test core_fast added [Issue #28] #30
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@IAlibay, can I bother you to review this, pretty please? |
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As with all the other tests, could you please add an example on a much smaller system that humans can look at and understand? For example:
To check gridding:
- 25 lipids in 5x5 grid, with x values of 0, 1, 2, 3, 4 and y values of 0, 1, 2, 3, 4
- 25 lipids in 5x5 grid, with x values of 0.5, 1.5, 2.5, 3.5, 4.5 and y values of 0, 1, 2, 3, 4
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- 25 lipids in 5x5 grid, with y values of 0.5, 1.5, 2.5, 3.5, 4.5 and x values of 0, 1, 2, 3, 4
- 25 lipids in 5x5 grid, with x values of 0.5, 1.5, 2.5, 3.5, 4.5 and y values of 0.5, 1.5, 2.5, 3.5, 4.5
- 25 lipids in 5x5 grid, with x values of -0.5, -1.5, 2.5, 3.5, 4.5 and y values of 0, 1, 2, 3, 4
- so on and so forth
- 50 lipids in 5x5 grid to check gridding of multiple lipids
- 50 lipids in 5x5 grid but all on one side of the box (like x > 2) to check gridding of uneven lipids
To check z-coord averaging
- z values of all 0
- z values of -1 and 1 (should average to 0 for the 50 lipid system, to check gridding)
- z values at the top of the box and bottom of the box (should average to 0, to check PBC)
Perhaps the other mentors @orbeckst @fiona-naughton @IAlibay have different perspectives, but IMO you will need to write these tests anyway for the new refactored code, and having them now will be an easy way to remember what does and doesn't work on your existing mdtraj code.
| z_calc = np.zeros([n_cells, n_cells]) | ||
| core_fast_leaflet(z_calc, "upper", mdtraj_po4, jump, n_cells, ["POPC"], md_ref_beads, max_width) | ||
| core_fast(mdtraj_po4, jump, n_cells, ["upper"], ["POPC"], md_ref_beads, max_width, 'test') | ||
| for z, z_test in zip(MEMBRANE_CURVATURE_DATA['z_avg_coords'], z_calc): |
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In unit testing we typically try to validate a single function in at least one test. Could you add tests where you check the functionality of core_fast and core_fast_leaflet separately in addition to this one?
Fixes issue #28
Changes
core_fastfunction incore.py.This PR helps to solve #17