def _generate_lattice_from_parameters(interaction_matrix: np.ndarray):
# make a graph from the interaction matrix.
# This should be replaced by from_adjacency_matrix of retworkx.
shape = interaction_matrix.shape
if len(shape) != 2 or shape[0] != shape[1]:
raise ValueError(
f"Invalid shape of `interaction_matrix`, {shape}, is given."
"It must be a square matrix.")
graph = PyGraph(multigraph=False)
graph.add_nodes_from(range(shape[0]))
for source_index in range(shape[0]):
for target_index in range(source_index, shape[0]):
weight = interaction_matrix[source_index, target_index]
if not weight == 0.0:
graph.add_edge(source_index, target_index, weight)
return Lattice(graph)
def from_json(cls, s: str) -> 'Topology':
"""Initializes from a JSON string."""
# load dict from JSON string
data = orjson.loads(s)
# validate type
_type = data.pop("type")
if _type != cls.__name__:
raise TypeError(f"cannot deserialize from type `{_type}`")
# initialize an empty graph
graph = PyGraph()
# process atoms
for atom in data["atoms"]:
graph.add_node(Atom.from_json(orjson.dumps(atom)))
# process bonds
for bond in data["bonds"]:
bond = Bond.from_json(orjson.dumps(bond))
graph.add_edge(bond.indices[0], bond.indices[1], edge=bond)
# return instance
return cls(graph)