switch from depth first to nx bfs algorithm (#333)

* switch from depth first to nx bfs algorithm

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

ipsuite/geometry/unwrap.py

@@ -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
 
 
@@ -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]: