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Faster LENS calculation using FastNS #29

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Faster LENS calculation using FastNS #29

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ec6a817
Faster LENS calculation using FastNS
tulga-rdn Aug 25, 2024
de0b5a4
Fix typos and bugs
tulga-rdn Aug 26, 2024
806ff2a
Merge pull request #1 from tulga-rdn/tulga-rdn-patch-1
tulga-rdn Aug 26, 2024
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23 changes: 15 additions & 8 deletions src/dynsight/_internal/lens/lens.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
from MDAnalysis import AtomGroup, Universe

import numpy as np
from MDAnalysis.lib.NeighborSearch import AtomNeighborSearch
from MDAnalysis.lib.nsgrid import FastNS


def list_neighbours_along_trajectory(
Expand Down Expand Up @@ -34,15 +34,22 @@ def list_neighbours_along_trajectory(
if trajslice is None:
trajslice = slice(None)
neigh_list_per_frame = []

for _ in input_universe.universe.trajectory[trajslice]:
neigh_search = AtomNeighborSearch(
input_universe.atoms, box=input_universe.dimensions
)
atom_pos = input_universe.atoms.positions
box_dim = input_universe.dimensions
gridsearch = FastNS(cutoff, atom_pos, box=box_dim, pbc=True)
max_cutoff = gridsearch._prepare_box(box=box_dim, pbc=True)
if cutoff > max_cutoff:
cutoff = max_cutoff
fastns_results = gridsearch.self_search()
pairs = fastns_results.get_pairs()
neigh_list_per_atom = [[] for _ in range(len(input_universe.atoms))]
for x, y in pairs:
neigh_list_per_atom[x].append(y)
neigh_list_per_atom[y].append(x)
neigh_list_per_frame.append(neigh_list_per_atom)

neigh_list_per_atom = [
neigh_search.search(atom, cutoff) for atom in input_universe.atoms
]
neigh_list_per_frame.append([at.ix for at in neigh_list_per_atom])
return neigh_list_per_frame


Expand Down
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