Assignment 3 - Chemistry Solver

Due: 2018-05-04

Your next assignment is to develop an ODE solver that follows the evolution of the nine species of H, H+, H-, He, He+, He++, H2, H2+ and e-.

You can use the Grackle method paper for this assignment.

• Look up the chemical kinetic rate equations
• Develop a right-hand side calculation. You may do this by hand, or using SymPy as we did in class.
• Calculate the rate coefficients as a function of temperature; you can assume an ideal gas law for the temperature.
• Utilize the SciPy integrators to evolve a network of reactions drawn from the Grackle methods paper.

You will have until May 4. (May the Fourth be with you.)

You should produce the following items:

• Python code that runs from the command line that accepts
  • Initial H ionization fraction
  • Initial He ionization fraction
  • Molecular hydrogen fraction
  • Density
  • Time to evolve to
  • Integrator to use inside scipy.integrate.ode
• An integrator that updates based on some safety factor until the time is reached
• A set of visualizations that show overall change in the various fractions.
• A writeup

Write-Up

Your code must be documented; this does not mean extensive comments, but it does mean that each routine must have a brief outline of what it is doing. You must also provide a notebook or other report that walks through how to utilize the code and what to expect.

You must evaluate the following items:

• When is it slower and faster? When it is near equilibrium or far?
• Do you see any particularly interesting regions in phase space?
• What was easy or hard?