eon.geometry.process

Process-atom selection for recycling / active regions.

Module Contents

Functions

get_process_atoms

Indices of atoms that move significantly plus neighbor shells.

API

eon.geometry.process.get_process_atoms(r, p, epsilon_r: float = 0.2, nshells: int = 1) → List[int]

Indices of atoms that move significantly plus neighbor shells.

Mobile atoms: displacement > epsilon_r (PBC), else the single largest mover. Neighbor shells use covalent radii from :data:eon.atoms.elements with cutoff (r1+r2)*(1.2)*nshells, evaluated via a single vesin neighbor list at the max such cutoff, then filtered pair-wise.

Returns plain Python int indices (safe for recycling metadata repr/eval).