core.components.calculate.recipes.local_env

core.components.calculate.recipes.local_env#

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This source code is licensed under the MIT license found in the LICENSE file in the root directory of this source tree.

Functions#

construct_bond_matrix(→ numpy.ndarray)

Constructs a bond matrix for a given crystal structure.

Module Contents#

core.components.calculate.recipes.local_env.construct_bond_matrix(structure: pymatgen.core.Structure, nn_finder: pymatgen.analysis.local_env.NearNeighbors, site_permutations: numpy.typing.ArrayLike | None = None) → numpy.ndarray#

Constructs a bond matrix for a given crystal structure.

This function uses a near neigbor algorithm from pymatgen to determine bonds between atoms in the structure and creates an adjacency matrix where 1 indicates a bond between atoms and 0 indicates no bond.

Parameters:

  • structure – A pymatgen Structure object representing the crystal structure

  • nn_finder – A NearNeighbors instance to determine near neighbor lists

  • site_permutations – A numpy array containing the site permutations if the covalent matrix should be constructed with sites in an order different than the order in which they appear in the given structure

Returns:

A square matrix where matrix[i,j] = 1 if atoms i and j share a covalent bond,

and 0 otherwise

Return type:

np.ndarray

Contents