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

Translating Fix Widom into the 3Mar20 version

Once you download the current version (29Oct20) of LAMMPS, you need to copy the fix_widom.cpp and fix_widom.h files located in the src/MC folder to a temporary location. Use git reset –hard b3040db1e to revert back to the 3Mar20 version, and copy the fix_widom.cpp and fix_widom.h files back to the src/MC folder of this version, renamed as fix_widom_modified.cpp and fix_widom_modified.h, respectively.

Upon performing regular compilation (see Appendix A, Building LAMMPS with CMake) including the MC package, several errors are produced, some of which are shown in the following screenshot:

Figure 15.1 – A partial list of errors when compiling Fix Widom in the 3Mar20 version

As you can see, the errors can be categorized into the following:

  • Parsing input parameters with the Utils class
  • Identifying molecular systems using the Atom class
  • Additional function signatures in group.cpp
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