exatomic.algorithms.geometry module

Geometry

Functions for constructing molecular and solid state geometries with symmetry adapted or crystalline structures.

exatomic.algorithms.geometry.make_small_molecule(center, ligand, distance, geometry, offset=None, plane=None, axis=None, domains=None, unit='Angstrom', angle=None)[source]

A minimal molecule builder for simple one-center, homogeneous ligand molecules of various general chemistry molecular geometries. If ‘domains’ is not specified and geometry is ambiguous (like ‘bent’), it just guesses the simplest geometry (smallest number of domains).

Parameters:

  • center (str) – atomic symbol of central atom

  • ligand (str) – atomic symbol of ligand atoms

  • distance (float) – distance between central atom and ligand

  • geometry (str) – molecular geometry

  • offset (np.array) – 3-array of position of central atom

  • plane (str) – cartesian plane of molecule (eg. for ‘square_planar’)

  • axis (str) – cartesian axis of molecule (eg. for ‘linear’)

  • domains (int) – number of electronic domains

  • unit (str) – unit of distance (default ‘Angstrom’)

Returns:

df (Atom) – Atom table of small molecule