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switch from depth first to nx bfs algorithm #333

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merged 3 commits into from
Aug 20, 2024
Merged

switch from depth first to nx bfs algorithm #333

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52286c6
switch from depth first to nx bfs algorithm
M-R-Schaefer Aug 9, 2024
214f736
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 9, 2024
e478997
Merge branch 'main' into unwrap_fix
M-R-Schaefer Aug 20, 2024
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26 changes: 10 additions & 16 deletions ipsuite/geometry/unwrap.py
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Original file line number Diff line number Diff line change
@@ -1,7 +1,9 @@
import ase
import networkx as nx
import numpy as np
from ase.calculators.singlepoint import SinglePointCalculator

from ipsuite.geometry import graphs
from ipsuite.geometry.graphs import edges_from_atoms


Expand All @@ -24,26 +26,18 @@ def sort_atomic_edges(edges, idx):


def displace_neighbors(mol, edges):
for edge in edges:
dist = mol.get_distance(edge[0], edge[1], vector=True)
pdist = mol.get_distance(edge[0], edge[1], True, vector=True)
dist = mol.get_distance(edges[0], edges[1], vector=True)
pdist = mol.get_distance(edges[0], edges[1], True, vector=True)

displacement = dist - pdist
mol.positions[edge[1]] -= displacement
displacement = dist - pdist
mol.positions[edges[1]] -= displacement


def unwrap(atoms, edges, idx):
# TODO this should probably be width first, not depth first
current_edges = sort_atomic_edges(edges, idx)
displace_neighbors(atoms, current_edges)

next_idxs = current_edges[:, 1]

mask = np.all(edges != idx, axis=1)
filtered_edges = edges[mask]

for next_idx in next_idxs:
unwrap(atoms, filtered_edges, next_idx)
G = graphs.atoms_to_graph(atoms)
edges = nx.traversal.bfs_edges(G, idx)
for e in edges:
displace_neighbors(atoms, e)


def unwrap_system(atoms: ase.Atoms, components: list[np.ndarray]) -> list[ase.Atom]:
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