polyopening

A python tool to determine the opening angle of coordination polyhedra of solids and molecular systems.

Requirements

The following packages are required

• numpy >= 2.0,
• ase >= 3.25.0 (Atomic Simulation Environment)
• qc-grid >= 0.0.9

Installation

Usage

Set-up

from polyopening import PolyhedralOpeningAngle

get_angles = PolyhedralOpeningAngle(
    cutoff=cutoff,
    lebedev_degree=131,
    atom_type="C",
    neighbor_type=["C", "H"]
)

• cutoff: cutoff radius in Å for the first coordination shell of the reference atom. Can be a single float number for a global cutoff or a pair-wise element specific dictionary like cutoff = {('H', 'H'): 1.1, ('C', 'H'): 1.3, ('C', 'C'): 1.85} See also ASE neighbor_list.
• lebedev_degree: Determines the number of grid points for the Lebedev Quadrature. Maximum degree is 131 ( = 5810 grid points).
• atom_type: The element type, for which the opening angles are to be calculated. Can be a single string ("C") or a list of strings (["C", "H"]). If all atoms are to be determined, select "all".
• neighbor_type: The element type(s) to be taken into account when determining the coordination polyhedron. Same syntax as atom_type.

Run

angles = get_angles.compute(Atoms_object)

The calculation of the opening angles is executed by assigning an ASE Atoms object to the compute( ) function. Returns a 1D array with all the opening angles in [deg].

References

When using the code, please cite

L. Hückmann, J. Cottom, J. Meyer Adv. Phys. Res. 2024, 3, 2300109. https://doi.org/10.1002/apxr.202300109