def find_all_bonds(geometry, tol=0.2):
"""
Finds all bonds present in a geometry.
Parameters
-----------
geometry: sisl.Geometry
the structure where the bonds should be found.
tol: float
the fraction that the distance between atoms is allowed to differ from
the "standard" in order to be considered a bond.
Return
---------
np.ndarray of shape (nbonds, 2)
each item of the array contains the 2 indices of the atoms that participate in the
bond.
"""
pt = PeriodicTable()
bonds = []
for at in geometry:
neighs = geometry.close(at, R=[0.1, 3])[-1]
for neigh in neighs[neighs > at]:
summed_radius = pt.radius([
abs(geometry.atoms[at].Z),
abs(geometry.atoms[neigh % geometry.na].Z)
]).sum()
bond_thresh = (1 + tol) * summed_radius
if bond_thresh > fnorm(geometry[neigh] - geometry[at]):
bonds.append([at, neigh])
return np.array(bonds, dtype=int)
def test_geom_category_no_r():
hBN = honeycomb(1.42, Atom[5, 7]) * (10, 11, 1)
B = AtomZ(5)
B2 = AtomNeighbours(2, neighbour=B, R=1.43)
N = AtomZ(7)
N2 = AtomNeighbours(min=2, max=2, neighbour=N, R=(0.01, 1.43))
PT = PeriodicTable()
B3 = AtomNeighbours(3,
neighbour=B,
R=lambda atom: (0.01, PT.radius(atom.Z)))
N3 = AtomNeighbours(3, neighbour=N, R=1.43)
Nabove3 = AtomNeighbours(min=3, neighbour=N, R=1.43)
assert B != N2
assert N2 != N3
n2 = AtomNeighbours(2, R=1.43)
category = (B & B2) ^ (N & N2) ^ (B & B3) ^ (N & N3) ^ n2
cat = category.categorize(hBN)
