kgcnn.crystal package

Submodules

kgcnn.crystal.base module

class kgcnn.crystal.base.CrystalPreprocessor(output_graph_as_dict: bool = False, lattice: str = 'graph_lattice', species: str = 'node_number', coords: str = 'node_coordinates', charge: str = 'charge')[source]

Bases: Callable[[pymatgen.core.structure.Structure], networkx.classes.multidigraph.MultiDiGraph]

Base class for crystal preprocessors.

Concrete CrystalPreprocessors must be implemented as subclasses.

__call__(structure: Union[pymatgen.core.structure.Structure, kgcnn.graph.base.GraphDict]) → Union[networkx.classes.multidigraph.MultiDiGraph, kgcnn.graph.base.GraphDict][source]

Function to process crystal structures. Executes call .

Parameters

structure (Structure) – Crystal for which the graph representation should be calculated.

Raises

NotImplementedError – Should be implemented in a subclass.

Returns

Graph representation of the crystal.

Return type

MultiDiGraph

call(structure: pymatgen.core.structure.Structure) → networkx.classes.multidigraph.MultiDiGraph[source]

Should be implemented in a subclass.

Parameters

structure (Structure) – Crystal for which the graph representation should be calculated.

Raises

NotImplementedError – Should be implemented in a subclass.

Returns

Graph representation of the crystal.

Return type

MultiDiGraph

edge_attributes = []
get_config() → dict[source]

Returns a dictionary uniquely identifying the CrystalPreprocessor and its configuration.

Returns

A dictionary uniquely identifying the CrystalPreprocessor and its configuration.

Return type

dict

graph_attributes = []
hash() → str[source]

Generates a unique hash for the CrystalPreprocessor and its configuration.

Returns

A unique hash for the CrystalPreprocessor and its configuration.

Return type

str

node_attributes = []

kgcnn.crystal.graph_builder module

kgcnn.crystal.graph_builder._estimate_nn_radius_from_density(k: int, coordinates: numpy.ndarray, lattice: numpy.ndarray, empirical_tol_factor: float = 0.0)[source]

Rough estimate of the expected radius to find N nearest neighbours.

Parameters

  • k (int) – Number of neighbours.

  • coordinates (np.ndarray) – Coordinates array.

  • lattice (np.ndarray) – Lattice matrix.

  • empirical_tol_factor (float) – Tolerance factor for radius.

Returns

estimated radius

Return type

float

kgcnn.crystal.graph_builder._get_attr_from_graph(graph: networkx.classes.multidigraph.MultiDiGraph, attr_name: str, make_copy: bool = False) → Union[Any, numpy.ndarray][source]

Utility function to obtain graph-level information of the underlying crystal.

Parameters

  • graph (MultiDiGraph) – Networkx graph object.

  • attr_name (str) – Name of the attribute.

  • make_copy (bool) – Copy crystal-graph attribute.

Returns

Crystal information.

Return type

np.ndarray

kgcnn.crystal.graph_builder._get_cube(dim: int) → numpy.ndarray[source]

Generate a cubic mesh.

Parameters

dim (int) – Dimension for cubic mesh.

Returns

Cubic mesh.

Return type

np.ndarray

kgcnn.crystal.graph_builder._get_geometric_properties_of_unit_cell(coordinates: numpy.ndarray, lattice: numpy.ndarray)[source]

Diameter of a 3D unit cell and other properties.

Parameters

  • coordinates (np.ndarray) – Coordinates array.

  • lattice (np.ndarray) – Lattice matrix.

Returns

(center_unit_cell, max_diameter_cell, volume_unit_cell, density_unit_cell)

Return type

tuple

kgcnn.crystal.graph_builder._get_max_diameter(lattice: numpy.ndarray) → Union[float, numpy.ndarray][source]

Determine the max diameter of a lattice.

Parameters

lattice (np.ndarray) – Lattice matrix.

Returns

Max diameter of the lattice.

Return type

np.ndarray

kgcnn.crystal.graph_builder._get_mesh(size: Union[int, list, tuple], dim: int) → numpy.ndarray[source]

Utility function to create a numpy mesh grid with indices at last dimension.

Parameters

  • size (int, list) – Size of each dimension.

  • dim (int) – Dimension of the grid.

Returns

Mesh grid of form:

Return type

np.ndarray

kgcnn.crystal.graph_builder._get_super_cell_grid_frac_coords(lattice: numpy.ndarray, frac_coords: numpy.ndarray, size: Union[int, list, numpy.ndarray])[source]

Get frac coordinates for positions in a grid of unit cells that is a cubic super-cell.

..code - block:: python

import numpy as np from kgcnn.crystal.graph_builder import _get_super_cell_grid_frac_coords coordinates = _get_super_cell_grid_frac_coords(

np.array([[1.0, 0.0, 0.0], [0.0, 1.0, 0.5], [0.0, 0.5, 1.5]]), np.array([[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]]), [3, 3, 3]

) print(coordinates.shape) # (7, 7, 7, 2, 3)

Parameters

  • lattice (np.ndarray) – Lattice matrix.

  • frac_coords (np.ndarray) – Fractional coordinates of atoms in unit cell.

  • size (list) – Size of the super-cell in each dimension.

Returns

List of fractional coordinates of atoms in the super-cell.

Return type

np.ndarray

kgcnn.crystal.graph_builder._to_unit_cell(frac_coords)[source]

Converts fractional coords to be within the \([0,1)\) interval.

Parameters

frac_coords – Fractional coordinates to map into \([0,1)\) interval.

Returns

Fractional coordinates within the [0,1) interval.

kgcnn.crystal.graph_builder.add_edge_information(graph: networkx.classes.multidigraph.MultiDiGraph, inplace=False, frac_offset=False, offset=True, distance=True) → networkx.classes.multidigraph.MultiDiGraph[source]

Adds edge information, such as offset ( frac_offset, offset ) and distances ( distance ) to edges.

Parameters

  • graph (MultiDiGraph) – Graph for which to add edge information.

  • inplace (bool, optional) – Whether to add the edge information to the given graph or create a copy with added edges. Defaults to False.

  • frac_offset (bool, optional) – Whether to add fractional offsets (frac_offset attribute) to edges. Defaults to False.

  • offset (bool, optional) – Whether to add offsets (offset attribute) to edges. Defaults to True.

  • distance (bool, optional) – Whether to add distances (distance attribute) to edges. Defaults to True.

Returns

The graph with added edge information.

Return type

MultiDiGraph

kgcnn.crystal.graph_builder.add_knn_bonds(graph: networkx.classes.multidigraph.MultiDiGraph, k: int = 12, max_radius: float = 10.0, tolerance: Optional[float] = None, inplace: bool = False) → networkx.classes.multidigraph.MultiDiGraph[source]

Adds kNN-based edges to a unit cell graph.

Parameters

  • graph (MultiDiGraph) – The unit cell graph to add kNN-based edges to.

  • k (int, optional) – How many neighbors to add for each node. Defaults to 12.

  • max_radius (float, optional) – This parameter has no effect on the outcome of the graph. It may only on the runtime. The algorithm starts the kNN search in the environment the radius of max_radius. If the kth neighbor is not within this radius the algorithm is called again with twice the initial radius. Defaults to 10.

  • tolerance (Optional[float], optional) – If tolerance is not None, edges with distances of the k-th nearest neighbor plus the tolerance value are included in the graph. Defaults to None.

  • inplace (bool, optional) – Whether to add the edges to the given graph or create a copy with added edges. Defaults to False.

Returns

Graph with added edges.

Return type

MultiDiGraph

kgcnn.crystal.graph_builder.add_radius_bonds(graph: networkx.classes.multidigraph.MultiDiGraph, radius: float = 5.0, inplace: bool = False) → networkx.classes.multidigraph.MultiDiGraph[source]

Adds radius-based edges to a unit cell graph.

Parameters

  • graph (MultiDiGraph) – The unit cell graph to add radius-based edges to.

  • radius (float, optional) – Cutoff radius for each atom in Angstrom units. Defaults to 5.

  • inplace (bool, optional) – Whether to add the edges to the given graph or create a copy with added edges. Defaults to False.

Returns

Graph with added edges.

Return type

MultiDiGraph

kgcnn.crystal.graph_builder.add_voronoi_bonds(graph: networkx.classes.multidigraph.MultiDiGraph, min_ridge_area: Optional[float] = None, inplace: bool = False) → networkx.classes.multidigraph.MultiDiGraph[source]

Adds Voronoi-based edges to a unit cell graph.

Parameters

  • graph (MultiDiGraph) – The unit cell graph to add radius-based edges to.

  • min_ridge_area (Optional[float], optional) – Threshold value for ridge area between two Voronoi cells. If a ridge area between two voronoi cells is smaller than this value the corresponding edge between the atoms of the cells is excluded from the graph. Defaults to None.

  • inplace (bool, optional) – Whether to add the edges to the given graph or create a copy with added edges. Defaults to False.

Returns

Graph with added edges.

Return type

MultiDiGraph

kgcnn.crystal.graph_builder.get_ridge_area(ridge_points)[source]

Computes the ridge area given ridge points.

Beware that this function, assumes that the ridge points are (roughly) within a flat subspace plane in the 3 dimensional space. It computes the area of the convex hull of the points in three dimensions and then divides it by two, since both sides of the flat convex hull are included.

Parameters

ridge_points (np.ndarray) – Ridge points to calculate area for.

Returns

Ridge area for the given points.

Return type

float

kgcnn.crystal.graph_builder.get_symmetrized_graph(structure: Union[pymatgen.core.structure.Structure, pyxtal.pyxtal]) → networkx.classes.multidigraph.MultiDiGraph[source]

Builds a unit graph without any edges, but with symmetry information as node attributes.

Each node has a asymmetric_mapping attribute, which contains the id of the symmetry-equivalent atom in the asymmetric unit. Each node has a symmop attribute, which contains the affine matrix to generate the position (in fractional coordinates) of the atom, from its symmetry-equivalent atom position in the asymmetric unit. Each node has a multiplicity attribute, which contains the multiplicity of the atom (how many symmetry-equivalent atoms there are for this node). The resulting graph will have a spacegroup attribute, that specifies the spacegroup of the crystal.

Parameters

structure (Union[Structure, pyxtal]) – Crystal structure to convert to a graph.

Raises

ValueError – If the argument is not a pymatgen Structure or pyxtal object.

Returns

Unit graph with symmetry information, but without any edges for the crystal.

Return type

MultiDiGraph

kgcnn.crystal.graph_builder.pairwise_diff(coords1: numpy.ndarray, coords2: numpy.ndarray) → numpy.ndarray[source]

Get the pairwise offset difference between two vector sets.

Parameters

  • coords1 (np.ndarray) – Coordinates of shape (…, n, 3)

  • coords2 (np.ndarray) – Coordinates of shape (…, m, 3)

Returns

Difference values of shape (…, n, m, 3)

Return type

np.ndarray

kgcnn.crystal.graph_builder.prune_knn_bonds(graph: networkx.classes.multidigraph.MultiDiGraph, k: int = 12, tolerance: Optional[float] = None, inplace: bool = False) → networkx.classes.multidigraph.MultiDiGraph[source]

Prunes edges of a graph to only the k with the smallest distance value.

Parameters

  • graph (MultiDiGraph) – The unit cell graph with edges to prune.

  • k (int, optional) – How many neighbors each node should maximally have. Defaults to 12.

  • tolerance (Optional[float], optional) – If tolerance is not None, edges with distances of the k-th nearest neighbor plus the tolerance value are included in the graph. Defaults to None.

  • inplace (bool, optional) – Whether to add the edges to the given graph or create a copy with added edges. Defaults to False.

Returns

The graph with pruned edges.

Return type

MultiDiGraph

kgcnn.crystal.graph_builder.prune_radius_bonds(graph: networkx.classes.multidigraph.MultiDiGraph, radius: float = 4.0, inplace: bool = False) → networkx.classes.multidigraph.MultiDiGraph[source]

Prunes edges of a graph with larger distance than the specified radius.

Parameters

  • graph (MultiDiGraph) – The unit cell graph with edges to prune.

  • radius (float, optional) – Distance threshold. Edges with larger distance than this value are removed from the graph. Defaults to 4.

  • inplace (bool, optional) – Whether to add the edges to the given graph or create a copy with added edges. Defaults to False.

Returns

The graph with pruned edges.

Return type

MultiDiGraph

kgcnn.crystal.graph_builder.prune_voronoi_bonds(graph: networkx.classes.multidigraph.MultiDiGraph, min_ridge_area: Optional[float] = None, inplace: bool = False) → networkx.classes.multidigraph.MultiDiGraph[source]

Prunes edges of a graph with a voronoi ridge are smaller then the specified min_ridge_area.

Only works for graphs with edges that contain voronoi_ridge_area as edge attributes. :param graph: The unit cell graph with edges to prune. :type graph: MultiDiGraph :param min_ridge_area: Threshold value for ridge area between two Voronoi cells.

If a ridge area between two voronoi cells is smaller than this value the corresponding edge between the atoms of the cells is excluded from the graph. Defaults to None.

Parameters

inplace (bool, optional) – Whether to add the edges to the given graph or create a copy with added edges. Defaults to False.

Returns

The graph with pruned edges.

Return type

MultiDiGraph

kgcnn.crystal.graph_builder.remove_duplicate_edges(graph: networkx.classes.multidigraph.MultiDiGraph, inplace=False) → networkx.classes.multidigraph.MultiDiGraph[source]

Removes duplicate edges with same offset.

Parameters

  • graph (MultiDiGraph) – The unit cell graph with edges to remove.

  • inplace (bool, optional) – Whether to add the edges to the given graph or create a copy with added edges. Defaults to False.

Returns

The graph without duplicate edges.

Return type

MultiDiGraph

kgcnn.crystal.graph_builder.structure_to_empty_graph(structure: Union[pymatgen.core.structure.Structure, pyxtal.pyxtal], symmetrize: bool = False) → networkx.classes.multidigraph.MultiDiGraph[source]

Builds an unit graph without any edges.

Parameters

  • structure (Union[Structure, pyxtal]) – Crystal structure to convert to a graph. symmetrize (bool, optional): Whether to include symmetry information attributes (asymmetric_mapping, symmop, multiplicity attributes) in nodes and graph (spacegroup atribute). Defaults to False.

  • symmetrize (bool) – Whether to get symmetrized graph.

Raises

ValueError – If the argument is not a pymatgen Structure or pyxtal object.

Returns

Unit graph without any edges for the crystal.

Return type

MultiDiGraph

kgcnn.crystal.graph_builder.to_asymmetric_unit_graph(graph: networkx.classes.multidigraph.MultiDiGraph) → networkx.classes.multidigraph.MultiDiGraph[source]

Generates super cell graph representation from unit cell graph representation.

Parameters

graph (MultiDiGraph) – Unit cell graph to generate asymmetric unit graph for.

Returns

Corresponding asymmetric unit graph for the given unit cell graph.

Return type

MultiDiGraph

kgcnn.crystal.graph_builder.to_non_periodic_unit_cell(graph: networkx.classes.multidigraph.MultiDiGraph, add_reverse_edges: bool = True, inplace: bool = False) → networkx.classes.multidigraph.MultiDiGraph[source]

Generates non-periodic graph representation from unit cell graph representation.

Parameters

  • graph (MultiDiGraph) – Unit cell graph to generate non-periodic graph for.

  • add_reverse_edges (bool, optional) – Whether to add incoming edges to atoms that lie outside the central unit cell. Defaults to True.

  • inplace (bool, optional) – Whether to add distances (distance attribute) to edges. Defaults to False.

Returns

Corresponding non-periodic graph for the given unit cell graph.

Return type

MultiDiGraph

kgcnn.crystal.graph_builder.to_supercell_graph(graph: networkx.classes.multidigraph.MultiDiGraph, size) → networkx.classes.multidigraph.MultiDiGraph[source]

Generates super-cell graph representation from unit cell graph representation.

Parameters

  • graph (MultiDiGraph) – Unit cell graph to generate super cell graph for.

  • size (list) – How many cells the crystal will get expanded into each dimension.

Returns

Corresponding super cell graph for the given unit cell graph.

Return type

MultiDiGraph

kgcnn.crystal.preprocessor module

class kgcnn.crystal.preprocessor.AsymmetricUnitCell(output_graph_as_dict: bool = False, lattice: str = 'graph_lattice', species: str = 'node_number', coords: str = 'node_coordinates', charge: str = 'charge')[source]

Bases: Callable[[pymatgen.core.structure.Structure], networkx.classes.multidigraph.MultiDiGraph]

Preprocessor that builds asymmetric unit graphs without any edges for crystals.

call(structure: pymatgen.core.structure.Structure) → networkx.classes.multidigraph.MultiDiGraph[source]

Builds the crystal graph (networkx.MultiDiGraph) for the pymatgen structure.

Parameters

structure (Structure) – Structure to convert to a crystal graph.

Returns

Crystal graph for the provided crystal.

Return type

MultiDiGraph

edge_attributes = []
graph_attributes = ['lattice_matrix', 'spacegroup']
node_attributes = ['atomic_number', 'frac_coords', 'coords', 'asymmetric_mapping', 'symmop', 'multiplicity']
class kgcnn.crystal.preprocessor.KNNAsymmetricUnitCell(k: int = 12, tolerance: Optional[float] = 1e-09, **kwargs)[source]

Bases: Callable[[pymatgen.core.structure.Structure], networkx.classes.multidigraph.MultiDiGraph]

Preprocessor that builds asymmetric unit graphs with kNN-based edges for crystals.

__init__(k: int = 12, tolerance: Optional[float] = 1e-09, **kwargs)[source]

Initializes the crystal preprocessor.

Parameters

  • k (int, optional) – How many nearest neighbours to consider for edge selection. Defaults to 12.

  • tolerance (Optional[float], optional) – If tolerance is not None, edges with distances of the k-th nearest neighbor plus the tolerance value are included in the graph. Defaults to 1e-9.

call(structure: pymatgen.core.structure.Structure) → networkx.classes.multidigraph.MultiDiGraph[source]

Builds the crystal graph (networkx.MultiDiGraph) for the pymatgen structure.

Parameters

structure (Structure) – Structure to convert to a crystal graph.

Returns

Crystal graph for the provided crystal.

Return type

MultiDiGraph

edge_attributes = ['cell_translation', 'distance', 'symmop', 'offset']
graph_attributes = ['lattice_matrix', 'spacegroup']
node_attributes = ['atomic_number', 'frac_coords', 'coords', 'multiplicity']
class kgcnn.crystal.preprocessor.KNNNonPeriodicUnitCell(k=12, tolerance=1e-09, **kwargs)[source]

Bases: Callable[[pymatgen.core.structure.Structure], networkx.classes.multidigraph.MultiDiGraph]

Preprocessor that builds non-periodic graphs with kNN-based edges for crystals.

__init__(k=12, tolerance=1e-09, **kwargs)[source]

Initializes the crystal preprocessor.

Parameters

  • k (int, optional) – How many nearest neighbours to consider for edge selection. Defaults to 12.

  • tolerance (float, optional) – If tolerance is not None, edges with distances of the k-th nearest neighbor plus the tolerance value are included in the graph. Defaults to 1e-9.

call(structure: pymatgen.core.structure.Structure) → networkx.classes.multidigraph.MultiDiGraph[source]

Builds the crystal graph (networkx.MultiDiGraph) for the pymatgen structure.

Parameters

structure (Structure) – Structure to convert to a crystal graph.

Returns

Crystal graph for the provided crystal.

Return type

MultiDiGraph

edge_attributes = ['cell_translation', 'distance', 'offset']
graph_attributes = ['lattice_matrix']
node_attributes = ['atomic_number', 'frac_coords', 'coords']
class kgcnn.crystal.preprocessor.KNNSuperCell(k: int = 12, tolerance: Optional[float] = 1e-09, size: Optional[list] = None, **kwargs)[source]

Bases: Callable[[pymatgen.core.structure.Structure], networkx.classes.multidigraph.MultiDiGraph]

Preprocessor that builds super-cell graphs with kNN-based edges for crystals.

__init__(k: int = 12, tolerance: Optional[float] = 1e-09, size: Optional[list] = None, **kwargs)[source]

Initializes the crystal preprocessor.

Parameters

  • k (int, optional) – How many nearest neighbours to consider for edge selection. Defaults to 12.

  • tolerance (Optional[float], optional) – If tolerance is not None, edges with distances of the k-th nearest neighbor plus the tolerance value are included in the graph. Defaults to 1e-9.

  • size (list, optional) – How many cells the crystal will get expanded into each dimension. Defaults to [3,3,3].

call(structure: pymatgen.core.structure.Structure) → networkx.classes.multidigraph.MultiDiGraph[source]

Builds the crystal graph (networkx.MultiDiGraph) for the pymatgen structure.

Parameters

structure (Structure) – Structure to convert to a crystal graph.

Returns

Crystal graph for the provided crystal.

Return type

MultiDiGraph

edge_attributes = ['cell_translation', 'distance', 'offset']
graph_attributes = ['lattice_matrix']
node_attributes = ['atomic_number', 'frac_coords', 'coords']
class kgcnn.crystal.preprocessor.KNNUnitCell(k: int = 12, tolerance: Optional[float] = 1e-09, **kwargs)[source]

Bases: Callable[[pymatgen.core.structure.Structure], networkx.classes.multidigraph.MultiDiGraph]

Preprocessor that builds unit cell graphs with kNN-based edges for crystals.

__init__(k: int = 12, tolerance: Optional[float] = 1e-09, **kwargs)[source]

Initializes the crystal preprocessor.

Parameters

  • k (int, optional) – How many nearest neighbours to consider for edge selection. Defaults to 12.

  • tolerance (Optional[float], optional) – If tolerance is not None, edges with distances of the k-th nearest neighbor plus the tolerance value are included in the graph. Defaults to 1e-9.

call(structure: pymatgen.core.structure.Structure) → networkx.classes.multidigraph.MultiDiGraph[source]

Builds the crystal graph (networkx.MultiDiGraph) for the pymatgen structure.

Parameters

structure (Structure) – Structure to convert to a crystal graph.

Returns

Crystal graph for the provided crystal.

Return type

MultiDiGraph

edge_attributes = ['cell_translation', 'distance', 'offset']
graph_attributes = ['lattice_matrix']
node_attributes = ['atomic_number', 'frac_coords', 'coords']
class kgcnn.crystal.preprocessor.RadiusAsymmetricUnitCell(radius: float = 3.0, **kwargs)[source]

Bases: Callable[[pymatgen.core.structure.Structure], networkx.classes.multidigraph.MultiDiGraph]

Preprocessor that builds asymmetric unit graphs with radius-based edges for crystals.

__init__(radius: float = 3.0, **kwargs)[source]

Initializes the crystal preprocessor.

Parameters

radius (float, optional) – Cutoff radius for each atom in Angstrom units. Defaults to 3.0.

call(structure: pymatgen.core.structure.Structure) → networkx.classes.multidigraph.MultiDiGraph[source]

Builds the crystal graph (networkx.MultiDiGraph) for the pymatgen structure.

Parameters

structure (Structure) – Structure to convert to a crystal graph.

Returns

Crystal graph for the provided crystal.

Return type

MultiDiGraph

edge_attributes = ['cell_translation', 'distance', 'symmop', 'offset']
graph_attributes = ['lattice_matrix', 'spacegroup']
node_attributes = ['atomic_number', 'frac_coords', 'coords', 'multiplicity']
class kgcnn.crystal.preprocessor.RadiusNonPeriodicUnitCell(radius: float = 3.0, **kwargs)[source]

Bases: Callable[[pymatgen.core.structure.Structure], networkx.classes.multidigraph.MultiDiGraph]

Preprocessor that builds non-periodic graphs with radius-based edges for crystals.

__init__(radius: float = 3.0, **kwargs)[source]

Initializes the crystal preprocessor.

Parameters

radius (float, optional) – Cutoff radius for each atom in Angstrom units. Defaults to 3.0.

call(structure: pymatgen.core.structure.Structure) → networkx.classes.multidigraph.MultiDiGraph[source]

Builds the crystal graph (networkx.MultiDiGraph) for the pymatgen structure.

Parameters

structure (Structure) – Structure to convert to a crystal graph.

Returns

Crystal graph for the provided crystal.

Return type

MultiDiGraph

edge_attributes = ['cell_translation', 'distance', 'offset']
graph_attributes = ['lattice_matrix']
node_attributes = ['atomic_number', 'frac_coords', 'coords']
class kgcnn.crystal.preprocessor.RadiusSuperCell(radius: float = 3.0, size: Optional[list] = None, **kwargs)[source]

Bases: Callable[[pymatgen.core.structure.Structure], networkx.classes.multidigraph.MultiDiGraph]

Preprocessor that builds super-cell graphs with radius-based edges for crystals.

__init__(radius: float = 3.0, size: Optional[list] = None, **kwargs)[source]

Initializes the crystal preprocessor.

Parameters

  • radius (float, optional) – Cutoff radius for each atom in Angstrom units. Defaults to 3.0.

  • size (list, optional) – How many cells the crystal will get expanded into each dimension. Defaults to [3,3,3].

call(structure: pymatgen.core.structure.Structure) → networkx.classes.multidigraph.MultiDiGraph[source]

Builds the crystal graph (networkx.MultiDiGraph) for the pymatgen structure.

Parameters

structure (Structure) – Structure to convert to a crystal graph.

Returns

Crystal graph for the provided crystal.

Return type

MultiDiGraph

edge_attributes = ['cell_translation', 'distance', 'offset']
graph_attributes = ['lattice_matrix']
node_attributes = ['atomic_number', 'frac_coords', 'coords']
class kgcnn.crystal.preprocessor.RadiusUnitCell(radius: float = 3.0, **kwargs)[source]

Bases: Callable[[pymatgen.core.structure.Structure], networkx.classes.multidigraph.MultiDiGraph]

Preprocessor that builds unit cell graphs with radius-based edges for crystals.

__init__(radius: float = 3.0, **kwargs)[source]

Initializes the crystal preprocessor.

Parameters

radius (float, optional) – Cutoff radius for each atom in Angstrom units. Defaults to 3.0.

call(structure: pymatgen.core.structure.Structure) → networkx.classes.multidigraph.MultiDiGraph[source]

Builds the crystal graph (networkx.MultiDiGraph) for the pymatgen structure.

Parameters

structure (Structure) – Structure to convert to a crystal graph.

Returns

Crystal graph for the provided crystal.

Return type

MultiDiGraph

edge_attributes = ['cell_translation', 'distance', 'offset']
graph_attributes = ['lattice_matrix']
node_attributes = ['atomic_number', 'frac_coords', 'coords']
class kgcnn.crystal.preprocessor.UnitCell(output_graph_as_dict: bool = False, lattice: str = 'graph_lattice', species: str = 'node_number', coords: str = 'node_coordinates', charge: str = 'charge')[source]

Bases: Callable[[pymatgen.core.structure.Structure], networkx.classes.multidigraph.MultiDiGraph]

Preprocessor that builds unit cell graphs without any edges for crystals.

call(structure: pymatgen.core.structure.Structure) → networkx.classes.multidigraph.MultiDiGraph[source]

Builds the crystal graph (networkx.MultiDiGraph) for the pymatgen structure.

Parameters

structure (Structure) – Structure to convert to a crystal graph.

Returns

Crystal graph for the provided crystal.

Return type

MultiDiGraph

edge_attributes = []
graph_attributes = ['lattice_matrix']
node_attributes = ['atomic_number', 'frac_coords', 'coords']
class kgcnn.crystal.preprocessor.VoronoiAsymmetricUnitCell(min_ridge_area: Optional[float] = 0.0, **kwargs)[source]

Bases: Callable[[pymatgen.core.structure.Structure], networkx.classes.multidigraph.MultiDiGraph]

Preprocessor that builds asymmetric unit graphs with Voronoi-based edges for crystals.

__init__(min_ridge_area: Optional[float] = 0.0, **kwargs)[source]

Initializes the crystal preprocessor.

Parameters

min_ridge_area (Optional[float], optional) – Threshold value for ridge area between two Voronoi cells. If a ridge area between two voronoi cells is smaller than this value the corresponding edge between the atoms of the cells is excluded from the graph. Defaults to 0.0.

call(structure: pymatgen.core.structure.Structure) → networkx.classes.multidigraph.MultiDiGraph[source]

Builds the crystal graph (networkx.MultiDiGraph) for the pymatgen structure.

Parameters

structure (Structure) – Structure to convert to a crystal graph.

Returns

Crystal graph for the provided crystal.

Return type

MultiDiGraph

edge_attributes = ['cell_translation', 'distance', 'symmop', 'offset', 'voronoi_ridge_area']
graph_attributes = ['lattice_matrix', 'spacegroup']
node_attributes = ['atomic_number', 'frac_coords', 'coords', 'multiplicity']
class kgcnn.crystal.preprocessor.VoronoiNonPeriodicUnitCell(min_ridge_area: Optional[float] = 0.0, **kwargs)[source]

Bases: Callable[[pymatgen.core.structure.Structure], networkx.classes.multidigraph.MultiDiGraph]

Preprocessor that builds non-periodic graphs with Voronoi-based edges for crystals.

__init__(min_ridge_area: Optional[float] = 0.0, **kwargs)[source]

Initializes the crystal preprocessor.

Parameters

min_ridge_area (Optional[float], optional) – Threshold value for ridge area between two Voronoi cells. If a ridge area between two voronoi cells is smaller than this value the corresponding edge between the atoms of the cells is excluded from the graph. Defaults to 0.0.

call(structure: pymatgen.core.structure.Structure) → networkx.classes.multidigraph.MultiDiGraph[source]

Builds the crystal graph (networkx.MultiDiGraph) for the pymatgen structure.

Parameters

structure (Structure) – Structure to convert to a crystal graph.

Returns

Crystal graph for the provided crystal.

Return type

MultiDiGraph

edge_attributes = ['cell_translation', 'distance', 'offset', 'voronoi_ridge_area']
graph_attributes = ['lattice_matrix']
node_attributes = ['atomic_number', 'frac_coords', 'coords']
class kgcnn.crystal.preprocessor.VoronoiSuperCell(min_ridge_area: Optional[float] = 0.0, size: Optional[list] = None, **kwargs)[source]

Bases: Callable[[pymatgen.core.structure.Structure], networkx.classes.multidigraph.MultiDiGraph]

Preprocessor that builds super-cell graphs with Voronoi-based edges for crystals.

__init__(min_ridge_area: Optional[float] = 0.0, size: Optional[list] = None, **kwargs)[source]

Initializes the crystal preprocessor.

Parameters

  • min_ridge_area (Optional[float], optional) – Threshold value for ridge area between two Voronoi cells. If a ridge area between two voronoi cells is smaller than this value the corresponding edge between the atoms of the cells is excluded from the graph. Defaults to 0.0.

  • size (list, optional) – How many cells the crystal will get expanded into each dimension. Defaults to [3,3,3].

call(structure: pymatgen.core.structure.Structure) → networkx.classes.multidigraph.MultiDiGraph[source]

Builds the crystal graph (networkx.MultiDiGraph) for the pymatgen structure.

Parameters

structure (Structure) – Structure to convert to a crystal graph.

Returns

Crystal graph for the provided crystal.

Return type

MultiDiGraph

edge_attributes = ['cell_translation', 'distance', 'offset', 'voronoi_ridge_area']
graph_attributes = ['lattice_matrix']
node_attributes = ['atomic_number', 'frac_coords', 'coords']
class kgcnn.crystal.preprocessor.VoronoiUnitCell(min_ridge_area: Optional[float] = 0.0, **kwargs)[source]

Bases: Callable[[pymatgen.core.structure.Structure], networkx.classes.multidigraph.MultiDiGraph]

Preprocessor that builds unit cell graphs with Voronoi-based edges for crystals.

__init__(min_ridge_area: Optional[float] = 0.0, **kwargs)[source]

Initializes the crystal preprocessor.

Parameters

min_ridge_area (Optional[float], optional) – Threshold value for ridge area between two Voronoi cells. If a ridge area between two voronoi cells is smaller than this value the corresponding edge between the atoms of the cells is excluded from the graph. Defaults to 0.0.

call(structure: pymatgen.core.structure.Structure) → networkx.classes.multidigraph.MultiDiGraph[source]

Builds the crystal graph (networkx.MultiDiGraph) for the pymatgen structure.

Parameters

structure (Structure) – Structure to convert to a crystal graph.

Returns

Crystal graph for the provided crystal.

Return type

MultiDiGraph

edge_attributes = ['cell_translation', 'distance', 'offset', 'voronoi_ridge_area']
graph_attributes = ['lattice_matrix']
node_attributes = ['atomic_number', 'frac_coords', 'coords']

Module contents