aim2dat.strct.ext_manipulation

External manipulation methods.

Submodules

Package Contents

Functions

add_functional_group

Module that implements functions to change molecular or crystalline structures.
aim2dat.strct.ext_manipulation.add_functional_group(structure: aim2dat.strct.strct.Structure, wrap: bool = False, host_index: int = 0, functional_group: str = 'CH3', bond_length: float = 1.25, r_max: float = 15.0, cn_method: str = 'minimum_distance', min_dist_delta: float = 0.1, n_nearest_neighbours: int = 5, econ_tolerance: float = 0.5, econ_conv_threshold: float = 0.001, voronoi_weight_type: float = 'rel_solid_angle', voronoi_weight_threshold: float = 0.5, okeeffe_weight_threshold: float = 0.5, change_label: bool = False) → aim2dat.strct.strct.Structure

Add a functional group or an atom to a host site.

Parameters:

  • key (str, int, tuple or list) – Only used in the StructureOperations class. Specifies the key or list/tuple of keys of the underlying StructureCollection object.

  • wrap (bool (optional)) – Wrap atomic positions back into the unit cell.

  • host_index (int) – Index of the host site.

  • functional_group (str) – Functional group or element symbol of the added functional group or atom.

  • bond_length (float) – Bond length between the host atom and the base atom of the functional group.

  • r_max (float (optional)) – Cut-off value for the maximum distance between two atoms in angstrom.

  • cn_method (str (optional)) – Method used to calculate the coordination environment.

  • min_dist_delta (float (optional)) – Tolerance parameter that defines the relative distance from the nearest neighbour atom for the 'minimum_distance' method.

  • n_nearest_neighbours (int (optional)) – Number of neighbours that are considered coordinated for the 'n_neighbours' method.

  • econ_tolerance (float (optional)) – Tolerance parameter for the econ method.

  • econ_conv_threshold (float (optional)) – Convergence threshold for the econ method.

  • voronoi_weight_type (str (optional)) – Weight type of the Voronoi facets. Supported options are 'covalent_atomic_radius', 'area' and 'solid_angle'. The prefix 'rel_' specifies that the relative weights with respect to the maximum value of the polyhedron are calculated.

  • voronoi_weight_threshold (float (optional)) – Weight threshold to consider a neighbouring atom coordinated.

Returns:

aiida_scripst.strct.Structure – Structure with attached functional group.