aim2dat.strct.ext_manipulation.rotate_structure

Module that implements routines to add a functional group or adsorbed molecule to a structure.

Module Contents

Functions

rotate_structure(structure, angles[, vector, origin, ...])

Rotate structure. The rotation is either defined by a list of 3 angles or a rotation
aim2dat.strct.ext_manipulation.rotate_structure.rotate_structure(structure: aim2dat.strct.Structure, angles: float | list[float], vector: None | list[float] = None, origin: None | list[float] = None, site_indices: slice | list[int] = slice(None), wrap: bool = False, dist_threshold: dict | list | float | int | str | None = None, change_label: bool = False)

Rotate structure. The rotation is either defined by a list of 3 angles or a rotation vector and one angle.

Parameters:

  • structure (aim2dat.strct.Structure) – Structure to rotate.

  • angles (float or list of float) – Angles for the rotation in degree. Type list for 3 individual rotations around the x, y, and z directions, respectively. Type float for a rotation around a roation vector given by vector..

  • vector (list of float (optional)) – Rotation vector in cartesian coordinates, needs to be given if angles is single number.

  • origin (list of float (optional)) – Rotation center for the rotation in cartesian coordinates. If not given, the mean position of all sites that are rotated is used.

  • site_indices (list of int (optional)) – Indices of the sites to rotate. If not given, all sites of the structure are rotated.

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

  • dist_threshold (dict, list, float, int, str or None (optional)) – Check the distances between all site pairs to ensure that none of the changed atoms collide or are too far apart. For example, 0.8 to ensure a minimum distance of 0.8 for all site pairs. A list [0.8, 1.5] adds a check for the maximum distance as well. Giving a dictionary {("C", "H"): 0.8, (0, 4): 0.8} allows distance checks for individual pairs of elements or site indices. Specifying an atomic radius type as str, e.g. covalent+10 sets the minimum threshold to the sum of covalent radii plus 10%.

  • change_label (bool (optional)) – Add suffix to the label of the new structure highlighting the performed manipulation.

Returns:

aim2dat.strct.Structure – Rotated structure.

Raises:

  • ValueError – dist_threshold needs to have keys with length 2 containing site indices or element symbols.

  • ValueError – dist_threshold needs to have keys of type List[str/int] containing site indices or element symbols.

  • TypeError – dist_threshold needs to be of type int/float/list/tuple/dict or None.

  • ValueError – If any distance between atoms is outside the threshold.