Foundations of Programming and Software Engineering for Molecular Science

This course provides an overview of topics relevant to programming and creating software projects. Students will become familiar with tools and practices commonly used in software development such as version control, documentation, and testing. Central to this course is a hands-on molecular simulation project where students work in groups to create a software package using concepts taught in the course.

Pre-Bootcamp: Set-Up

Lesson Title	Questions	Objectives
Computer Set-Up	How do I set up my computer? How do I set up git and GitHub? What text editor should I use?	Use conda to create an environment and install packages. Install compilers for operating system. Set up credentials for GitHub.

Day 1

Lessons

Lesson Title	Questions	Objectives
Introduction to the Command Line	What is the command line? How can I navigate files and directories on the command line?	Learn basic shell commands for navigating and creating files and directories.
Introduction to Version Control with Git	What is version control? How do I use git to keep a record of my project? What is a branch and why would I use one? How do I tell git to ignore files?	Explain the purpose of version control Introduce common git commands. Understand how to view and check out previous versions of files.
Using GitHub	How is git different than GitHub? How do I use git and GitHub?	Explain difference between git and GitHub. Learn how to use and manage a repository on GitHub.
Code Collaboration using GitHub	How can others contribute to my project on GitHub? How can I contribute to the projects of others?	Explain collaboration workflow on GitHub. Understand how to open and review a pull request.

Discussions and Assignments

Type	Description
Discussion	Command Line and Git Review
Group Assignment	Submitting a Pull Request to a Central Repository

Day 2

Lessons

Lesson Title	Objectives	Questions
Intro to Monte Carlo Methods	Explain Monte Carlo methods. Apply Monte Carlo method to calculate pi. Apply Monte Carlo to calculate integrals	What are Monte Carlo methods? How can I use Monte Carlo to estimate pi?
The Lennard Jones Equation	Understand the Lennard Jones potential. Understand periodic boundary conditions.	How can Monte Carlo be applied to a thermodynamic problem? How do we model the interaction of nonbonded atoms?

Discussions and Assignments

Type	Description
Class Warm-up	Get to Know your Group
Group Assignment	Tasks: Monte Carlo Error,Lennard Jones,Distance Calculation
Individual Assignment 1	Contains the link to start Individual Assignment 1.

Day 3

Lessons

Lesson Title	Objectives	Questions
Lennard Jones Energy of Atomic System	Write Python code to calculate the Lennard Jones energy.	How do I use the Lennard Jones equation to calculate the energy of an atomic system?

Discussions and Assignments

Type	Description
Class Warm-up	Think Python and Energy Calculations
Group Discussion and Assignment	Simulation Cut-offs and Periodic Boundaries

Day 4

Lessons

Lesson Title	Objectives	Questions
Total Energy Comparison	Apply a cut-off and periodic boundaries to the energy calculation and compare it to values reported by NIST.	Does my total energy agree with the values reported from NIST?
Monte Carlo for a Lennard Jones Fluid	Use the Metropolis algorithm to sample configurations of LJ particles	How do I write a Monte Carlo simulation?

Discussions and Assignments

Type	Description
Class Warm-up	Explain XCKD and Code Changes
Group Assignment and Discussion	Acceptance probability, Performance, Starting configurations

Day 5

Lessons

Lesson Title	Objectives	Questions
Working with Numpy Arrays	Be able to name the differences between Python lists and numpy arrays. Understand the idea of broadcasting.	What are the differences between NumPy arrays and lists? How can I use NumPy to do calculations?
Rewriting the Distance Function	Rewrite calculate distance function for numpy arrays	How can I rewrite functions to take advantage of NumPy element-wise operation and broadcasting?
Creating a Python Module	Put Python code into a module (.py file) Import functions from our module.	What is a Python module?

Discussions and Assignments

Type	Description
Class Warm-up	Warm Up Quiz and Debugging
Group Assignment and Discussion	NumPy and MC Calculations
Individual Assignment 2	Individual Assignment 2

Day 6

Lessons

Lesson Title	Objectives	Questions
Introduction to C++	Explain static and dynamic typing Explain basic C++ structure and syntax, comparing/contrasting with python Introduce compiling from the command line	What is the difference between compiled and interpreted languages? What are the main advantages of C++ vs python? What are some similarities between python and C++?
First C++ Program	Be able to write and build a minimal C++ program Be able to debug compiler errors	How do I write and compile a minimal C++ program? What are the basic constructs of C++? How do I handle compile errors?

Discussions and Assignments

Type	Description
Class Warm-up	Counting function calls
Group Assignment	Python and C++ Discussion and Integration via Summation

Day 7

Lessons

Lesson Title	Objectives	Questions
Common data types	Learn about the built-in data types in C++, and what they are used for	What are the common, built-in data types in C++pointers and references in C++ When should I use each data type?
Arrays, Pointers, Memory, and Vectors	To learn about pointers To learn about different ways of representing lists/arrays of data	What are pointers and references in C++ Why/when should I use a pointer or reference? Pitfalls of using pointer

Discussions and Assignments

Type	Description
Class Warm-up	Programming Design Recipe
Group Assignment	Monte Carlo C++ rewrite
Individual Assignment	Individual Assignment 3

Day 8

Lessons

Lesson Title	Objectives	Questions
Function Calling and Arguments	Learn about C++ functions and argument passing Learn about the const keyword Learn about returning multiple things from a function	How do functions differ in C++ and Python? How are arguments passed in C++? How can we protect variables (and function arguments) from changing?
Namespaces	Learn about grouping functions and objects with namespaces	How can we group functions together under a single collection? How can I prevent collisions with functions having the same name in other libraries?
Exceptions	Learn about throwing and catching exception in C++	How do we handle major errors in C++? How do exceptions differ from python?

Discussions and Assignments

Type	Description
Class Warm-up	UC Berkeley Libraries
Group Assignment	Monte Carlo C++ rewrite
Final Project	Final Project Assignment

Day 9

Lessons

Lesson Title	Objectives	Questions
Multi-file projects	Learn how the C++ compiler preprocesses files Learn the difference between header and source files Learn how to include intra-project header files	How can we split a large C++ project into multiple files

Discussions and Assignments

Type	Description
Class Warm-up	Python and C++ - Function Arguments
Individual Assignment	Individual Assignment 4