Fix issue #159 #160
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Fix issue #159 #160
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chryswoods
approved these changes
Feb 9, 2024
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This PR closes #159 by ensuring that vector components that are sufficiently close to zero following a reduction are set to exactly zero. This solves the issue of conversion to OpenMM, which requires that the first vector lies exactly on the x-axis and the second is exactly in the x-y plane. Non-zero values generated by our code seem to be on the order of 1e-16, so we could probably make the tolerance smaller if needed. (The OpenMM Python API uses 1e-6 as the small value.)
An alternative approach to this would be to leave the
TrinclinicBoxclass untouched and simply zero the values when setting the box vectors in the Sire to OpenMM code. Let me know if you'd prefer that approach, since this issue seems to be (at present) OpenMM specific due to the way they check for reduced form.I've cancelled the CI since it's been tested locally via some problematic
somd1inputs. Feel free to consume into one of the other PRs if you're happy.