_activeforce.h.
  • The existing files that are modified are fix_addforce.cpp, fix_addforce.h, and compute_bond_local.cpp.
  • The methods that are modified are constructor, post_force().
  • The input parameters are fMagnitude, and direction.
  • The other quantities introduced in this section can be seen in a full list in Figure 10.9 under post_force().
  • The LAMMPS syntax is fix FIX_NAME GROUP activeforce FMAGNITUDE DIRECTION (we'll review the syntax in this section).

In this section, we will create an active force in Fix Activeforce that applies a specified magnitude of force along the direction defined by two bonded atoms.

Theory (active force on bonded atoms)

An active force is generated by an atom and acts on the same atom. In this example, the active force acts on an...