def test_clusters_from_file(self):
clusters1 = clusters_from_file(
filename="tests/STRUCTURE_FILES/POSCAR_2_clusters.vasp",
rcut=4.0,
elements={"Li"},
)
tort.tort_mod.tear_down()
clusters2 = clusters_from_file(
filename="tests/STRUCTURE_FILES/POSCAR_2_clusters.vasp",
rcut=3.5,
elements={"Li"},
)
tort.tort_mod.tear_down()
self.assertEqual(len(clusters1), 1)
self.assertEqual(len(clusters2), 2)
def test_cluster_periodic(self):
clusters1 = clusters_from_file(
filename="tests/STRUCTURE_FILES/POSCAR_2_clusters.vasp",
rcut=4.0,
elements={"Li"},
)
tort.tort_mod.tear_down()
clusters2 = clusters_from_file(
filename="tests/STRUCTURE_FILES/POSCAR_2_clusters.vasp",
rcut=3.5,
elements={"Li"},
)
tort.tort_mod.tear_down()
self.assertEqual(clusters1.pop().periodic, 3)
if clusters2.pop().periodic == 3:
self.assertEqual(clusters2.pop().periodic, 0)
else:
self.assertEqual(clusters2.pop().periodic, 3)
def test_periodic(self):
clusters1 = clusters_from_file(
filename="tests/STRUCTURE_FILES/POSCAR_periodic_1.vasp",
rcut=4.0,
elements={"Li"},
)
clusters2 = clusters_from_file(
filename="tests/STRUCTURE_FILES/POSCAR_periodic_2.vasp",
rcut=4.0,
elements={"Li"},
)
clusters3 = clusters_from_file(
filename="tests/STRUCTURE_FILES/POSCAR_periodic_3.vasp",
rcut=4.0,
elements={"Li"},
)
self.assertEqual(clusters1.pop().periodic, 1)
self.assertEqual(clusters2.pop().periodic, 2)
self.assertEqual(clusters3.pop().periodic, 3)
def test_torture_cluster(self, value):
cluster = clusters_from_file(filename="tests/STRUCTURE_FILES/" + value,
rcut=4.0,
elements={"Li"})
clusterf = cluster.pop()
clusterf.grow_cluster()
clusterf.torture_fort()
tort.tort_mod.tear_down()
self.assertEqual(
set([
node.tortuosity
for node in clusterf.return_key_nodes(key="Halo", value=False)
]),
set([4, 3, 3, 3, 3, 3, 3, 3]),
)
def test_graph_from_structure(self):
clusters1 = clusters_from_file(
filename="tests/STRUCTURE_FILES/POSCAR_2_clusters.vasp",
rcut=4.0,
elements={"Li"},
)
structure = Structure.from_file("tests/STRUCTURE_FILES/POSCAR_2_clusters.vasp")
graph = graph_from_structure(structure, rcut=4.0, elements={"Li"})
neigh_set_1 = set(
[frozenset(node.neighbours_ind) for node in clusters1.pop().nodes]
)
neigh_set_2 = set(
[frozenset(node.neighbours_ind) for node in graph.clusters.pop().nodes]
)
self.assertEqual(neigh_set_1, neigh_set_2)
def test_graph_from_file(self):
graph = graph_from_file(
filename="tests/STRUCTURE_FILES/POSCAR_2_clusters.vasp",
rcut=4.0,
elements={"Li"},
)
tort.tort_mod.tear_down()
clusters = clusters_from_file(
filename="tests/STRUCTURE_FILES/POSCAR_2_clusters.vasp",
rcut=4.0,
elements={"Li"},
)
tort.tort_mod.tear_down()
c_nodes = set([node.index for node in clusters.pop().nodes])
g_nodes = set([node.index for node in graph.clusters.pop().nodes])
self.assertEqual(g_nodes, c_nodes)
def test_minimal_cluster(self, value):
graph = graph_from_file(filename="tests/STRUCTURE_FILES/" + value,
rcut=4.0,
elements={"Li"})
cluster = clusters_from_file(filename="tests/STRUCTURE_FILES/" + value,
rcut=4.0,
elements={"Li"})
clusterf = cluster.pop()
clusterf.grow_cluster()
clusterf.torture_fort()
graph.torture()
self.assertEqual(
set([c.tortuosity for c in graph.minimal_clusters]),
set([c.tortuosity for c in list(graph.clusters)]),
)
def test_output_clusters_cif(self):
graph = graph_from_file(
filename="tests/STRUCTURE_FILES/POSCAR_2_clusters.vasp",
rcut=4.0,
elements={"Li"},
)
graph.output_clusters(fmt="cif")
subprocess.run("mv *CLUS* tests/STRUCTURE_FILES/", shell=True)
clusters = clusters_from_file(
filename="tests/STRUCTURE_FILES/POSCAR_CLUS_0.cif",
rcut=4.0,
elements={"Li"},
)
c_nodes = set([node.index for node in clusters.pop().nodes])
g_nodes = set([node.index for node in graph.clusters.pop().nodes])
self.assertEqual(g_nodes, c_nodes)
