quemb.kbe.autofrag.autogen

quemb.kbe.autofrag.autogen(mol, kpt, frozen_core=True, be_type='be2', write_geom=False, unitcell=1, gamma_2d=False, gamma_1d=False, long_bond=False, perpend_dist=4.0, perpend_dist_tol=0.001, nx=False, ny=False, nz=False, iao_valence_basis=None, interlayer=False, print_frags=True)

Automatic cell partitioning

Partitions a unitcell into overlapping fragments as defined in BE atom-based fragmentations. It automatically detects branched chemical chains and ring systems and partitions accordingly. For efficiency, it only checks two atoms for connectivity (chemical bond) if they are within 3.5 Angstrom. This value is hardcoded as normdist. Two atoms are defined as bonded if they are within 1.8 Angstrom (1.2 for Hydrogen atom). This is also hardcoded as bond & hbond. Neighboring unitcells are used in the fragmentation, exploiting translational symmetry.

Parameters:

  • mol (Cell) – pyscf.pbc.gto.cell.Cell object. This is required for the options, ‘autogen’, and ‘chain’ as frag_type.

  • kpt (list of int) – Number of k-points in each lattice vector dimension.

  • frozen_core (bool, optional) – Whether to invoke frozen core approximation. Defaults to True.

  • be_type (str, optional) – Specifies the order of bootstrap calculation in the atom-based fragmentation. Supported values are ‘be1’, ‘be2’, ‘be3’, and ‘be4’. Defaults to ‘be2’.

  • write_geom (bool, optional) – Whether to write a ‘fragment.xyz’ file which contains all the fragments in Cartesian coordinates. Defaults to False.

  • iao_valence_basis (str, optional) – Name of minimal basis set for IAO scheme. ‘sto-3g’ is sufficient for most cases. Defaults to None.

  • valence_only (bool, optional) – If True, all calculations will be performed in the valence basis in the IAO partitioning. This is an experimental feature. Defaults to False.

  • print_frags (bool, optional) – Whether to print out the list of resulting fragments. Defaults to True.

  • interlayer (bool) – Whether the periodic system has two stacked monolayers.

  • long_bond (bool) – For systems with longer than 1.8 Angstrom covalent bond, set this to True otherwise the fragmentation might fail.

Returns:

  • fsites (list of list of int) – List of fragment sites where each fragment is a list of LO indices.

  • edgsites (list of list of list of int) – List of edge sites for each fragment where each edge is a list of LO indices.

  • center (list of list of int) – List of center indices for each edge.

  • edge_idx (list of list of list of int) – List of edge indices for each fragment where each edge index is a list of LO indices.

  • center_idx (list of list of list of int) – List of center indices for each fragment where each center index is a list of LO indices.

  • centerf_idx (list of list of int) – List of center fragment indices.

  • ebe_weight (list of list) – Weights for each fragment. Each entry contains a weight and a list of LO indices.