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21:10:10
drmeister
Seriously - there are few things in life that give me as much joy as programming.
21:10:49
drmeister
That's an octree visualized on top of the molecule that I constructed on top of it.
21:11:37
drmeister
The octree's are working pretty much. But they are missing some close contacts that I can see when I compare every atom to every other atom (slow). I'm debugging why.
21:15:30
drmeister
Purple balls are collisions that the octree code is identifying. Yellow balls are close contacts from comparing every atom to every other atom. If they agreed then all yellow balls would be hidden within purple ones.
21:22:26
drmeister
To rapidly identify where atoms overlap with each other without having to carry out N(N-1)/2 distance calculations.
21:24:10
drmeister
But it's not working perfectly. I should get the same results with octrees vs the slow N(N-1)/2 comparisons.
21:25:09
drmeister
The molecule coming up from the bottom has atoms that get really close to the atoms in the octree. The green ball is the atom coming from the bottom that has a collision with an atom in the octree.
21:26:44
drmeister
With interactive Common Lisp running in jupyterlab and nglview I can debug this shit because I can visualize everything.
21:30:37
drmeister
To quote the fictional character Mark Whatney - "[I'm] sciencing the shit out of this"
21:40:12
Shinmera
octrees are O(logn) in the best case, but it can degenerate to O(n) if it's bounded and degenerate.
21:43:39
Shinmera
Oh wait, I mistook what you wrote, obviously querying everyone is going to be O(nlogn) vs O(n^2)
21:51:21
selwyn
drmeister: i must have asked before but i've forgotten the answer: do you ever use quantum or semiclassical methods in cando?
23:20:18
kpoeck_
Latest code with updates for clasp there in https://github.com/sionescu/bordeaux-threads