quemb.molbe.fragment.fragpart

class quemb.molbe.fragment.fragpart(frag_type='autogen', closed=False, iao_valence_basis=None, valence_only=False, print_frags=True, write_geom=False, be_type='be2', frag_prefix='f', connectivity='euclidean', mol=None, frozen_core=False, cutoff=20.0, remove_nonnunique_frags=True, additional_args=None)

Fragment/partitioning definition

Interfaces two main fragmentation functions (autogen & chain) 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', 'hchain_simple', 'chain']) – Name of fragmentation function. ‘chemgen’, ‘autogen’, ‘graphgen’, ‘hchain_simple’, and ‘chain’ are supported. Defaults to ‘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 (Mole | None) – 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.

  • valence_only (bool) – If this option is set to True, all calculation will be performed in the valence basis in the IAO partitioning. This is an experimental feature.

  • 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.

  • remove_nonunique_frags – Whether to remove fragments which are strict subsets of another fragment in the system. True by default.

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

  • connectivity (str) – Keyword string specifying the distance metric to be used for edge weights in the fragment adjacency graph. Currently supports “euclidean” (which uses the square of the distance between atoms in real space to determine connectivity within a fragment.)

  • cutoff (float) – Atoms with an edge weight beyond cutoff will be excluded from the shortest_path calculation. This is crucial when handling very large systems, where computing the shortest paths from all to all becomes non-trivial. Defaults to 20.0.

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

Methods

__init__([frag_type, closed, ...])

chain(mol[, frozen_core, closed])

Hard coded linear chain fragment constructor

hchain_simple()

Hard coded fragmentation feature