\(\newcommand{\AA}{\text{Å}}\)

lmodea_k.Cluster#

class Cluster(crystal=None, cluster_dim=None, custom_cutoffs=None, allowed_formulae=None)#

Describes a cluster (non-periodic supercell) built from a unit cell.

Parameters:

crystal (Crystal) – A Crystal object representing the unit cell.
dim (list of int, optional) – Number of unit cells along each lattice vector, default is [3, 3, 3].
custom_cutoffs (list of tuples, optional) – List of ((element1, element2), (min_cutoff, max_cutoff)) tuples that override the default bonding cutoffs.

Raises:

ValueError – If a Crystal object is not provided.

Notes

The cluster geometry is fixed after construction; derived data such as distance matrices and bond graphs are cached and assume immutable coordinates.

__init__(crystal=None, cluster_dim=None, custom_cutoffs=None, allowed_formulae=None)#

Methods

`__init__`([crystal, cluster_dim, ...])
`expand_eigenvectors_and_masses`(L, wavevector)	Expand primitive-cell eigenvectors and masses to the 3×3×3 cluster.
`find_cluster_indices`(pc_indices, Rl)	Return indices i such that:
`find_molecule_containing`(atom_idx)	Return the complete covalent molecule (connected component) containing the given cluster atom index.

Attributes

`Rl`	Lattice index (integer offsets) for each cluster atom.
`all_angles`	List of angles (A, B, C) with B in center cell, cluster indices.
`all_bonds`	List of covalent bonds as (a, b) cluster-index tuples (a < b).
`all_dihedrals`	List of dihedrals (A, B, C, D) with B in center cell, cluster indices.
`all_molecules`	Return all unique molecules in the cluster as lists of cluster atom indices.
`all_rings`	List of chordless rings as lists of cluster atom indices (all in center cell).
`asymm_unit_map`	Map from primitive-cell atom index to asymmetric unit index.
`bond_graph`	Adjacency list of covalent bonds (cluster indices).
`cell_real`	Real-space lattice vectors (3x3, Å).
`coords`	Cartesian coordinates of cluster atoms (Å).
`cutoffs`	Bond cutoff dictionary (including any user overrides).
`dim`	Number of unit cells along each lattice vector (list of int).
`distance_matrix`	Full pairwise distance matrix for cluster atoms in Å (natoms x natoms).
`hbond_graph`	Adjacency list of hydrogen bonds (cluster indices).
`hydrogen_bonds`	List of hydrogen bonds as (a, b) cluster-index tuples (a < b).
`pc_coords_cart`	Cartesian coordinates of primitive-cell atoms.
`pc_coords_frac`	Fractional coordinates of primitive-cell atoms.
`pc_index_map`	Map from cluster atom index to primitive-cell atom index.
`pc_masses`	Atomic masses of primitive-cell atoms.
`pc_natoms`	Number of atoms in the primitive cell.
`pc_symbols`	Element symbols in the primitive cell.

lmodea_k.Cluster