megnet.data.local_env module¶
-
class
AllAtomPairs
[source]¶ Bases:
pymatgen.analysis.local_env.NearNeighbors
Get all combinations of atoms as bonds in a molecule
-
get_nn_info
(molecule: pymatgen.core.structure.Molecule, n: int) → Dict[source]¶ Get all near-neighbor sites as well as the associated image locations and weights of the site with index n.
- Parameters
structure (Structure) – input structure.
n (integer) – index of site for which to determine near-neighbor information.
- Returns
- each dictionary provides information
about a single near neighbor, where key ‘site’ gives access to the corresponding Site object, ‘image’ gives the image location, and ‘weight’ provides the weight that a given near-neighbor site contributes to the coordination number (1 or smaller), ‘site_index’ gives index of the corresponding site in the original structure.
- Return type
siw (list of dicts)
-
-
class
MinimumDistanceNNAll
(cutoff: float = 4.0)[source]¶ Bases:
pymatgen.analysis.local_env.MinimumDistanceNN
Determine bonded sites by fixed cutoff
- Args:.
- cutoff (float): cutoff radius in Angstrom to look for trial
near-neighbor sites (default: 4.0).
Args: tol (float): tolerance parameter for neighbor identification
(default: 0.1).
- cutoff (float): cutoff radius in Angstrom to look for trial
near-neighbor sites (default: 10.0).
- get_all_sites (boolean): If this is set to True then the neighbor
sites are only determined by the cutoff radius, tol is ignored
-
get_nn_info
(structure: pymatgen.core.structure.Structure, n: int) → Dict[source]¶ Get all near-neighbor sites as well as the associated image locations and weights of the site with index n using the closest neighbor distance-based method.
- Parameters
structure (Structure) – input structure.
n (integer) – index of site for which to determine near neighbors.
- Returns
- tuples, each one
of which represents a neighbor site, its image location, and its weight.
- Return type
siw (list of tuples (Site, array, float))