quemb.kbe.fragment.fragpart.__init__

fragpart.__init__(natom=0, frag_type='autogen', unitcell=1, gamma_2d=False, gamma_1d=False, interlayer=False, long_bond=False, perpend_dist=4.0, perpend_dist_tol=0.001, nx=False, ny=False, nz=False, kpt=None, iao_valence_basis=None, be_type='be2', mol=None, frozen_core=False, self_match=False, allcen=True)

Fragment/partitioning definition

Interfaces two main fragmentation functions (autogen & polychain) in MolBE. It defines edge & center for density matching and energy estimation. It also forms the base for IAO/PAO partitioning for a large basis set bootstrap calculation. Fragments are constructed based on atoms within a unitcell.

Parameters:

  • frag_type (str) – Name of fragmentation function. ‘autogen’, ‘hchain_simple’, and ‘chain’ are supported. Defaults to ‘autogen’ For systems with only hydrogen, use ‘chain’; everything else should use ‘autogen’

  • be_type (str) – Specifies order of bootsrap calculation in the atom-based fragmentation. ‘be1’, ‘be2’, ‘be3’, & ‘be4’ are supported. Defaults to ‘be2’ For a simple linear system A-B-C-D, be1 only has fragments [A], [B], [C], [D] be2 has [A, B, C], [B, C, D] ben …

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

  • iao_valence_basis (str) – Name of minimal basis set for IAO scheme. ‘sto-3g’ suffice for most cases.

  • frozen_core (bool) – Whether to invoke frozen core approximation. This is set to False by default

  • print_frags (bool) – Whether to print out list of resulting fragments. True by default

  • write_geom (bool) – Whether to write ‘fragment.xyz’ file which contains all the fragments in cartesian coordinates.

  • kpt (list of int) – No. of k-points in each lattice vector direction. This is the same as kmesh.

  • 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.