def test_disorder(lim=8):
from numpy import all, array, dot
from numpy.random import random, randint
from numpy.linalg import det
from pylada.crystal import binary, supercell
from pylada.vff import build_tree
lattice = binary.zinc_blende()
for i in xrange(10):
cell = randint(-lim, lim, (3,3))
while det(cell) == 0: cell = randint(-lim, lim, (3,3))
a = supercell(lattice, dot(lattice.cell, cell))
b = build_tree(a, overlap=0.8)
ids = [id(node.center) for node in b]
connections = array([ sorted([ids.index(id(n.center)) for n, v in node])
for node in b ])
epsilon = random((3,3)) * 0.1
epsilon = epsilon + epsilon.T
a.cell += dot(epsilon, a.cell)
for atom in a: atom.pos += dot(epsilon, atom.pos)
b = build_tree(a, overlap=0.8)
c = array([ sorted([ids.index(id(n.center)) for n, v in node])
for node in b ])
assert all(connections == c)
b = build_tree(a, overlap=0.8)
for atom in a: atom.pos += random(3) * 0.05 - 0.025
c = array([ sorted([ids.index(id(n.center)) for n, v in node])
for node in b ])
assert all(connections == c)
return a
def test_single_counting():
from pylada.crystal import binary, supercell
from pylada.vff import build_tree
a = binary.zinc_blende()
a = supercell(binary.zinc_blende(), [[4, 0, 0], [0, 2, 0], [0, 0, 1]])
b = build_tree(a, overlap=0.5)
n = 0
for center in b:
for endpoint, vector in center.sc_bond_iter():
n += 1
for other, v in endpoint.sc_bond_iter(): assert other is not center
assert id(center) in [id(c) for c, v in endpoint]
assert n == 2 * len(a)
def test_angle():
from pylada.crystal import binary, supercell
from pylada.vff import build_tree
a = binary.zinc_blende()
a = supercell(binary.zinc_blende(), [[4, 0, 0], [0, 2, 0], [0, 0, 1]])
b = build_tree(a, overlap=0.5)
for center in b:
ids = [id(u.center) for u, d in center]
angles = set([(id(u.center), id(v.center)) for (u, d), (v, d) in center.angle_iter()])
for i, ida in enumerate(ids[:-1]):
for idb in ids[i+1:]:
if (ida, idb) in angles: assert (idb, ida) not in angles
else: assert (idb, ida) in angles
assert len(angles) == 6
def test_tree():
from numpy import all, array, dot, sum, any
from pylada.crystal import binary, supercell
from pylada.vff import build_tree
a = binary.zinc_blende()
a = supercell(binary.zinc_blende(), [[2, 0, 0], [0, 2, 0], [0, 0, 1]])
b = build_tree(a, overlap=0.5)
for center in b:
positions = []
for i, (bond, vector) in enumerate(center):
position = bond.pos + dot(a.cell, vector)
assert abs(sum((position - center.pos)**2) - 0.25*0.25*3) < 1e-8
assert all( [any(abs(array(p) - position[None, :]) > 1e-8) for p in positions] )
positions.append(position)
assert i == 3
