Bond length and angle distributions #32
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## master #32 +/- ##
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+ Coverage 99.55% 99.62% +0.07%
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Files 5 5
Lines 224 270 +46
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+ Hits 223 269 +46
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jennyfothergill
approved these changes
Jan 12, 2022
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| pos1_unwrap = pos1 + (img1 * snap.configuration.box[:3]) | ||
| pos2_unwrap = pos2 + (img2 * snap.configuration.box[:3]) | ||
| pos3_unwrap = pos3 + (img3 * snap.configuration.box[:3]) |
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you could use freud unwrap if you wanted to support non-orthogonal boxes, but it's not urgent
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yeah, I thought about that as well. I say we can add that later if the need arises.
jennyfothergill
approved these changes
Jan 12, 2022
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This PR creates 2 functions. One that returns the bond lengths for a given bond pair, and one that returns bond angles for a given angle triplet. It allows the user to accumulate lengths and angles over a range of snapshots for better sampling.
A quick note about handling PBCs: I chose to use the periodic images stored in the gsd file to unwrap positions before finding the bond vectors. I think the other option would be to check if a vector is larger than half the box and correct it using the box length, but I'm not sure how to do that if we don't have a cubic volume. IMO, unwrapping the relevant positions first seems like the best option.