Dr. Shafat Mubin - Extending and Modifying LAMMPS Writing Your Own Source Code: A pragmatic guide to extending LAMMPS as per custom simulation requirements

A pragmatic guide to extending LAMMPS as per custom simulation requirements

Dr. Shafat Mubin

Jichen Li

BIRMINGHAMMUMBAI

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All praise is to Allah, the most merciful, the most gracious.

Dr. Shafat Mubin

To all the people who make the world better.

Jichen Li

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Many users of LAMMPS think of it as a tool that provides various features; they likely never look at the source code itself, which is a perfectly fine way to use it. But if you want LAMMPS to do something a little different than what it already does, or you have an idea for something completely new that LAMMPS could do, and you either don't know where to start or want a big-picture view of how to go about it, then this book is for you.

It gives a gentle introduction to how the LAMMPS source code is structured, how to find the code that corresponds to specific features of a LAMMPS input script so you can see how it works, and how to modify or write new code to implement new options or new commands that you want to add to LAMMPS. Most importantly, in my view, it gives some concrete and non-trivial examples of features in different categories (what LAMMPS calls styles) that could be added in the code.

If you follow the step-by-step explanations and instructions provided in this book, you will have a sound understanding of how to do the preceding activities yourself for some new idea you care about in your own research. In fact, about 95% of the LAMMPS source code are styles, which the developers or users added to the code in the same manner and for the same reasons. They wanted to alter an existing model, formulate a new one, or measure a new property, so that LAMMPS could be used to tackle a new problem.

Finally, if you follow the methodologies explained in this book and write some new code for LAMMPS that you think will be useful to others, I hope you will consider submitting it on the LAMMPS GitHub site for possible inclusion in the distribution. That is how many features in current LAMMPS came to be. And it is how its user community continues to help the code grow and become a more useful tool.

Dr. Steven Plimpton

Lead developer of LAMMPS

Dr. Shafat Mubin (PhD in physics, Penn State) is an assistant professor of physics at Valdosta State University. Since his graduate student days, he has worked with molecular simulations primarily using LAMMPS and has investigated a variety of simulation systems employing a wide array of techniques. He possesses extensive experience in writing custom routines and extending the LAMMPS source code and hosts his own website to instruct and demonstrate how to do so to other users. At present, he is engaged in computational physics research, including molecular simulations, and endeavors to train undergraduate students in computational techniques to help them better prepare for careers in physics.

I want to thank the people who have supported me, especially Farhana.

Jichen Li (graduated from Qingdao University of Science and Technology) is now studying for his masters degree at the University of Science and Technology of China. He has used LAMMPS to conduct molecular simulations to explore the relationship between polymer microstructure and macro mechanical and rheological properties. He has developed several modeling and post-processing frameworks for LAMMPS and possesses a thorough understanding of its program architecture. He is dedicated to community learning and contributes to the community through his website, where he has written several columns and tutorials for LAMMPS beginners. At present, he is working on trans-scale simulation and the combination of deep learning and simulation.

I would like to thank my parents for their encouragement, Peiyuan Wang, for his support, and my tutor, Jianhui Song, who led me to the field of molecular dynamics.

Jie Peng is a postdoc from the School of Material Science at Purdue University, US. He has great experience in the area of physics and material engineering. He graduated from the Shanghai Jiao Tong University (China) with a bachelors and a masters degree, and obtained his PhD from the University of Maryland (US) in May 2019. He likes working in interdisciplinary areas where he can see the fundamental science behind materials behavior while being able to exploit his knowledge to make use of these materials. He studies the least amount of energy that is transferred in materials electrons and phonons. The goal is to understand the law of energy transfer at the nanoscale, at which most modern devices operate cell phones, computers, and so on.