$$ \newcommand{\Oof}[1]{\mathcal{O}(#1)} \newcommand{\F}{\boldsymbol{F}} \newcommand{\J}{\boldsymbol{J}} \newcommand{\x}{\boldsymbol{x}} \renewcommand{\c}{\boldsymbol{c}} $$

Contents
- Preface
- Why learn programming?
- Target audience and background knowledge
- Numerical methods
- The computer language: Python
- How this book is different
- Supplementary materials
- Acknowledgments
- The first few steps
- What is a program? And what is programming?
- A Python program with variables
- The program
- Dissection of the program
- Why not just use a pocket calculator?
- Why you must use a text editor to write programs
- Installation of Python
- Write and run your first program
- A Python program with a library function
- A Python program with vectorization and plotting
- More basic concepts
- Using Python interactively
- Arithmetics, parentheses and rounding errors
- Variables and objects
- Integer division
- Formatting text and numbers
- Arrays
- Plotting
- Error messages and warnings
- Input data
- Symbolic computations
- Concluding remarks
- Exercises
- Exercise 1: Error messages
- Exercise 2: Volume of a cube
- Exercise 3: Area and circumference of a circle
- Exercise 4: Volumes of three cubes
- Exercise 5: Average of integers
- Exercise 6: Interactive computing of volume and area
- Exercise 7: Peculiar results from division
- Exercise 8: Update variable at command prompt
- Exercise 9: Formatted print to screen
- Exercise 10: Python documentation and random numbers
- Basic constructions
- If tests, colon and indentation
- Functions
- For loops
- While loops
- Lists and tuples - alternatives to arrays
- Reading from and writing to files
- Exercises
- Exercise 11: Errors with colon, indent, etc.
- Exercise 12: Compare integers a and b
- Exercise 13: Functions for circumference and area of a circle
- Exercise 14: Function for area of a rectangle
- Exercise 15: Area of a polygon
- Exercise 16: Average of integers
- Exercise 17: While loop with errors
- Exercise 18: Area of rectangle versus circle
- Exercise 19: Find crossing points of two graphs
- Exercise 20: Sort array with numbers
- Exercise 21: Compute $ \pi $
- Exercise 22: Compute combinations of sets
- Exercise 23: Frequency of random numbers
- Remarks
- Exercise 24: Game 21
- Exercise 25: Linear interpolation
- Exercise 26: Test straight line requirement
- Exercise 27: Fit straight line to data
- Remarks
- Exercise 28: Fit sines to straight line
- Remarks
- Exercise 29: Count occurrences of a string in a string
- Remarks
- Computing integrals
- Basic ideas of numerical integration
- Computational example
- The composite trapezoidal rule
- The general formula
- Implementation
- Specific or general implementation?
- Implementation with functions
- Solving our specific problem in a session
- Solving our specific problem in a program
- Making a module
- Alternative flat special-purpose implementation
- The composite midpoint method
- The idea
- The general formula
- Implementation
- Comparing the trapezoidal and the midpoint methods
- Testing
- Problems with brief testing procedures
- Proper test procedures
- Hand-computed results
- Solving a problem without numerical errors
- Demonstrating correct convergence rates
- Finite precision of floating-point numbers
- Constructing unit tests and writing test functions
- Hand-computed numerical results
- Solving a problem without numerical errors
- Demonstrating correct convergence rates
- Vectorization
- Vectorizing the midpoint rule
- Vectorizing the trapezoidal rule
- Measuring computational speed
- Double and triple integrals
- The midpoint rule for a double integral
- Derivation via one-dimensional integrals
- Direct derivation
- Programming a double sum
- Reusing code for one-dimensional integrals
- Verification via test functions
- The midpoint rule for a triple integral
- Theory
- Implementation
- Monte Carlo integration for complex-shaped domains
- The Monte Carlo integration algorithm
- Implementation
- Verification
- Test function for function with random numbers
- Integral over a circle
- Exercises
- Exercise 30: Hand calculations for the trapezoidal method
- Exercise 31: Hand calculations for the midpoint method
- Exercise 32: Compute a simple integral
- Exercise 33: Hand-calculations with sine integrals
- Exercise 34: Make test functions for the midpoint method
- Exercise 35: Explore rounding errors with large numbers
- Exercise 36: Write test functions for $ \int_0^4\sqrt{x}dx $
- Remarks
- Exercise 37: Rectangle methods
- Exercise 38: Adaptive integration
- Remarks
- Exercise 39: Integrating x raised to x
- Exercise 40: Integrate products of sine functions
- Exercise 41: Revisit fit of sines to a function
- Exercise 42: Derive the trapezoidal rule for a double integral
- Exercise 43: Compute the area of a triangle by Monte Carlo integration
- Solving ordinary differential equations
- Population growth
- Derivation of the model
- Numerical solution
- Programming the Forward Euler scheme; the special case
- Understanding the Forward Euler method
- Programming the Forward Euler scheme; the general case
- Making the population growth model more realistic
- Verification: exact linear solution of the discrete equations
- Spreading of diseases
- Spreading of a flu
- A Forward Euler method for the differential equation system
- Programming the numerical method; the special case
- Outbreak or not
- Abstract problem and notation
- Programming the numerical method; the general case
- Time-restricted immunity
- Incorporating vaccination
- Discontinuous coefficients: a vaccination campaign
- Oscillating one-dimensional systems
- Derivation of a simple model
- Numerical solution
- Programming the numerical method; the special case
- A magic fix of the numerical method
- The 2nd-order Runge-Kutta method (or Heun's method)
- Software for solving ODEs
- The 4th-order Runge-Kutta method
- The algorithm
- Application
- Implementation
- Derivation
- More effects: damping, nonlinearity, and external forces
- The Euler-Cromer scheme
- The 4-th order Runge-Kutta method
- Illustration of linear damping
- Illustration of linear damping with sinusoidal excitation
- Spring-mass system with sliding friction
- A finite difference method; undamped, linear case
- A finite difference method; linear damping
- Exercises
- Exercise 44: Geometric construction of the Forward Euler method
- Exercise 45: Make test functions for the Forward Euler method
- Exercise 46: Implement and evaluate Heun's method
- Exercise 47: Find an appropriate time step; logistic model
- Exercise 48: Find an appropriate time step; SIR model
- Exercise 49: Model an adaptive vaccination campaign
- Exercise 50: Make a SIRV model with time-limited effect of vaccination
- Exercise 51: Refactor a flat program
- Exercise 52: Simulate oscillations by a general ODE solver
- Exercise 53: Compute the energy in oscillations
- Exercise 54: Use a Backward Euler scheme for population growth
- Exercise 55: Use a Crank-Nicolson scheme for population growth
- Exercise 56: Understand finite differences via Taylor series
- Exercise 57: Use a Backward Euler scheme for oscillations
- Remarks
- Exercise 58: Use Heun's method for the SIR model
- Exercise 59: Use Odespy to solve a simple ODE
- Exercise 60: Set up a Backward Euler scheme for oscillations
- Exercise 61: Set up a Forward Euler scheme for nonlinear and damped oscillations
- Exercise 62: Discretize an initial condition
- Solving partial differential equations
- Finite difference methods
- Reduction of a PDE to a system of ODEs
- Construction of a test problem with known discrete solution
- Implementation: Forward Euler method
- Application: heat conduction in a rod
- Vectorization
- Using Odespy to solve the system of ODEs
- Implicit methods
- Exercises
- Exercise 63: Simulate a diffusion equation by hand
- Exercise 64: Compute temperature variations in the ground
- Exercise 65: Compare implicit methods
- Exercise 66: Explore adaptive and implicit methods
- Exercise 67: Investigate the $ \theta $ rule
- Remarks
- Exercise 68: Compute the diffusion of a Gaussian peak
- Remarks
- Exercise 69: Vectorize a function for computing the area of a polygon
- Exercise 70: Explore symmetry
- Remarks
- Exercise 71: Compute solutions as $ t\rightarrow\infty $
- Remarks
- Exercise 72: Solve a two-point boundary value problem
- Solving nonlinear algebraic equations
- Brute force methods
- Brute force root finding
- Numerical algorithm
- Implementation
- Brute force optimization
- Numerical algorithm
- Implementation
- Model problem for algebraic equations
- Newton's method
- Deriving and implementing Newton's method
- Making a more efficient and robust implementation
- The secant method
- The bisection method
- Rate of convergence
- Solving multiple nonlinear algebraic equations
- Abstract notation
- Taylor expansions for multi-variable functions
- Newton's method
- Implementation
- Exercises
- Exercise 73: Understand why Newton's method can fail
- Exercise 74: See if the secant method fails
- Exercise 75: Understand why the bisection method cannot fail
- Exercise 76: Combine the bisection method with Newton's method
- Exercise 77: Write a test function for Newton's method
- Exercise 78: Solve nonlinear equation for a vibrating beam
- Appendix: Getting access to Python
- Required software
- Anaconda and Spyder
- Spyder on Mac
- Installation of additional packages
- How to write and run a Python program
- The need for a text editor
- Text editors
- Terminal windows
- Using a plain text editor and a terminal window
- Spyder
- The SageMathCloud and Wakari web services
- Basic intro to SageMathCloud
- Basic intro to Wakari
- Installing your own Python packages
- Writing IPython notebooks
- A simple program in the notebook
- Mixing text, mathematics, code, and graphics
- References

Anaconda and Spyder

Anaconda is a free Python distribution produced by Continuum Analytics and contains about 200 Python packages, as well as Python itself, for doing a wide range of scientific computations. Anaconda can be downloaded from http://continuum.io/downloads. Choose Python version 2.7.

The Integrated Development Environment (IDE) Spyder is included with Anaconda and is our recommended tool for writing and running Python programs on Mac and Windows, unless you have preference for a plain text editor for writing programs and a terminal window for running them.

Spyder on Mac

Spyder is started by typing spyder in a (new) Terminal application. If you get an error message unknown locale, you need to type the following line in the Terminal application, or preferably put the line in your $HOME/.bashrc Unix initialization file:

export LANG=en_US.UTF-8; export LC_ALL=en_US.UTF-8

Installation of additional packages

Anaconda installs the pip tool that is handy to install additional packages. In a Terminal application on Mac or in a PowerShell terminal on Windows, write

pip install --user packagename