Foregrounding the Code: Computational Chemistry Instructional Activities Using a Highly Readable Fluid Simulation Code,Journal of Chemical Education

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Foregrounding the Code: Computational Chemistry Instructional Activities Using a Highly Readable Fluid Simulation Code
Journal of Chemical Education ( IF 2.5 ) Pub Date : 2023-02-07 , DOI: 10.1021/acs.jchemed.2c00838
Gianmarc Grazioli ₁ , Adam Ingwerson ₁ , David Santiago ₁ , Patrick Regan ₁ , Heekun Cho ₁

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Computational chemistry instructional activities are often based around students running chemical simulations via a graphical user interface (GUI). GUI-based activities offer many advantages, as they enable students to run chemical simulations with a few mouse clicks. Although these activities are excellent for introducing students to the capabilities of chemical simulations, the disadvantage is that the students’ experience is not representative of how professional computational chemists work. Just as it is important that students in an organic chemistry instructional lab gain hands-on experience with equipment commonly used by professional organic chemists, students of computational chemistry must gain hands-on experience with coding, as professional computational chemists do not rely on GUIs; we write code. Motivated by the need for instructional activities that provide hands-on experience with computer code, a pair of activities were created around a free lightweight (runs on standard laptops) open-source Lennard-Jones (LJ) fluid simulation code written in Python, a programming language that prioritizes readability. The first activity, aimed at undergraduate physical chemistry lab courses, involves students writing Python code in a Jupyter Notebook that is used to run LJ simulations and fit a van der Waals gas model to data produced by the LJ fluid simulations. The second is a jigsaw activity, aimed at advanced undergraduate or graduate students, where students are assigned different sections of the LJ fluid simulation code, and must demonstrate the functionality of their section to the class by both giving an oral presentation and sharing a Jupyter Notebook demonstration of their own design.

中文翻译：

突出代码：使用高度可读的流体模拟代码的计算化学教学活动

计算化学教学活动通常基于学生通过图形用户界面 (GUI) 运行化学模拟。基于 GUI 的活动具有许多优势，因为它们使学生只需单击几下鼠标即可运行化学模拟。虽然这些活动非常适合向学生介绍化学模拟的能力，但缺点是学生的经验并不能代表专业计算化学家的工作方式。正如有机化学教学实验室的学生获得专业有机化学家常用设备的实践经验很重要一样，计算化学的学生也必须获得编码方面的实践经验，因为专业计算化学家不依赖 GUI；我们写代码。出于对提供计算机代码实践经验的教学活动的需求，围绕一个免费的轻量级（在标准笔记本电脑上运行）开源 Lennard-Jones (LJ) 流体模拟代码创建了一对活动，该代码是用 Python 编写的，一个优先考虑可读性的编程语言。第一项活动针对本科物理化学实验室课程，涉及学生在 Jupyter 笔记本中编写 Python 代码，该笔记本用于运行 LJ 模拟并将范德瓦尔斯气体模型拟合到 LJ 流体模拟产生的数据。第二个是拼图活动，针对高年级本科生或研究生，学生被分配到 LJ 流体模拟代码的不同部分，

更新日期：2023-02-07

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