def test_cluster_is_not_neighbouring(self):
sites = [Mock(spec=Site), Mock(spec=Site)]
sites[0].p_neighbours = [Mock(spec=Site)]
sites[1].p_neighbours = [Mock(spec=Site)]
clusters = [Cluster([sites[0]]), Cluster([sites[1]])]
self.assertEqual(clusters[0].is_neighbouring(clusters[1]), False)
self.assertEqual(clusters[1].is_neighbouring(clusters[0]), False)
def test_cluster_is_not_periodically_contiguous(self):
sites = [Mock(spec=Site), Mock(spec=Site), Mock(spec=Site)]
sites[0].r = np.array([0.0, 0.0, 0.0])
sites[1].r = np.array([1.0, 0.0, 0.0])
sites[2].r = np.array([2.0, 0.0, 0.0])
sites[0].p_neighbours = [sites[1]]
sites[1].p_neighbours = [sites[0], sites[2]]
sites[2].p_neighbours = [sites[1]]
cluster = Cluster(sites)
self.assertEqual(cluster.is_periodically_contiguous()[0], False)
def test_cluster_edges(self):
sites = [
Mock(spec=Site),
Mock(spec=Site),
Mock(spec=Site),
Mock(spec=Site)
]
sites[0].r = np.array([0.0, 0.0, 1.0])
sites[1].r = np.array([1.0, 1.0, 0.0])
sites[2].r = np.array([0.0, 1.0, 1.0])
sites[3].r = np.array([1.0, 0.0, 0.0])
sites[0].p_neighbours = [sites[1], sites[2], sites[3]]
sites[1].p_neighbours = [sites[0], sites[2], sites[3]]
sites[2].p_neighbours = [sites[0], sites[1], sites[3]]
sites[3].p_neighbours = [sites[0], sites[1], sites[2]]
min_x = (sites[0], sites[2])
max_x = (sites[1], sites[3])
min_y = (sites[0], sites[3])
max_y = (sites[1], sites[2])
min_z = (sites[1], sites[3])
max_z = (sites[0], sites[2])
cluster = Cluster(sites)
for s in cluster.sites_at_edges()[0]:
self.assertEqual(s in min_x, True)
for s in cluster.sites_at_edges()[1]:
self.assertEqual(s in max_x, True)
for s in cluster.sites_at_edges()[2]:
self.assertEqual(s in min_y, True)
for s in cluster.sites_at_edges()[3]:
self.assertEqual(s in max_y, True)
for s in cluster.sites_at_edges()[4]:
self.assertEqual(s in min_z, True)
for s in cluster.sites_at_edges()[5]:
self.assertEqual(s in max_z, True)
def test_cluster_merge_with_blocked_neighbour(self):
sites = [
Mock(spec=Site),
Mock(spec=Site),
Mock(spec=Site),
Mock(spec=Site)
]
sites[0].p_neighbours = [sites[1], sites[2]]
sites[2].p_neighbours = [sites[0], sites[3]]
cluster1 = Cluster([sites[0]])
cluster2 = Cluster([sites[2]])
cluster1.neighbours = cluster1.neighbours - set([sites[1]])
combined_cluster = cluster1.merge(cluster2)
self.assertEqual(combined_cluster.sites, set([sites[0], sites[2]]))
self.assertEqual(combined_cluster.neighbours, set([sites[3]]))
def test_cluster_is_initialised(self):
sites = [
Mock(spec=Site),
Mock(spec=Site),
Mock(spec=Site),
Mock(spec=Site)
]
cluster_sites = sites[0:2]
neighbour_sites = sites[2:4]
sites[0].p_neighbours = [sites[1], sites[2], sites[3]]
sites[1].p_neighbours = [sites[0], sites[2]]
cluster = Cluster(cluster_sites)
self.assertEqual(cluster.sites, set(cluster_sites))
self.assertEqual(cluster.neighbours, set(neighbour_sites))
def test_cluster_remove_sites_from_neighbours(self):
sites = [Mock(spec=Site), Mock(spec=Site), Mock(spec=Site)]
sites[0].p_neighbours = [sites[1], sites[2]]
sites[1].label = 'A'
sites[2].label = 'B'
cluster = Cluster([sites[0]])
cluster.remove_sites_from_neighbours('A')
self.assertEqual(cluster.neighbours, set([sites[2]]))
cluster.remove_sites_from_neighbours(['B'])
self.assertEqual(cluster.neighbours, set())
def test_cluster_size(self):
sites = [Mock(spec=Site), Mock(spec=Site)]
sites[0].p_neighbours = [Mock(spec=Site)]
sites[1].p_neighbours = [Mock(spec=Site)]
cluster = Cluster(sites)
self.assertEqual(cluster.size(), 2)