Physics 212, 2019: Lecture 13

From Ilya Nemenman: Theoretical Biophysics @ Emory
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Back to Physics 212, 2019: Computational Modeling.

Finishing up dynamical systems analysis

See previous lecture.

Verification of models

Look for small parameters! -- More in class.

Your code must be verified by running it for roughly as many independent special cases (where you know what the output should be) as there are parameters. The test cases should not be arbitrary, but the should meaningfully check the special values of the parameters.

Good coding practices

  1. Passing a variable number of arguments to a function, and how to further pass them alone in the context of ODE solvers, for example. See GrowthFunctions, Integrators, and Module 2 for details, or Sec 5.8, and specifically 5.8.3 in the textbook.
  2. You show avoid editing arguments to a function inside the function. Read Sec D.3 of the textbook for details.
  3. If you choose to edit arguments to a function inside the function, then don't return these changed variables at the same time: either edit the original object (argument), or make a copy (return), but not both at the same time.
  4. Always check that your while loops are not infinite.
  5. Use constants by their name (even if they only appear once), and not by their numerical values. Define constants in the preamble.
  6. Write floating point numbers explicitly as 1.0 and not 1, for example.
  7. Vectorize your math. See Sec 3.2.1 in the textbook.
  8. We talked about Scopes and name spaces, Sec E1 through E5.