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 the Andersen thermostat

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

  • These are the new files that have been created: fix_temp_andersen.cpp and fix_temp_andersen.h
  • These are the existing files that have been modified: fix_temp_berendsen.cpp and fix_temp_berendsen.h.
  • These are the methods that have been modified: constructor, and end_of_step()
  • These are the input parameters: andFreq, seedMB, sigmaMB
  • These are the other quantities introduced: random, me
  • LAMMPS syntax: fix FIX_NAME GROUP temp/andersen FREQUENCY SEED SIGMA (we'll review this syntax later in this section)

In this section, we will write a fix to apply the Andersen thermostat that adjusts the temperature of particles by assigning random velocities to them at specified intervals.

Theory – Andersen thermostat

Based on the concept of velocity and momentum adjustments upon stochastic collisions in an atomistic system, the Andersen thermostat...