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Update TIP5P comparison #1744
Update TIP5P comparison #1744
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mattwthompson
commented
Oct 13, 2023
- Tag issue being addressed
- Add tests
- Update docstrings/documentation, if applicable
- Lint codebase
- Update changelog
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I noticed that 1) a lot of notebook prose was deleted in this PR and 2) that this up-pins to interchange >=0.3.16 while #1754 to fix examples CI down-pins to interchange ==0.3.14, so I'm not sure whether this is ready to merge. I'm assigning @Yoshanuikabundi as a reviewer for this one (though if I misread this and this could supersede #1754 I can take it sooner) |
There will need to be some updates to this notebook when the dust settles in Interchange, but it will look different than the current state - I'll re-open and re-trigger review with the web UI when it's done, nothing to worry about or work on here until then |
" [[0.0, 0.0, 0.0], [-0.7815, 0.5526, 0.0], [0.7815, 0.5526, 0.0]] * unit.angstrom\n", | ||
" bond_length\n", | ||
" * Quantity(\n", | ||
" [\n", | ||
" [0.0, 0.0, 0.0],\n", | ||
" [-sin(theta / 2), cos(theta / 2), 0.0],\n", | ||
" [sin(theta / 2), cos(theta / 2), 0.0],\n", | ||
" ]\n", | ||
" )\n", |
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I'm convinced this is the cause of the years-long energy difference we've been observing
In [1]: from openff.units import *
In [2]: from math import *
In [3]: bond_length = Quantity(0.9572, unit.angstrom)
In [4]: theta = Quantity(104.52, unit.degree).to(unit.radian)
In [5]: bond_length * Quantity(
...: [
...: [0.0, 0.0, 0.0],
...: [-sin(theta / 2), cos(theta / 2), 0.0],
...: [sin(theta / 2), cos(theta / 2), 0.0],
...: ],
...: )
Out[5]:
array([[ 0. , 0. , 0. ],
[-0.75695033, 0.58588228, 0. ],
[ 0.75695033, 0.58588228, 0. ]]) <Unit('angstrom')>