def test_init(self):
# Generic connected component not using EnvironmentNodes
# (as_dict won't work on such a ConnectedComponent instance)
cc = ConnectedComponent(environments=['a', 'b', 'c', 'd', 'e', 'f'],
links=[('a', 'b', 0), ('a', 'c', 0),
('b', 'c', 0), ('a', 'a', 0),
('a', 'b', 1), ('c', 'd'), ('c', 'd'),
('c', 'd'), ('d', 'e'), ('e', 'f')],
environments_data={
'a': {
'var1': 2,
'var2': 3
},
'b': {
'var1': 3
}
},
links_data={
('c', 'b'): {
'bcinfo': 2
},
('a', 'b', 1): {
'ab1info': 4
},
('d', 'c'): {
'dcinfo': 8
}
})
assert isinstance(cc.graph, nx.MultiGraph)
nodes = list(cc.graph.nodes())
assert set(nodes) == {'a', 'b', 'c', 'd', 'e', 'f'}
edges = cc.graph.edges()
assert len(edges) == 10
assert cc.graph['a']['b'] == {0: {}, 1: {'ab1info': 4}}
assert cc.graph['b']['a'] == {0: {}, 1: {'ab1info': 4}}
assert cc.graph['c']['b'] == {0: {'bcinfo': 2}}
assert cc.graph['b']['c'] == {0: {'bcinfo': 2}}
assert len(cc.graph['c']['d']) == 3
assert cc.graph['c']['d'][0] == {'dcinfo': 8}
assert cc.graph['c']['d'][1] == {'dcinfo': 8}
assert cc.graph['c']['d'][2] == {'dcinfo': 8}
assert cc.graph.nodes(data=True)['a'] == {'var1': 2, 'var2': 3}
assert cc.graph.nodes(data=True)['b'] == {'var1': 3}
assert cc.graph.nodes(data=True)['c'] == {}
# Make a deep copy of the graph to actually check that the objects are different instances
mygraph = copy.deepcopy(cc.graph)
assert isinstance(
mygraph,
nx.MultiGraph) # Check that it is indeed the same type of graph
cc2 = ConnectedComponent(graph=mygraph)
assert set(list(mygraph.nodes())) == set(list(cc2.graph.nodes()))
assert set(list(mygraph.edges())) == set(list(cc2.graph.edges()))
assert len(cc2.graph) == 6
def test_serialization_private_methods(self):
# Testing _edgekey_to_edgedictkey
key = ConnectedComponent._edgekey_to_edgedictkey(3)
assert key == '3'
with pytest.raises(RuntimeError,
match=r'Cannot pass an edge key which is a str '
r'representation of an int\x2E'):
key = ConnectedComponent._edgekey_to_edgedictkey('5')
key = ConnectedComponent._edgekey_to_edgedictkey('mykey')
assert key == 'mykey'
with pytest.raises(
ValueError,
match=r'Edge key should be either a str or an int\x2E'):
key = ConnectedComponent._edgekey_to_edgedictkey(0.2)
def test_serialization_private_methods(self):
# Testing _edgekey_to_edgedictkey
key = ConnectedComponent._edgekey_to_edgedictkey(3)
assert key == "3"
with pytest.raises(
RuntimeError,
match=r"Cannot pass an edge key which is a str "
r"representation of an int\x2E",
):
key = ConnectedComponent._edgekey_to_edgedictkey("5")
key = ConnectedComponent._edgekey_to_edgedictkey("mykey")
assert key == "mykey"
with pytest.raises(
ValueError,
match=r"Edge key should be either a str or an int\x2E"):
key = ConnectedComponent._edgekey_to_edgedictkey(0.2)
def get_connected_components(self, environments_symbols=None, only_atoms=None):
connected_components = []
env_subgraph = self.environment_subgraph(environments_symbols=environments_symbols, only_atoms=only_atoms)
for component_nodes in nx.connected_components(env_subgraph):
graph = env_subgraph.subgraph(component_nodes).copy()
connected_components.append(ConnectedComponent.from_graph(graph))
return connected_components
def test_init(self):
# Generic connected component not using EnvironmentNodes
# (as_dict won't work on such a ConnectedComponent instance)
cc = ConnectedComponent(
environments=["a", "b", "c", "d", "e", "f"],
links=[
("a", "b", 0),
("a", "c", 0),
("b", "c", 0),
("a", "a", 0),
("a", "b", 1),
("c", "d"),
("c", "d"),
("c", "d"),
("d", "e"),
("e", "f"),
],
environments_data={
"a": {
"var1": 2,
"var2": 3
},
"b": {
"var1": 3
}
},
links_data={
("c", "b"): {
"bcinfo": 2
},
("a", "b", 1): {
"ab1info": 4
},
("d", "c"): {
"dcinfo": 8
},
},
)
assert isinstance(cc.graph, nx.MultiGraph)
nodes = list(cc.graph.nodes())
assert set(nodes) == {"a", "b", "c", "d", "e", "f"}
edges = cc.graph.edges()
assert len(edges) == 10
assert cc.graph["a"]["b"] == {0: {}, 1: {"ab1info": 4}}
assert cc.graph["b"]["a"] == {0: {}, 1: {"ab1info": 4}}
assert cc.graph["c"]["b"] == {0: {"bcinfo": 2}}
assert cc.graph["b"]["c"] == {0: {"bcinfo": 2}}
assert len(cc.graph["c"]["d"]) == 3
assert cc.graph["c"]["d"][0] == {"dcinfo": 8}
assert cc.graph["c"]["d"][1] == {"dcinfo": 8}
assert cc.graph["c"]["d"][2] == {"dcinfo": 8}
assert cc.graph.nodes(data=True)["a"] == {"var1": 2, "var2": 3}
assert cc.graph.nodes(data=True)["b"] == {"var1": 3}
assert cc.graph.nodes(data=True)["c"] == {}
# Make a deep copy of the graph to actually check that the objects are different instances
mygraph = copy.deepcopy(cc.graph)
assert isinstance(
mygraph,
nx.MultiGraph) # Check that it is indeed the same type of graph
cc2 = ConnectedComponent(graph=mygraph)
assert set(list(mygraph.nodes())) == set(list(cc2.graph.nodes()))
assert set(list(mygraph.edges())) == set(list(cc2.graph.edges()))
assert len(cc2.graph) == 6
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)