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/learningmatter-mit/atomisticskills/chem-vibrationnpx skills add learningmatter-mit/AtomisticSkills --skill chem-vibrationgit clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkillsWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/learningmatter-mit/atomisticskills/chem-vibration)<a href="https://agentmods.dev/skills/learningmatter-mit/atomisticskills/chem-vibration"><img src="https://agentmods.dev/badge/skills/learningmatter-mit/atomisticskills/chem-vibration.svg" alt="Measured on agentmods" height="20"></a>What 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 | $0.00027 | $0.01354 |
| Opus 5 | $0.00014 | $0.00677 |
| Sonnet 5 | $0.00005 | $0.00271 |
| Haiku 4.5 | $0.00003 | $0.00135 |
Grade A, and why
chem-vibration scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 4d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 118 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Molecular Vibration Analysis Skill
Goal
Calculate the vibrational frequencies ($\nu$), normal modes, and zero-point energy (ZPE) of non-periodic (finite) systems — molecules, clusters, and adsorbates — within the harmonic approximation using Machine Learning Interatomic Potentials (MLIPs).
[!IMPORTANT] This skill is for molecules and finite systems only. For periodic crystals, use the phonon skill instead.
Background
In the harmonic approximation, the potential energy surface near a local minimum is approximated as $V \approx V_0 + \frac{1}{2} \sum_{ij} H_{ij} \Delta r_i \Delta r_j$, where $H_{ij} = \frac{\partial^2 V}{\partial r_i \partial r_j}$ is the Hessian (force constant) matrix. Diagonalizing the mass-weighted Hessian yields $3N$ eigenvalues: for a nonlinear molecule, $3N-6$ are real vibrational modes (and $3N-5$ for linear molecules), while the remaining eigenvalues correspond to translational and rotational degrees of freedom (near zero).
1. Prerequisites
- An MLIP wrapper must be available (
MACEWrapper,MatGLWrapper, orFAIRCHEMWrapper). - ASE must be installed in the relevant conda environment.
- The input structure must be a molecule or cluster (non-periodic). Periodic systems should use mat-phonon.
2. Choosing a Foundation Potential
[!IMPORTANT]
- Use OMAT or MatPES trained models (e.g.,
MACE-OMAT-0-small). These are optimized for forces and give reliable Hessians.- The harmonic approximation requires a well-converged equilibrium geometry. Always relax with tight force tolerance (fmax ≤ 0.001 eV/Å) before computing vibrations.
Refer to the foundation-potentials skill for details.
3. Calculation Workflow
Step 1: Prepare a molecule
Use ASE's built-in molecule database or provide a structure file:
# Built-in molecules: H2O, CO2, CH4, NH3, CH3OH, C2H6, etc.
# Or provide a .xyz / .cif / POSCAR file
What ships with it
3 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.
- 4d ago First seen · 118 lines · 27 tokens per session scan A 346c7bfdf42c
chem-vibration is a skill published in the GitHub repository learningmatter-mit/AtomisticSkills (158 stars, last pushed today), licensed MIT. It adds 27 tokens to every session and 1,354 once invoked, about $0.0001 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 2026-08-30.
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