Monte Carlo example issues

[mattagape]

1. what do we mean by density?

2. In MonteCarlo::random_agent(), what does enumerate() do?

3. In energy(), what is the coefficient for? It doesn't seem to be Beta, the coefficient mentioned above.

4. In accept_change(), how do we know that we should implement the following line? return exp(-(successor - prior) / self.temperature) > uniform()

5. What does this do? import sys sys.path.append('DiffusionExample')

6. In def test_move_particle_one_over(): "change" should be "changed"

7. In same function, what does multiply.reduce do?

8. In def test_equal_probability(): energy = MagicMock() But in def test_accept_change(): energy = MagicMock Do the missing brackets matter?

9. In def test_equal_probability(): It looks like changes_at_zero is a list of booleans. I'm not sure what the next line is doing or how: assert count_nonzero(changes_at_zero),etc.

10. In def test_accept_change(): please explain the final assertion.

NB Maybe some of this code isn't essential to be understood line-by-line??

11. In def test_main_algorithm(): I don't really understand what the Mocks are doing with their side effects This relates to issue 86

12. Error at end of page - UsageError: Cell magic %%cmd not found. - presumably it should be %%bash, although if we're not going to be using notebooks I guess this error doesn't matter

[ageorgou]

• Problem statement:

  • Steps 5-8 look like they should be nested under 4? It's fine as it is, but the ":" at the end of 4 makes it seem that way to me.
  • Step 6 should be the other way around: /beta controls how likely we are to move from more to less favourable states. We always accept proposed moves to more favourable states.
  • Steps 7-8: I would make it clearer that what we are doing here is accepting the move with probability P_0.
  • Step 8: I don't think "anyway" fits here

• Instructions (in bullet points):

  • Capitalise first letters
  • Missing period at last bullet point

• Solution:

  • Why the spaces in the start and end of docstrings?
  • In simulate: Change string formatting from 'Energy = %f'% energy to 'Energy = {}'.format(energy)?
  • In docstring of test_move_particle_one_over: "Check density is change" -> "changed"
  • In docstring of test_input_sanity: "Check incorrect input do fail" -> "Check incorrect inputs [do] fail" (or something else). Also missing period at the end.
  • In docstring of test_accept_change: Missing period at the end
  • In test_accept_change: In final lines, strange comma in assertion? Also don't need the float in Python 3(?)
  • In test_main_algorithm: Missing spaces between list elements in last line