Chapter 0 Python Jupyter Notebooks Scientific Computing For

Python is a popular programming language available on all major computer platforms, including macOS, Linux, and Windows. It is a scripting language, which means that the moment the user presses the Return key or Run, the Python software interprets and runs the code. This is in contrast to a compiled language like C, where the code must first be translated into binary (i.e., machine language) before it can be run. On-the-fly interpretation makes Python quick to use and often provides the user with rapid results. This is ideal for scientific data analysis, where the user is routinely making changes to the processing and visualization of the data. Python is free, open-source software and is maintained by the non-profit Python Software Foundation.

This is appealing for two major reasons. The first is that it is widely, freely, and irrevocably available to anyone who wants to use it, regardless of budget. With proprietary software, which is more and more commonly offered under a subscription model, if a company stops offering or updating a software package, it may simply become unavailable, leaving users without the software... Second, it is open source, so anyone can inspect and modify the code. This allows anyone to review the code to ensure it does what it claims instead of relying on the assertions of the software distributor. Another reason to use Python over other options, free or otherwise, is the power and the community support available to Python users.

Python is a common and popular programming language that has been applied to a wide variety of applications, including data analysis, visualization, machine learning, robotics, web scraping, 3D graphics, and more. As a result, there is a large community built around Python that provides valuable support for those who need assistance. If you are stuck on a problem or have a question, a quick internet search will likely provide the answer. Common internet forums include stackexchange.com or stackoverflow.com among others. If you have a question or need help on something, you are probably not the first person to ask that question. Along with Python, this book uses the IPython environment and Jupyter notebooks as a medium for running and sharing Python code.

More details are given below on Jupyter notebooks, but for now, know that they provide interactive environments ideal for scientific computing. In addition, we will use a variety of free, open-source libraries to provide collections of useful functions for scientific data processing, analysis, and visualization. Think of a library as an add-on or tool pack for Python, and there are many to choose from. Software installation instructions may have changed since these instructions were written and may vary depending on the operating system. The following is the textbook used for the Scientific Computing Chemists course intended to teach chemists and chemistry students basic computer programming in Python and Jupyter Notebooks and advanced tools for the processing, visualization,... This book serves as an introduction to coding for chemists.

A chapter outline is provided below. The book starts with a streamlined introduction to Python for chemists followed by introducing powerful computing tools and numerous applications to chemistry. This book assumes that the student or reader has no prior programming experience and has at least one year of undergraduate chemistry background and ideally some very basic spectroscopy/spectrometry (i.e., NMR, IR, UV-vis, and... All software used (e.g., Python, NumPy, SciPy, etc.) is free and open source software and runs on macOS, Windows, and Linux. This book is periodically updated to fix typos, account for new software versions, and add new content. The most recent version can be viewed using the link above, downloaded, or forked using Git or GitHub.

Reports of errors and information on how people are using this book are always welcome. The book is copyright © 2017-2025 Charles J. Weiss and is released under the CC BY-NC-SA 4.0 license. All files with the book are also copyright and released under the CC BY-NC-SA 4.0 license unless otherwise noted (see README.txt files for more information). Answer keys to exercises are available to instructors upon request by emailing me using your school email address. The answer keys are © Charles J.

Weiss and are not released under a Creative Commons license. Estimated time to complete: 60 to 90 minutes. Welcome to the online materials for this online course on programming in Python for mathematical computing (a.k.a. scientific computing). This first unit is an introduction to some basic features of the Python software that we will be using. Specifically, we use Python 3, and even more specifically, Python version 3.9 or higher.

We start directly with Jupyter notebooks via the tool JupyterLab as a way to use Python interactively like a scientific calculator, and aim to work with these notebooks as much as possible. Later, we will also learn the more advanced code development tools offered by the Integrated Development Environment Spyder. This supports both both interactive use of Python and also working with files of Python code: creating, opening and editing files, running and debugging code, and so on. It has more advanced tools for developing Python code than the Jupyter notebook system, so for more substantial programming tasks it can be better to develop code within Spyder — even if that code... Attribution-NonCommercial-ShareAlike CC BY-NC-SA This book serves as an introduction to coding for chemists.

The tools employed in this book are the powerful and popular combination of Jupyter notebooks and the Python programming language. No background beyond first-year college chemistry and occasionally some very basic spectroscopy (for advanced chapters) is assumed for most of this book. This book starts with a brief primer on Jupyter notebooks in chapter 0 and computer programming with Python in chapters 1 and 2. If you already have a background in these tools, feel free to skip ahead. The rest of the book dives into applications of Python to solving chemical problems. Python and Jupyter were chosen for a variety of reasons, including that they are:

Learning to use a number of popular Python scientific libraries to solve chemical problems is one of the themes of this book. A Python library can be thought of as a tool pack with premade functions for performing common tasks in scientific data processing, analysis, and visualization. For example, the matplotlib library provides a variety of functions for creating a wide range of plots, while the scikit-learn library contains functions and resources for machine learning. Dr. Charlie Weiss' interests span the areas of organic and inorganic chemistry, along with scientific computing. He earned a bachelor's degree from Carleton College, Ph.D.

from Northwestern University and completed his postdoctoral work in the electrocatalysis group at Pacific Northwest National Laboratory. His research has historically centered around the development of organometallic complexes and catalysts for organic reactions, but has more recently moved into digital data analysis and visualization using Python and Jupyter notebooks. His GitHub page is at github.com/weisscharlesj. An online text used for a Scientific Computing chemistry course[1] intended to teach undergraduate chemistry students basic coding in Python and Jupyter Notebooks and advanced tools for processing, visualization, and analysis of digital data. This text assumes that the students have no prior programming experience and have at least one year of undergraduate chemistry background and some very basic spectroscopy/spectrometry (i.e., NMR, IR, UV-vis, and GC/MS) background. All software used (e.g., Python, NumPy, SciPy, etc…) is free and open source software.

[1] J. Chem. Educ. 2017, 94, 592-597 DOI: 10.1021/acs.jchemed.7b00078 and J. Chem. Educ.

2017, 94, 1904-1910 DOI: 10.1021/acs.jchemed.7b00395 Scientific Computing for Chemists with Python https://github.com/weisscharlesj/SciCompforChemists Scientific computing utilizes computers to aid in scientific tasks such as data processing and digital simulations, among others. The well-developed field of computational chemistry is part of scientific computing and focuses on utilizing computing to simulate chemical phenomena and calculate properties. However, there is less focus in the field of chemistry on the data processing side of computing, so this book strives to fill this void by introducing the reader to tools and methods for...

This book serves as an introduction to coding for chemists. The tools employed in this book are the powerful and popular combination of Jupyter notebooks and the Python programming language. No background beyond first-year college chemistry and occasionally some very basic spectroscopy (for advanced chapters) is assumed for most of this book. This book starts with a brief primer on Jupyter notebooks in chapter 0 and computer programming with Python in chapters 1 and 2. If you already have a background in these tools, feel free to skip ahead. The rest of the book dives into applications of Python to solving chemical problems.

Python and Jupyter were chosen for a variety of reasons, including that they are: Powerful and well-suited for solving chemical problems Cross-platform (e.g., runs on Windows, macOS, and Linux) Supplemented with numerous, specialized libraries for handling specific types of data or problems (e.g., machine learning) Supported by a helpful and welcoming community A set of lectures on scientific computing with Python, using IPython notebooks.

To open these notebooks in IPython, download the files to a directory on your computer and from that directory run: This will open a new page in your browser with a list of the available notebooks. Should this error [TerminalIPythonApp] WARNING | File not found: u'notebook' pop up, please install Jupyter by following the instructions and execute the following command to run the notebook: A PDF file containing all the lectures is available here: Scientific Computing with Python This is an experimental repo for Scientific Computing for Chemists with Python. See Scientific Computing for Chemists with Python for the updated version of this book.

This book and all associated files are copyright © 2022 Charles J. Weiss and are released under under the CC BY-NC-SA 4.0 license. Scientific Computing for Chemists: An Undergraduate Course in Simulations, Data Processing, and Visualization J. Chem. Educ. 2017, 94, 592-597 DOI: 10.1021/acs.jchemed.7b00078

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