structure-perturbation

name	structure-perturbation
description	Apply random/Gaussian/scaled-random displacements to atomic structures, single or batch.
when_to_use	Use when generating perturbed structures for MLIP training data, NEB starts, finite-temperature initial configurations, or to stress-test a relaxed structure.
entry	scripts/structure_perturbation.py

Structure Perturbation

Two CLI sub-commands:

• perturb_structure — produce one perturbed copy with stats.
• batch_perturb — produce many (different seeds) for dataset generation.

python3 scripts/structure_perturbation.py perturb_structure \
  --input-file Fe_bcc.extxyz --displacement-magnitude 0.1 --perturbation-mode gaussian --seed 42

python3 scripts/structure_perturbation.py batch_perturb \
  --input-file Fe_bcc.extxyz --num-structures 50 --displacement-magnitude 0.05

Modes: random (uniform), gaussian (std = magnitude), scaled_random (scaled by per-element covalent radius).