def convert(self,
structure: Structure,
state_attributes: List = None) -> Dict:
"""
Take a pymatgen structure and convert it to a index-type graph representation
The graph will have node, distance, index1, index2, where node is a vector of Z number
of atoms in the structure, index1 and index2 mark the atom indices forming the bond and separated by
distance.
For state attributes, you can set structure.state = [[xx, xx]] beforehand or the algorithm would
take default [[0, 0]]
Args:
state_attributes: (list) state attributes
structure: (pymatgen structure)
(dictionary)
"""
state_attributes = state_attributes or getattr(
structure, 'state', None) or np.array([[0.0, 0.0]],
dtype='float32')
atoms = self.get_atom_features(structure)
index1, index2, _, bonds = get_graphs_within_cutoff(
structure, self.nn_strategy.cutoff)
if np.size(np.unique(index1)) < len(atoms):
raise RuntimeError("Isolated atoms found in the structure")
return {
'atom': atoms,
'bond': bonds,
'state': state_attributes,
'index1': index1,
'index2': index2
}
def convert(self, structure: Structure, state_attributes: List = None) -> Dict:
"""
Take a pymatgen structure and convert it to a index-type graph representation
The graph will have node, distance, index1, index2, where node is a vector of Z number
of atoms in the structure, index1 and index2 mark the atom indices forming the bond and separated by
distance.
For state attributes, you can set structure.state = [[xx, xx]] beforehand or the algorithm would
take default [[0, 0]]
Args:
state_attributes: (list) state attributes
structure: (pymatgen structure)
(dictionary)
"""
state_attributes = (
state_attributes or getattr(structure, "state", None) or np.array([[0.0, 0.0]], dtype="float32")
)
atoms = self.get_atom_features(structure)
index1, index2, _, bonds = get_graphs_within_cutoff(structure, self.nn_strategy.cutoff)
if len(index1) == 0:
raise RuntimeError("The cutoff is too small, resulting in " "material graph with no bonds")
if np.size(np.unique(index1)) < len(atoms):
logger.warning("Isolated atoms found in the structure. The " "cutoff radius might be small")
return {"atom": atoms, "bond": bonds, "state": state_attributes, "index1": index1, "index2": index2}
def test_model_load(self):
s = Structure(Lattice.cubic(3.6), ["Mo", "Mo"], [[0.5, 0.5, 0.5], [0, 0, 0]])
center_indices, neighbor_indices, images, distances = get_graphs_within_cutoff(s, 4)
self.assertListEqual(
center_indices.tolist(),
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1],
)