def test_equal(self):
s = self.get_structure("SiO2")
en = EnvironmentNode(central_site=s[0],
i_central_site=0,
ce_symbol="T:4")
en1 = EnvironmentNode(central_site=s[2],
i_central_site=0,
ce_symbol="T:4")
assert en == en1
assert not en.everything_equal(en1)
en2 = EnvironmentNode(central_site=s[0],
i_central_site=3,
ce_symbol="T:4")
assert en != en2
assert not en.everything_equal(en2)
en3 = EnvironmentNode(central_site=s[0],
i_central_site=0,
ce_symbol="O:6")
assert en == en3
assert not en.everything_equal(en3)
en4 = EnvironmentNode(central_site=s[0],
i_central_site=0,
ce_symbol="T:4")
assert en == en4
assert en.everything_equal(en4)
def test_cycle(self):
e1 = EnvironmentNode(central_site="Si", i_central_site=0, ce_symbol="T:4")
e2 = EnvironmentNode(central_site="Si", i_central_site=3, ce_symbol="T:4")
e3 = EnvironmentNode(central_site="Si", i_central_site=2, ce_symbol="T:4")
e4 = EnvironmentNode(central_site="Si", i_central_site=5, ce_symbol="T:4")
e5 = EnvironmentNode(central_site="Si", i_central_site=1, ce_symbol="T:4")
# Tests of SimpleGraphCycle with EnvironmentNodes
c1 = SimpleGraphCycle([e2])
c2 = SimpleGraphCycle([e2])
self.assertEqual(c1, c2)
c1 = SimpleGraphCycle([e1])
c2 = SimpleGraphCycle([e2])
self.assertNotEqual(c1, c2)
c1 = SimpleGraphCycle([e1, e2, e3])
c2 = SimpleGraphCycle([e2, e1, e3])
self.assertEqual(c1, c2)
c2 = SimpleGraphCycle([e2, e3, e1])
self.assertEqual(c1, c2)
c1 = SimpleGraphCycle([e3, e2, e4, e1, e5])
c2 = SimpleGraphCycle([e1, e4, e2, e3, e5])
self.assertEqual(c1, c2)
c2 = SimpleGraphCycle([e2, e3, e5, e1, e4])
self.assertEqual(c1, c2)
c1 = SimpleGraphCycle([e2, e3, e4, e1, e5])
c2 = SimpleGraphCycle([e2, e3, e5, e1, e4])
self.assertNotEqual(c1, c2)
# Tests of MultiGraphCycle with EnvironmentNodes
c1 = MultiGraphCycle([e1], [2])
c2 = MultiGraphCycle([e1], [2])
self.assertEqual(c1, c2)
c2 = MultiGraphCycle([e1], [1])
self.assertNotEqual(c1, c2)
c2 = MultiGraphCycle([e2], [2])
self.assertNotEqual(c1, c2)
c1 = MultiGraphCycle([e1, e2], [0, 1])
c2 = MultiGraphCycle([e1, e2], [1, 0])
self.assertEqual(c1, c2)
c2 = MultiGraphCycle([e2, e1], [1, 0])
self.assertEqual(c1, c2)
c2 = MultiGraphCycle([e2, e1], [0, 1])
self.assertEqual(c1, c2)
c2 = MultiGraphCycle([e2, e1], [2, 1])
self.assertNotEqual(c1, c2)
c1 = MultiGraphCycle([e1, e2, e3], [0, 1, 2])
c2 = MultiGraphCycle([e2, e1, e3], [0, 2, 1])
self.assertEqual(c1, c2)
c2 = MultiGraphCycle([e2, e3, e1], [1, 2, 0])
self.assertEqual(c1, c2)
def from_dict(cls, d):
"""
Reconstructs the ConnectedComponent object from a dict representation of the
ConnectedComponent object created using the as_dict method.
Args:
d (dict): dict representation of the ConnectedComponent object
Returns:
ConnectedComponent: The connected component representing the links of a given set of environments.
"""
nodes_map = {
inode_str: EnvironmentNode.from_dict(nodedict) for inode_str, (nodedict, nodedata) in d["nodes"].items()
}
nodes_data = {inode_str: nodedata for inode_str, (nodedict, nodedata) in d["nodes"].items()}
dod = {}
for e1, e1dict in d["graph"].items():
dod[e1] = {}
for e2, e2dict in e1dict.items():
dod[e1][e2] = {
cls._edgedictkey_to_edgekey(ied): cls._retuplify_edgedata(edata) for ied, edata in e2dict.items()
}
graph = nx.from_dict_of_dicts(dod, create_using=nx.MultiGraph, multigraph_input=True)
nx.set_node_attributes(graph, nodes_data)
nx.relabel_nodes(graph, nodes_map, copy=False)
return cls(graph=graph)
def test_as_dict(self):
s = self.get_structure("SiO2")
en = EnvironmentNode(central_site=s[2],
i_central_site=2,
ce_symbol="T:4")
en_from_dict = EnvironmentNode.from_dict(en.as_dict())
assert en.everything_equal(en_from_dict)
if bson is not None:
bson_data = bson.BSON.encode(en.as_dict())
en_from_bson = EnvironmentNode.from_dict(bson_data.decode())
assert en.everything_equal(en_from_bson)
def test_periodicity(self):
en1 = EnvironmentNode(central_site="Si",
i_central_site=3,
ce_symbol="T:4")
en2 = EnvironmentNode(central_site="Ag",
i_central_site=5,
ce_symbol="T:4")
en3 = EnvironmentNode(central_site="Ag",
i_central_site=8,
ce_symbol="O:6")
en4 = EnvironmentNode(central_site="Fe",
i_central_site=23,
ce_symbol="C:8")
graph = nx.MultiGraph()
graph.add_nodes_from([en1, en2, en3])
graph.add_edge(
en1,
en2,
start=en1.isite,
end=en2.isite,
delta=(0, 0, 0),
ligands=[(2, (0, 0, 1), (0, 0, 1)), (1, (0, 0, 1), (0, 0, 1))],
)
graph.add_edge(
en1,
en3,
start=en1.isite,
end=en2.isite,
delta=(0, 0, 0),
ligands=[(10, (0, 0, 1), (0, 0, 1)), (11, (0, 0, 1), (0, 0, 1))],
)
cc = ConnectedComponent(graph=graph)
assert cc.is_0d
assert not cc.is_1d
assert not cc.is_2d
assert not cc.is_3d
assert not cc.is_periodic
assert cc.periodicity == "0D"
graph = nx.MultiGraph()
graph.add_nodes_from([en1, en2, en3])
graph.add_edge(
en1,
en2,
start=en1.isite,
end=en2.isite,
delta=(0, 0, 0),
ligands=[(2, (0, 0, 1), (0, 0, 1)), (1, (0, 0, 1), (0, 0, 1))],
)
graph.add_edge(
en1,
en3,
start=en1.isite,
end=en3.isite,
delta=(0, 0, 0),
ligands=[(10, (0, 0, 1), (0, 0, 1)), (11, (0, 0, 1), (0, 0, 1))],
)
graph.add_edge(
en2,
en3,
start=en2.isite,
end=en3.isite,
delta=(0, 0, 1),
ligands=[(2, (0, 0, 1), (0, 0, 1)), (1, (0, 0, 1), (0, 0, 1))],
)
cc = ConnectedComponent(graph=graph)
assert not cc.is_0d
assert cc.is_1d
assert not cc.is_2d
assert not cc.is_3d
assert cc.is_periodic
assert cc.periodicity == "1D"
graph = nx.MultiGraph()
graph.add_nodes_from([en1, en2, en3])
graph.add_edge(
en1,
en2,
start=en1.isite,
end=en2.isite,
delta=(0, 0, 1),
ligands=[(2, (0, 0, 1), (0, 0, 1)), (1, (0, 0, 1), (0, 0, 1))],
)
graph.add_edge(
en1,
en3,
start=en1.isite,
end=en3.isite,
delta=(0, 0, 0),
ligands=[(10, (0, 0, 1), (0, 0, 1)), (11, (0, 0, 1), (0, 0, 1))],
)
graph.add_edge(
en2,
en3,
start=en2.isite,
end=en3.isite,
delta=(0, 0, -1),
ligands=[(2, (0, 0, 1), (0, 0, 1)), (1, (0, 0, 1), (0, 0, 1))],
)
cc = ConnectedComponent(graph=graph)
assert cc.periodicity == "0D"
# Test errors when computing periodicity
graph = nx.MultiGraph()
graph.add_nodes_from([en1, en2, en3])
graph.add_edge(
en1,
en1,
start=en1.isite,
end=en1.isite,
delta=(0, 0, 1),
ligands=[(2, (0, 0, 1), (0, 0, 1)), (1, (0, 0, 1), (0, 0, 1))],
)
graph.add_edge(
en1,
en1,
start=en1.isite,
end=en1.isite,
delta=(0, 0, 1),
ligands=[(2, (0, 0, 1), (0, 0, 1)), (1, (0, 0, 1), (0, 0, 1))],
)
cc = ConnectedComponent(graph=graph)
with pytest.raises(
ValueError,
match=r"There should not be self loops with the same "
r"\x28or opposite\x29 delta image\x2E",
):
cc.compute_periodicity_all_simple_paths_algorithm()
graph = nx.MultiGraph()
graph.add_nodes_from([en1, en2, en3])
graph.add_edge(
en1,
en1,
start=en1.isite,
end=en1.isite,
delta=(3, 2, -1),
ligands=[(2, (0, 0, 1), (0, 0, 1)), (1, (0, 0, 1), (0, 0, 1))],
)
graph.add_edge(
en1,
en1,
start=en1.isite,
end=en1.isite,
delta=(-3, -2, 1),
ligands=[(2, (0, 0, 1), (0, 0, 1)), (1, (0, 0, 1), (0, 0, 1))],
)
cc = ConnectedComponent(graph=graph)
with pytest.raises(
ValueError,
match=r"There should not be self loops with the same "
r"\x28or opposite\x29 delta image\x2E",
):
cc.compute_periodicity_all_simple_paths_algorithm()
graph = nx.MultiGraph()
graph.add_nodes_from([en1, en2, en3])
graph.add_edge(
en1,
en1,
start=en1.isite,
end=en1.isite,
delta=(0, 0, 0),
ligands=[(2, (0, 0, 1), (0, 0, 1)), (1, (0, 0, 1), (0, 0, 1))],
)
cc = ConnectedComponent(graph=graph)
with pytest.raises(
ValueError,
match=r"There should not be self loops with delta image = "
r"\x280, 0, 0\x29\x2E",
):
cc.compute_periodicity_all_simple_paths_algorithm()
# Test a 2d periodicity
graph = nx.MultiGraph()
graph.add_nodes_from([en1, en2, en3, en4])
graph.add_edge(
en1,
en2,
start=en1.isite,
end=en2.isite,
delta=(0, 0, 0),
ligands=[(2, (0, 0, 1), (0, 0, 1)), (1, (0, 0, 1), (0, 0, 1))],
)
graph.add_edge(
en1,
en3,
start=en1.isite,
end=en3.isite,
delta=(0, 0, 0),
ligands=[(2, (0, 0, 1), (0, 0, 1)), (1, (0, 0, 1), (0, 0, 1))],
)
graph.add_edge(
en4,
en2,
start=en4.isite,
end=en2.isite,
delta=(0, 0, 0),
ligands=[(2, (0, 0, 1), (0, 0, 1)), (1, (0, 0, 1), (0, 0, 1))],
)
graph.add_edge(
en3,
en4,
start=en4.isite,
end=en3.isite,
delta=(0, 0, 0),
ligands=[(2, (0, 0, 1), (0, 0, 1)), (1, (0, 0, 1), (0, 0, 1))],
)
graph.add_edge(
en3,
en4,
start=en4.isite,
end=en3.isite,
delta=(0, -1, 0),
ligands=[(2, (0, 0, 1), (0, 0, 1)), (1, (0, 0, 1), (0, 0, 1))],
)
graph.add_edge(
en3,
en2,
start=en2.isite,
end=en3.isite,
delta=(-1, -1, 0),
ligands=[(2, (0, 0, 1), (0, 0, 1)), (1, (0, 0, 1), (0, 0, 1))],
)
cc = ConnectedComponent(graph=graph)
assert not cc.is_0d
assert not cc.is_1d
assert cc.is_2d
assert not cc.is_3d
assert cc.is_periodic
assert cc.periodicity == "2D"
assert np.allclose(
cc.periodicity_vectors,
[np.array([0, 1, 0]), np.array([1, 1, 0])])
assert type(cc.periodicity_vectors) is list
assert cc.periodicity_vectors[0].dtype is np.dtype(int)
# Test a 3d periodicity
graph = nx.MultiGraph()
graph.add_nodes_from([en1, en2, en3, en4])
graph.add_edge(
en1,
en2,
start=en1.isite,
end=en2.isite,
delta=(0, 0, 0),
ligands=[(2, (0, 0, 1), (0, 0, 1)), (1, (0, 0, 1), (0, 0, 1))],
)
graph.add_edge(
en1,
en3,
start=en1.isite,
end=en3.isite,
delta=(0, 0, 0),
ligands=[(2, (0, 0, 1), (0, 0, 1)), (1, (0, 0, 1), (0, 0, 1))],
)
graph.add_edge(
en4,
en2,
start=en4.isite,
end=en2.isite,
delta=(0, 0, 0),
ligands=[(2, (0, 0, 1), (0, 0, 1)), (1, (0, 0, 1), (0, 0, 1))],
)
graph.add_edge(
en3,
en4,
start=en4.isite,
end=en3.isite,
delta=(0, 0, 0),
ligands=[(2, (0, 0, 1), (0, 0, 1)), (1, (0, 0, 1), (0, 0, 1))],
)
graph.add_edge(
en3,
en4,
start=en4.isite,
end=en3.isite,
delta=(0, -1, 0),
ligands=[(2, (0, 0, 1), (0, 0, 1)), (1, (0, 0, 1), (0, 0, 1))],
)
graph.add_edge(
en3,
en2,
start=en2.isite,
end=en3.isite,
delta=(-1, -1, 0),
ligands=[(2, (0, 0, 1), (0, 0, 1)), (1, (0, 0, 1), (0, 0, 1))],
)
graph.add_edge(
en3,
en3,
start=en3.isite,
end=en3.isite,
delta=(-1, -1, -1),
ligands=[(2, (0, 0, 1), (0, 0, 1)), (1, (0, 0, 1), (0, 0, 1))],
)
cc = ConnectedComponent(graph=graph)
assert not cc.is_0d
assert not cc.is_1d
assert not cc.is_2d
assert cc.is_3d
assert cc.is_periodic
assert cc.periodicity == "3D"
assert np.allclose(
cc.periodicity_vectors,
[np.array([0, 1, 0]),
np.array([1, 1, 0]),
np.array([1, 1, 1])],
)
assert type(cc.periodicity_vectors) is list
assert cc.periodicity_vectors[0].dtype is np.dtype(int)
def test_serialization(self):
lat = Lattice.hexagonal(a=2.0, c=2.5)
en1 = EnvironmentNode(
central_site=PeriodicSite("Si",
coords=np.array([0.0, 0.0, 0.0]),
lattice=lat),
i_central_site=3,
ce_symbol="T:4",
)
en2 = EnvironmentNode(
central_site=PeriodicSite("Ag",
coords=np.array([0.0, 0.0, 0.5]),
lattice=lat),
i_central_site=5,
ce_symbol="T:4",
)
en3 = EnvironmentNode(
central_site=PeriodicSite("Ag",
coords=np.array([0.0, 0.5, 0.5]),
lattice=lat),
i_central_site=8,
ce_symbol="O:6",
)
graph = nx.MultiGraph()
graph.add_nodes_from([en1, en2, en3])
graph.add_edge(
en1,
en2,
start=en1.isite,
end=en2.isite,
delta=(0, 0, 0),
ligands=[(2, (0, 0, 1), (0, 0, 1)), (1, (0, 0, 1), (0, 0, 1))],
)
graph.add_edge(
en1,
en3,
start=en1.isite,
end=en2.isite,
delta=(0, 0, 0),
ligands=[(10, (0, 0, 1), (0, 0, 1)), (11, (0, 0, 1), (0, 0, 1))],
)
cc = ConnectedComponent(graph=graph)
ref_sorted_edges = [[en1, en2], [en1, en3]]
sorted_edges = sorted([sorted(e) for e in cc.graph.edges()])
assert sorted_edges == ref_sorted_edges
ccfromdict = ConnectedComponent.from_dict(cc.as_dict())
ccfromjson = ConnectedComponent.from_dict(
json.loads(json.dumps(cc.as_dict())))
loaded_cc_list = [ccfromdict, ccfromjson]
if bson is not None:
bson_data = bson.BSON.encode(cc.as_dict())
ccfrombson = ConnectedComponent.from_dict(bson_data.decode())
loaded_cc_list.append(ccfrombson)
for loaded_cc in loaded_cc_list:
assert loaded_cc.graph.number_of_nodes() == 3
assert loaded_cc.graph.number_of_edges() == 2
assert set(list(cc.graph.nodes())) == set(
list(loaded_cc.graph.nodes()))
assert sorted_edges == sorted(
[sorted(e) for e in loaded_cc.graph.edges()])
for ii, e in enumerate(sorted_edges):
assert cc.graph[e[0]][e[1]] == loaded_cc.graph[e[0]][e[1]]
for node in loaded_cc.graph.nodes():
assert isinstance(node.central_site, PeriodicSite)
def test_str(self):
s = self.get_structure("SiO2")
en = EnvironmentNode(central_site=s[2],
i_central_site=2,
ce_symbol="T:4")
assert str(en) == "Node #2 Si (T:4)"
def test_str(self):
s = self.get_structure('SiO2')
en = EnvironmentNode(central_site=s[2],
i_central_site=2,
ce_symbol='T:4')
assert str(en) == 'Node #2 Si (T:4)'