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Apply random/Gaussian/scaled-random displacements to atomic structures, single or batch.
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Based on SOC occupation classification
Build common bulk crystal structures (FCC/BCC/HCP/diamond/zincblende/...) using ASE.
Build a coherent lattice-matched interface between two bulk structures using the pymatgen ZSL algorithm.
Workflow, lattice-matching strategies, and pitfalls for building interfaces between two crystals/surfaces.
Strategies for searching, filtering, and downloading structures from the Materials Project (MP) database.
Workflow for building Metal-Organic Framework (MOF) structures (MOF-5, Cu-BTC, IRMOF series, custom).
Methods for building isolated molecules (ASE database, SMILES via RDKit, organometallics, endohedral cages, NEB pathways).
| 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 |
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).