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mphoward
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mphoward
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Overall looks good! I have two comments below, and there is a documentation build error that needs fixing. We should merge this branch before #80, as I think you will be able to use this method to implement the change in from_hoomd_gsd?
src/lammpsio/box.py
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| # Extract tilt factors | ||
| xy, xz, yz = arr[0, 1], arr[0, 2], arr[1, 2] | ||
| tilt = [xy, xz, yz] if numpy.any([xy, xz, yz]) else None |
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This is one area of LAMMPS that is slightly grey. You may want to have a triclinic box that has zero tilt factors, say in order to allow the box to deform later.
Should we add a default argument like check_orthorhombic=True or force_triclinic=False that will cause this check to occur? And otherwise, accept the tilts as they come from the matrix?
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Good point! I've implemented a force_triclinic argument to cover this scenario!
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I've made these tweaks and fixed the documentation! This should go in before #80, and then I'll made the edits there! |
mphoward
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mphoward
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Thanks! One small comment, then this can be merged.
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Adds a method to create a
lammpio.Boxobject from a box matrix.