ase — independently scanned and version-tracked by SaferSkills.
SaferSkills independently audited ase (Agent Skill) and scored it 100/100 (green). The audit ran 55 deterministic rules across Security, Supply Chain, Maintenance, Transparency, and Community; it found 0 high-severity and 0 lower-severity findings. The full rule-by-rule trace and per-finding evidence are below. Free, methodology-open.
Findings & checks · 0 flagged
Every scanned point with the score it earned and what moved between them.
First recorded scan — no prior version to compare against.
The primary manifest — the file an agent reads to learn what this artifact does.
ASE 3.24.0 (December 2024). Central object: Atoms. Calculators are decoupled — swap between EMT, xTB, ORCA, GPAW without changing workflow.
from ase import Atoms
from ase.build import molecule
from ase.calculators.emt import EMT
from ase.optimize import BFGS
# Build water molecule
atoms = molecule('H2O')
atoms.calc = EMT() # fast toy calculator
# Geometry optimization
opt = BFGS(atoms, trajectory='h2o.traj', logfile='opt.log')
opt.run(fmax=0.05) # eV/Å convergence criterion
print(atoms.get_potential_energy()) # eV
print(atoms.get_forces()) # eV/Å| Task | Reference |
|---|---|
| Atoms object, cell, PBC, building molecules/surfaces/bulk | references/atoms-structures.md |
| Calculators: EMT, ORCA, xTB, GPAW, LAMMPS, config | references/calculators.md |
| Geometry optimization, constraints, filters, unit cells | references/optimization.md |
| Molecular dynamics: NVE/NVT/NPT, thermostats, trajectories | references/molecular-dynamics.md |
| NEB, climbing image, IDPP, AutoNEB, barrier extraction | references/neb-transitions.md |
| Vibrations, phonons, IR, ZPE, thermochemistry | references/vibrations-analysis.md |
| Module | Import | Role |
|---|---|---|
Atoms | from ase import Atoms | Core structure object |
units | from ase import units | Unit conversions (eV, Å, fs…) |
io | from ase import io | Read/write all formats |
build | from ase.build import … | molecule, bulk, surface, slab |
optimize | from ase.optimize import BFGS, FIRE, LBFGS | Geometry optimizers |
md | from ase.md.verlet import VelocityVerlet | Molecular dynamics |
mep | from ase.mep import NEB, DyNEB | Minimum energy paths |
vibrations | from ase.vibrations import Vibrations | Normal modes |
phonons | from ase.phonons import Phonons | Phonon dispersion |
constraints | from ase.constraints import FixAtoms, FixBondLength | Constraints |
filters | from ase.filters import ExpCellFilter, FrechetCellFilter | Cell optimization |
db | from ase.db import connect | ASE database |
pip install ase # latest (3.24.0+)
conda install -c conda-forge ase
# Verify
python -c "import ase; print(ase.__version__)"from ase import units
units.eV # 1.0 (internal unit)
units.Hartree # 27.2114 eV
units.kcal / units.mol # 0.04336 eV
units.fs # femtosecond in ASE time units
units.bar # pressure
units.Bohr # 0.529177 Åase + scientific-skills:rowan — cloud QM (DFT, pKa) for heavy calculationsase + scientific-skills:pymatgen — materials/crystallography workflowschem_qm.py — ORCA/Gaussian input gen + output parsingscientific-skills:biopython — PDB structure loading for biomolecular systems~30 seconds. Free. No account. Every finding cites a rule and a line of evidence.