Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx agentmods add skills/kdevos12/alkyl/asenpx skills add Kdevos12/ALKYL --skill asegit clone --depth 1 https://github.com/Kdevos12/ALKYLWhat it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5 | $0.00055 | $0.01057 |
| Opus 5 | $0.00028 | $0.00528 |
| Sonnet 5 | $0.00011 | $0.00211 |
| Haiku 4.5 | $0.00006 | $0.00106 |
Grade A, and why
ase scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 2d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 97 lines — stays where its author put it; the contents beside it link to each section on GitHub.
ASE — Atomic Simulation Environment
ASE 3.24.0 (December 2024). Central object: Atoms. Calculators are decoupled — swap between EMT, xTB, ORCA, GPAW without changing workflow.
When to Use This Skill
- Building and manipulating atomic structures (molecules, surfaces, bulk, slabs)
- Geometry optimization (DFT, semi-empirical, force fields)
- Molecular dynamics: NVE, NVT (Langevin, Berendsen), NPT
- Transition state search: NEB, climbing image, AutoNEB
- Vibrational analysis, IR spectra, zero-point energy, thermochemistry
- Interfacing with ORCA, GPAW, xTB, VASP, LAMMPS, Quantum ESPRESSO
- Reading/writing structure files: CIF, XYZ, TRAJ, SDF, PDB, VASP POSCAR
Quick Start
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
Router — What to Read
| 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 |
Key Modules
| 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 |
What ships with it
6 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 2d ago First seen · 97 lines · 55 tokens per session scan A d4f6b503c0a0
ase is a skill published in the GitHub repository Kdevos12/ALKYL (6 stars, last pushed 5mo ago), licensed MIT. It adds 55 tokens to every session and 1,057 once invoked, about $0.0003 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.
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