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

Prerequisites

Before starting the debugging process, a test LAMMPS executable file should be built. When building with CMake (see Appendix A, Building LAMMPS with CMake), adding a –D CMAKE_BUILD_TYPE=Debug flag assists in the debugging process since it does not optimize out any variable, that is, the compiler does not eliminate intermediate values.

After CMake configuration, it is fine if C++ flags only show up as –g in the build configuration. Also, it is advisable to rename the executable from lmp to lmp_test to distinguish it accordingly. The following screenshot shows the build configuration after executing the CMake configuration:

Figure 13.1 – Screenshot showing the build configuration by CMake

As you can see, having created an executable, we will apply debugging tools to analyze the purpose of the sbmask() method in pair_lj_cut.cpp. A data file (test.data) is created to construct a linear polymer chain consisting of 5 bonded atoms...