def check(structure, center, tolerance=1e-8):
from numpy import abs, sqrt, all
from pylada.crystal.cppwrappers import coordination_shells
# check we get the coordination_shells of zinc-blende.
neighs = coordination_shells(structure, 5, center, tolerance);
assert len(neighs) == 5
assert len(neighs[0]) == 4
for atom, diff, dist in neighs[0]:
assert abs(dist - sqrt(3.0) * 0.25) < tolerance
assert all(abs(abs(diff) - 0.25) < tolerance)
assert len(neighs[1]) == 12
for atom, diff, dist in neighs[1]:
assert abs(dist - sqrt(2.0) * 0.5) < tolerance
assert len([0 for u in diff if abs(u) < tolerance]) == 1
assert len([0 for u in diff if abs(abs(u)-0.5) < tolerance]) == 2
assert len(neighs[2]) == 12
for atom, diff, dist in neighs[2]:
assert abs(dist - sqrt(0.75*0.75+2.*0.25*0.25)) < tolerance
assert len([0 for u in diff if abs(abs(u)-0.25) < tolerance]) == 2
assert len([0 for u in diff if abs(abs(u)-0.75) < tolerance]) == 1
assert len(neighs[3]) == 6
for atom, diff, dist in neighs[3]:
assert abs(dist - 1.) < tolerance
assert len([0 for u in diff if abs(u) < tolerance]) == 2
assert len([0 for u in diff if abs(abs(u)-1.) < tolerance]) == 1
assert len(neighs[4]) == 12
for atom, diff, dist in neighs[4]:
assert abs(dist - sqrt(2*0.75*0.75+0.25*0.25)) < tolerance
assert len([0 for u in diff if abs(abs(u)-0.75) < tolerance]) == 2
assert len([0 for u in diff if abs(abs(u)-0.25) < tolerance]) == 1
def check(structure, center, tolerance=1e-8):
from numpy import abs, sqrt, all
from pylada.crystal.cppwrappers import coordination_shells
# check we get the coordination_shells of zinc-blende.
neighs = coordination_shells(structure, 5, center, tolerance);
assert len(neighs) == 5
assert len(neighs[0]) == 4
for atom, diff, dist in neighs[0]:
assert abs(dist - sqrt(3.0) * 0.25) < tolerance
assert all(abs(abs(diff) - 0.25) < tolerance)
assert len(neighs[1]) == 12
for atom, diff, dist in neighs[1]:
assert abs(dist - sqrt(2.0) * 0.5) < tolerance
assert len([0 for u in diff if abs(u) < tolerance]) == 1
assert len([0 for u in diff if abs(abs(u)-0.5) < tolerance]) == 2
assert len(neighs[2]) == 12
for atom, diff, dist in neighs[2]:
assert abs(dist - sqrt(0.75*0.75+2.*0.25*0.25)) < tolerance
assert len([0 for u in diff if abs(abs(u)-0.25) < tolerance]) == 2
assert len([0 for u in diff if abs(abs(u)-0.75) < tolerance]) == 1
assert len(neighs[3]) == 6
for atom, diff, dist in neighs[3]:
assert abs(dist - 1.) < tolerance
assert len([0 for u in diff if abs(u) < tolerance]) == 2
assert len([0 for u in diff if abs(abs(u)-1.) < tolerance]) == 1
assert len(neighs[4]) == 12
for atom, diff, dist in neighs[4]:
assert abs(dist - sqrt(2*0.75*0.75+0.25*0.25)) < tolerance
assert len([0 for u in diff if abs(abs(u)-0.75) < tolerance]) == 2
assert len([0 for u in diff if abs(abs(u)-0.25) < tolerance]) == 1
def check_against_neighbors(structure, tolerance=1e-8):
from numpy import abs, sqrt, all
from pylada.crystal.cppwrappers import coordination_shells, neighbors
a = neighbors(structure, 150, [0,0,0], tolerance)
result = []
fn = a[0][2]
i = 0
for atom, trans, dist in a:
if abs(fn-dist) < tolerance: i+=1; continue
result.append([i, fn])
i = 1
fn = dist
b = coordination_shells(structure, 150, [0,0,0], tolerance)
for x, y in zip(result, b):
assert len(y) == x[0]
assert abs(y[0][2] - x[1]) < tolerance
def check_against_neighbors(structure, tolerance=1e-8):
from numpy import abs, sqrt, all
from pylada.crystal.cppwrappers import coordination_shells, neighbors
a = neighbors(structure, 150, [0,0,0], tolerance)
result = []
fn = a[0][2]
i = 0
for atom, trans, dist in a:
if abs(fn-dist) < tolerance: i+=1; continue
result.append([i, fn])
i = 1
fn = dist
b = coordination_shells(structure, 150, [0,0,0], tolerance)
for x, y in zip(result, b):
assert len(y) == x[0]
assert abs(y[0][2] - x[1]) < tolerance