def test_solid_angle(self):
self.nn.targets = None
for n in range(len(self.s)):
angle = 0
for nn in self.nn.get_voronoi_polyhedra(self.s, n).values():
angle += nn['solid_angle']
self.assertAlmostEqual(4 * np.pi, angle)
self.assertEqual(solid_angle([0,0,0], [[1,0,0],[-1,0,0],[0,1,0]]), pi)
def test_solid_angle(self):
self.nn.targets = None
for n in range(len(self.s)):
angle = 0
for nn in self.nn.get_voronoi_polyhedra(self.s, n).values():
angle += nn['solid_angle']
self.assertAlmostEqual(4 * np.pi, angle)
self.assertEqual(solid_angle([0, 0, 0], [[1, 0, 0], [-1, 0, 0], [0, 1, 0]]), pi)
def analyze_vol_interstice(center_coords, nn_coords, center_r,
nn_rs, convex_hull_simplices):
"""Analyze the volume interstices in the tetrahedra formed by center
atom and neighbor convex hull triplets.
Args:
center_coords ([float]): Central atomic coordinates.
nn_coords (array-like, shape (N, 3)): Nearest Neighbors' coordinates
center_r (float): central atom's radius.
nn_rs ([float]): Nearest Neighbors' radii.
convex_hull_simplices (array-like, shape (M, 3)): Indices of points
forming the simplicial facets of convex hull.
Returns:
volume_interstice_list ([float]): Volume interstice list.
"""
volume_interstice_list = list()
triplet_set = [(0, 1, 2), (1, 0, 2), (2, 0, 1)]
for facet_indices in convex_hull_simplices:
facet_coords = nn_coords[facet_indices]
facet_rs = nn_rs[facet_indices]
solid_angles = list()
for triplet in triplet_set:
s_a = solid_angle(facet_coords[triplet[0]],
np.array([facet_coords[triplet[1]],
facet_coords[triplet[2]],
center_coords]))
solid_angles.append(s_a)
# calculate neighbors' packed volume in the tetrahedron
packed_volume = 0
for s_a, nn_r in zip(solid_angles, facet_rs):
packed_volume += s_a / 3 * pow(nn_r, 3)
# add center atom's volume in the tetrahedron
center_solid_angle = solid_angle(center_coords, facet_coords)
packed_volume += center_solid_angle / 3 * pow(center_r, 3)
volume = vol_tetra(center_coords, *facet_coords)
volume_interstice = 1 - packed_volume / volume
volume_interstice_list.append(volume_interstice
if volume_interstice > 0 else 0)
return volume_interstice_list