Energy Calculator
benchflow-ai/skillsbench
Calculate per-second RMS energy from audio files. An agent skill from benchflow-ai/skillsbench.
Calculate vibrational frequencies, normal modes, zero-point energy, and IR spectra of molecules and clusters using MLIPs.
MITAuto-check passed
Install Chem Vibration
$ npx skills add learningmatter-mit/AtomisticSkills --skill chem-vibration -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install learningmatter-mit/AtomisticSkills chem-vibration --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/chem-vibration .claude/skills/chem-vibration && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "chem-vibration" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/chem-vibration into .claude/skills/chem-vibration/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "chem-vibration", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/chem-vibrationType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add learningmatter-mit/AtomisticSkills --skill chem-vibration -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install learningmatter-mit/AtomisticSkills chem-vibration --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/chem-vibration .agents/skills/chem-vibration && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "chem-vibration" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/chem-vibration into .agents/skills/chem-vibration/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "chem-vibration", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add learningmatter-mit/AtomisticSkills --skill chem-vibration -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install learningmatter-mit/AtomisticSkills chem-vibration --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/chem-vibration .cursor/skills/chem-vibration && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "chem-vibration" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/chem-vibration into .cursor/skills/chem-vibration/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "chem-vibration", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/learningmatter-mit/AtomisticSkills.git --path skills/chem-vibration--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add learningmatter-mit/AtomisticSkills --skill chem-vibration -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install learningmatter-mit/AtomisticSkills chem-vibration --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/chem-vibration .gemini/skills/chem-vibration && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "chem-vibration" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/chem-vibration into .gemini/skills/chem-vibration/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "chem-vibration", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install learningmatter-mit/AtomisticSkills chem-vibrationInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add learningmatter-mit/AtomisticSkills --skill chem-vibration -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/chem-vibration .github/skills/chem-vibration && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "chem-vibration" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/chem-vibration into .github/skills/chem-vibration/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "chem-vibration", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add learningmatter-mit/AtomisticSkills --skill chem-vibration -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install learningmatter-mit/AtomisticSkills chem-vibration --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/chem-vibration .opencode/skills/chem-vibration && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "chem-vibration" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/chem-vibration into .opencode/skills/chem-vibration/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "chem-vibration", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
chem-vibration- GitHub stars
- 176
- Token cost
- ~1.3k tokens
- SKILL.md length
- 457 words
- Files
- 4 (incl. scripts)
- Skills in repo
- 129
- Repo updated
- First seen
- Licence
- MIT
At a glance
Calculate vibrational frequencies, normal modes, zero-point energy, and IR spectra of molecules and clusters using MLIPs.
- Works in 6 steps: Prerequisites → Choosing a Foundation Potential → Calculation Workflow → …
- SKILL.md covers Goal, Background, 1. Prerequisites and 2. Choosing a Foundation…, plus 4 more sections
- Runs Python scripts from its folder
What it does
Chem Vibration is an agent skill from learningmatter-mit/AtomisticSkills. Calculate vibrational frequencies, normal modes, zero-point energy, and IR spectra of molecules and clusters using MLIPs.
Its SKILL.md is about 1.3k tokens, which your agent loads only when the skill is triggered. The skill folder holds 6 other files, including scripts (for example `examples/H2O/README.md`, `examples/H2O/vibration_results.json` and `scripts/calculate_vibrations.py`).
The repository describes itself as: Integrating AtomisticSkills into Agentic IDEs (Cursor, Claude Code, Codex, Google Antigravity, Hermes Agent, etc). The licence is MIT.
Example prompts
- “/chem-vibration”
Requirements
- Python 3
Workflow steps
6 steps, taken from the step headings in SKILL.md.
What it can do on your machine
Read from SKILL.md and the folder at commit 6257444. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Ships 1 file in scripts/ (Python), which the agent can run.
From the folder's file list and the shell code blocks in SKILL.md.
Network
Links to these hosts (documentation or services it may open):
github.com
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Chem Vibration loads about 1.3k tokens when it runs. Until then it costs about 34 tokens; SKILL.md has 457 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.
SKILL.md
The full file from learningmatter-mit/AtomisticSkills at commit 6257444, republished under its MIT licence (© learningmatter-mit). 457 words, ~1,265 tokens.
Download SKILL.mdSave it as
.claude/skills/chem-vibration/SKILL.md (or your agent's skills folder). This skill also uses 3 other files; get the full folder from GitHub.- name
- chem-vibration
- description
- Calculate vibrational frequencies, normal modes, zero-point energy, and IR spectra of molecules and clusters using MLIPs.
- metadata.category
- chemistry
- metadata.venv
- mlip
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 is included in the
mlipandfairchemenvironments. - 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 fileStep 2: Run vibration analysis
${CLAUDE_SKILL_DIR}/../../venv/run mlip python ${CLAUDE_SKILL_DIR}/scripts/calculate_vibrations.py \
--molecule H2O \
--model_type mace \
--model_name MACE-OMAT-0-small \
--output_dir research/my_folder/vibrationsWith a structure file instead:
${CLAUDE_SKILL_DIR}/../../venv/run mlip python ${CLAUDE_SKILL_DIR}/scripts/calculate_vibrations.py \
--structure path/to/molecule.xyz \
--model_type mace \
--model_name MACE-OMAT-0-small \
--no_relax \
--output_dir research/my_folder/vibrationsKey Parameters:
--molecule: ASE built-in molecule name (e.g.,H2O,CO2,CH4)--structure: Path to structure file (alternative to--molecule)--delta: Finite-difference displacement in Å (default: 0.01)--nfree: Number of displacements per degree of freedom, 2 or 4 (default: 2)--relax / --no_relax: Whether to relax before vibration analysis (default: relax)--fmax: Force convergence for relaxation (default: 0.001 eV/Å)
Show full SKILL.md (160 more words)Show less
4. Output Files
vibration_results.json: Summary including:frequencies_cm1: All frequencies in cm⁻¹frequencies_meV: All frequencies in meVreal_modes: Indices and frequencies of real vibrational modesimaginary_modes: Indices and frequencies of imaginary modes (should be near zero)zero_point_energy_eV: Zero-point energy in eVn_atoms,formula,is_linear
vib.N.traj: Trajectory files for each vibrational mode (for visualization)
5. Examples
See examples/H2O/ for a water molecule vibration analysis.
${CLAUDE_SKILL_DIR}/../../venv/run mlip python ${CLAUDE_SKILL_DIR}/scripts/calculate_vibrations.py \
--molecule H2O \
--model_type mace \
--model_name MACE-OMAT-0-small \
--output_dir ${CLAUDE_SKILL_DIR}/examples/H2OExpected H2O vibrational modes (experimental reference):
| Mode | Type | Experimental (cm⁻¹) |
|---|---|---|
| Bending | ν₂ | ~1595 |
| Symmetric stretch | ν₁ | ~3657 |
| Asymmetric stretch | ν₃ | ~3756 |
6. Constraints
- Molecule/cluster only: This skill applies the harmonic approximation to finite systems. For periodic crystals, use mat-phonon.
- Equilibrium required: The structure MUST be at a local minimum (forces ≈ 0). Large residual forces invalidate the harmonic approximation.
- Harmonic approximation: Only valid near equilibrium. Accuracy degrades for large-amplitude motions and near dissociation.
- Environments: Scripts require an environment with MLIP packages (
venv/run <venv> ...):mlipfor MACE and MatGL/CHGNet modelsfairchemfor FairChem/UMA models
Author: Bowen Deng Contact: GitHub @learningmatter-mit
© learningmatter-mit, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
SKILL.md and 3 other files (scripts) in skills/chem-vibration of learningmatter-mit/AtomisticSkills.
- SKILL.md
- examples/H2O/README.md
- examples/H2O/vibration_results.json
- scripts/calculate_vibrations.py
Open the folder on GitHubat commit 6257444
Compare with similar skills
Chem Vibration next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Chem Vibration this skilllearningmatter-mit/AtomisticSkills | 176 | — | ~1.3k | Automated safety check: Pass | MIT | |
| Energy Calculatorbenchflow-ai/skillsbench | 1.8k | — | ~437 | Automated safety check: Pass | Apache-2.0 | |
| Bio Free Energy CalculationsGPTomics/bioSkills | 1.2k | 1 repos | ~4.5k | Automated safety check: Pass | MIT | |
| Dynamic Workflow Modeaffaan-m/ECC | 275k | 1 repos | ~1.3k | Automated safety check: Pass | MIT | |
| Agent GitHub Modesruvnet/ruflo | 74k | 2 repos | ~1.7k | Automated safety check: Pass | MIT | |
| Consent Modethedaviddias/Front-End-Checklist | 74k | — | ~425 | Automated safety check: Pass | MIT |
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Questions about Chem Vibration
What does Chem Vibration do?
Calculate vibrational frequencies, normal modes, zero-point energy, and IR spectra of molecules and clusters using MLIPs. Chem Vibration is an agent skill from learningmatter-mit/AtomisticSkills. Calculate vibrational frequencies, normal modes, zero-point energy, and IR spectra of molecules and clusters using MLIPs.
How do I install Chem Vibration in Claude Code?
Run `npx skills add learningmatter-mit/AtomisticSkills --skill chem-vibration -a claude-code`. Or copy the skill folder (skills/chem-vibration in learningmatter-mit/AtomisticSkills) into .claude/skills/chem-vibration in your project. Claude Code loads it when a task matches its description.
How do I install Chem Vibration in Codex?
Run `npx skills add learningmatter-mit/AtomisticSkills --skill chem-vibration -a codex`. Or copy the skill folder (skills/chem-vibration in learningmatter-mit/AtomisticSkills) into .agents/skills/chem-vibration in your project. Codex loads it when a task matches its description.
Can I use Chem Vibration in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add learningmatter-mit/AtomisticSkills --skill chem-vibration -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/chem-vibration, .gemini/skills/chem-vibration, .github/skills/chem-vibration and .opencode/skills/chem-vibration in your project.
What does Chem Vibration need to run?
Going by SKILL.md and its folder, Chem Vibration needs Python for the scripts in its folder. Our summary lists: Python 3.
Does Chem Vibration access the network?
SKILL.md names 1 domain. As links in the text: github.com. This is read from the text; nothing was executed.
Is Chem Vibration safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.
What licence does Chem Vibration use?
Chem Vibration is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Chem Vibration use?
About 1.3k tokens (SKILL.md is roughly 5.1k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
What are the alternatives to Chem Vibration?
Skills that share tags, products or a category with Chem Vibration: Energy Calculator (benchflow-ai/skillsbench, 1.8k stars), Bio Free Energy Calculations (GPTomics/bioSkills, 1.2k stars), Dynamic Workflow Mode (affaan-m/ECC, 275k stars) and Agent GitHub Modes (ruvnet/ruflo, 74k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Chem Vibration?
learningmatter-mit (a GitHub organization) maintains it in learningmatter-mit/AtomisticSkills, which has 176 GitHub stars. The repository holds 129 skills in this directory. The repository was last updated on October 7, 2026.
Source: learningmatter-mit/AtomisticSkills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.