quemb.molbe.fragment.fragmentate

quemb.molbe.fragment.fragmentate(mol, *, frag_type='autogen', iao_valence_basis=None, print_frags=True, write_geom=False, n_BE=2, frag_prefix='f', frozen_core=False, additional_args=None)

Fragment/partitioning definition

Interfaces the fragmentation functions 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.

Parameters:

  • frag_type (Literal['chemgen', 'graphgen', 'autogen']) – Name of fragmentation function. ‘chemgen’, ‘autogen’, and ‘graphgen’ are supported. Defaults to ‘autogen’.

  • n_BE (int, optional) – Specifies the order of bootstrap calculation in the atom-based fragmentation, i.e. BE(n). For a simple linear system A-B-C-D, BE(1) only has fragments [A], [B], [C], [D] BE(2) has [A, B, C], [B, C, D] ben …

  • mol (Mole) – This is required for the following frag_type options: "chemgen", "graphgen", "autogen"

  • iao_valence_basis (str | None) – 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.

  • frag_prefix (str) – Prefix to be appended to the fragment datanames. Useful for managing fragment scratch directories.

  • additional_args (AutogenArgs | ChemGenArgs | GraphGenArgs | None) – Additional arguments for different fragmentation functions.

Return type:

FragPart