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

Reviewing the compute heat flux class

In this section, we will study the source code for the compute heat flux class, which is contained in compute_heat_flux.cpp and compute_heat_flux.h.

The compute heat flux class accepts the per-atom kinetic energy, per-atom potential energy, and per-atom stress to calculate the heat flow (J). This can be calculated as follows:

In this equation, represents the sum of kinetic and potential energies of atom i, represents the velocity vector of atom i, represents the stress tensor of atom i, and V represents the volume occupied by the atoms in consideration. The summation of is the convective part of the heat flux, while the summation of is the virial part of the heat flux.

Therefore, this compute needs to read the kinetic energy, potential energy, and stress of atoms dynamically, and this is facilitated by feeding these quantities as other computes. So, effectively, compute heat flux accepts three other computes as input parameters...