structuretoolkit.build.geometry.repulse

structuretoolkit.build.geometry.repulse(structure: Atoms, min_dist: float = 1.5, step_size: float = 0.2, axis: int | None = None, iterations: int = 100, inplace: bool = False) → Atoms

Iteratively displace atoms apart until all interatomic distances exceed a minimum threshold.

For each pair of atoms closer than min_dist, the atom is displaced away from its nearest neighbour by up to step_size along the direction of the interatomic vector. The loop repeats until all nearest-neighbour distances satisfy the minimum criterion or the iteration limit is reached.

Parameters:

• structure (ase.Atoms) – Structure to modify.

• min_dist (float) – Minimum interatomic distance (in Å) to enforce between every pair of atoms. Defaults to 1.5.

• step_size (float) – Maximum displacement (in Å) applied to a single atom per iteration. Smaller values give smoother convergence but require more iterations. Defaults to 0.2.

• axis (int or None) – Cartesian axis index (0, 1, or 2) along which displacements are restricted. When None (default) displacements are applied in all three directions.

• iterations (int) – Maximum number of displacement steps before raising a RuntimeError. Defaults to 100.

• inplace (bool) – If True, the positions of structure are modified directly. If False (default), a copy is made and the original is left unchanged.

Returns:

The structure with adjusted atomic positions. This is the same object as structure when inplace=True, or a new copy otherwise.

Return type:

ase.Atoms

Raises:

RuntimeError – If the minimum distance criterion is not satisfied within iterations steps.