Cantera Ignition Delay
K-Dense-AI/scientific-agent-skills
Runs Cantera constant-volume or constant-pressure ignition simulations and reports temperature-based ignition delay with mechanism provenance and checks.
Query the Crystallography Open Database (COD) and other OPTIMADE-compliant databases for experimental crystal structures.
Install Mat DB Optimade
$ npx skills add learningmatter-mit/AtomisticSkills --skill mat-db-optimade -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install learningmatter-mit/AtomisticSkills mat-db-optimade --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/mat-db-optimade .claude/skills/mat-db-optimade && 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 "mat-db-optimade" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/mat-db-optimade into .claude/skills/mat-db-optimade/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "mat-db-optimade", 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/mat-db-optimadeType 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 mat-db-optimade -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install learningmatter-mit/AtomisticSkills mat-db-optimade --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/mat-db-optimade .agents/skills/mat-db-optimade && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "mat-db-optimade" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/mat-db-optimade into .agents/skills/mat-db-optimade/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "mat-db-optimade", 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 mat-db-optimade -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install learningmatter-mit/AtomisticSkills mat-db-optimade --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/mat-db-optimade .cursor/skills/mat-db-optimade && 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 "mat-db-optimade" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/mat-db-optimade into .cursor/skills/mat-db-optimade/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "mat-db-optimade", 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/mat-db-optimade--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 mat-db-optimade -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install learningmatter-mit/AtomisticSkills mat-db-optimade --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/mat-db-optimade .gemini/skills/mat-db-optimade && 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 "mat-db-optimade" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/mat-db-optimade into .gemini/skills/mat-db-optimade/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "mat-db-optimade", 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 mat-db-optimadeInstalls 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 mat-db-optimade -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/mat-db-optimade .github/skills/mat-db-optimade && 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 "mat-db-optimade" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/mat-db-optimade into .github/skills/mat-db-optimade/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "mat-db-optimade", 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 mat-db-optimade -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 mat-db-optimade --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/mat-db-optimade .opencode/skills/mat-db-optimade && 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 "mat-db-optimade" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/mat-db-optimade into .opencode/skills/mat-db-optimade/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "mat-db-optimade", 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
mat-db-optimade- GitHub stars
- 176
- Token cost
- ~634 tokens
- SKILL.md length
- 244 words
- Files
- 8 (incl. scripts)
- Skills in repo
- 129
- Repo updated
- First seen
- Licence
- MIT
At a glance
Query the Crystallography Open Database (COD) and other OPTIMADE-compliant databases for experimental crystal structures.
- Tasks that involve Physical and earth sciences
- SKILL.md covers Goal, Instructions, Constraints and References
- Runs Python scripts from its folder
What it does
Mat DB Optimade is an agent skill from learningmatter-mit/AtomisticSkills. Query the Crystallography Open Database (COD) and other OPTIMADE-compliant databases for experimental crystal structures.
Its SKILL.md is about 630 tokens, which your agent loads only when the skill is triggered. The skill folder holds 12 other files, including scripts (for example `examples/query-aflow/README.md`, `examples/query-aflow/results_aflow.json` and `examples/query-cod/README.md`).
It sits in Research & Science, covering Physical and earth sciences. The repository describes itself as: Integrating AtomisticSkills into Agentic IDEs (Cursor, Claude Code, Codex, Google Antigravity, Hermes Agent, etc). The licence is MIT.
When your agent uses it
- Tasks that involve Physical and earth sciences
Example prompts
- “/mat-db-optimade”
Requirements
- Python 3
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):
doi.orggithub.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
Mat DB Optimade loads about 634 tokens when it runs. Until then it costs about 34 tokens; SKILL.md has 244 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). 244 words, ~634 tokens.
Download SKILL.mdSave it as
.claude/skills/mat-db-optimade/SKILL.md (or your agent's skills folder). This skill also uses 7 other files; get the full folder from GitHub.- name
- mat-db-optimade
- description
- Query the Crystallography Open Database (COD) and other OPTIMADE-compliant databases for experimental crystal structures.
- metadata.category
- materials
- metadata.venv
- cpu
mat-db-optimade
Goal
To query experimental crystal structures (e.g. from the Crystallography Open Database - COD, NOMAD) using the standardized REST API provided by OPTIMADE, and to extract the structural data and metadata in a JSON format.
Instructions
Step 1. Querying an OPTIMADE Database
Use the query_optimade.py script to fetch structure data based on standard OPTIMADE query language filters.
${CLAUDE_SKILL_DIR}/../../venv/run cpu python ${CLAUDE_SKILL_DIR}/scripts/query_optimade.py \
results.json \
--filter 'elements HAS ALL "Na", "Cl"' \
--provider cod \
--max_results 5Parameters:
output: Path to the output JSON file where results will be stored.--filter: The OPTIMADE filter string. (e.g.,elements HAS ALL "O", "Ti").--provider: Comma-separated list of database providers. Defaults tocod.--max_results: Maximum number of structures to pull per provider. Defaults to 10.
Supported Database Providers (Common short IDs)
When using the --provider parameter, you can provide the following short string identifiers for well-known databases:
cod– Crystallography Open Database: The largest open-access collection of experimentally determined crystal structures.nmd– NOMAD: Comprehensive repository of both theoretical methods and experimental configurations.aflow– AFLOW: Automatic-FLOW Computational Materials Data Repository.mp– Materials Project: Well-known theoretical stable/unstable materials repository based on DFT.oqmd– Open Quantum Materials Database: High-throughput DFT database of thermodynamic and structural properties.jarvis– JARVIS: Joint Automated Repository for Various Integrated Simulations.
Constraints
- Environments: The scripts require the
cpuenvironment. - Provider Status: Sometimes specific providers (like Aflow or NOMAD) may experience API downtime. If a provider fails, the
optimadeclient will log warnings.
References
- Andersen, C. W., et al. "OPTIMADE, an API for exchanging materials data." Scientific Data, 8, 217 (2021). DOI
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 7 other files (scripts) in skills/mat-db-optimade of learningmatter-mit/AtomisticSkills.
- SKILL.md
- examples/query-aflow/README.md
- examples/query-aflow/results_aflow.json
- examples/query-cod/README.md
- examples/query-cod/results.json
- examples/query-nomad/README.md
- examples/query-nomad/results_nomad.json
- scripts/query_optimade.py
Open the folder on GitHubat commit 6257444
Compare with similar skills
Mat DB Optimade 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 |
|---|---|---|---|---|---|---|
| Mat DB Optimade this skilllearningmatter-mit/AtomisticSkills | 176 | — | ~634 | Automated safety check: Pass | MIT | |
| Cantera Ignition DelayK-Dense-AI/scientific-agent-skills | 48k | 2 repos | ~2.2k | Automated safety check: Pass | MIT | |
| AstropyzLanqing/codex-claude-academic-skills | 4.6k | 14 repos | ~2.9k | Automated safety check: Pass | BSD-3-Clause | |
| PymatgenzLanqing/codex-claude-academic-skills | 4.6k | 12 repos | ~5k | Automated safety check: Pass | MIT | |
| Weathertrpc-group/trpc-agent-go | 1.8k | 9 repos | ~591 | Automated safety check: Pass | Apache-2.0 | |
| Pymol VisualizationChatMol/ChatMol | 372 | — | ~1.2k | Automated safety check: Pass | MIT |
Similar skills
Astropy
zLanqing/codex-claude-academic-skills
Comprehensive Python library for astronomy and astrophysics.
Pymatgen
zLanqing/codex-claude-academic-skills
Materials science toolkit. An agent skill from zLanqing/codex-claude-academic-skills.
Weather
trpc-group/trpc-agent-go
Get current weather and forecasts via wttr.in or Open-Meteo.
Pymol Visualization
ChatMol/ChatMol
Generate publication-quality molecular visualization images using PyMOL.
Review
Muuuun/luxas
Write domain-authentic review articles that synthesize rather than stack.
More from learningmatter-mit/AtomisticSkills
All 129 skills in this repoDrug Binding Site Definition
learningmatter-mit/AtomisticSkills
Define a docking search box (center coordinates + box dimensions in Angstroms) from a co-crystal ligand, binding-site residues, or a saved JSON specification.
Drug Complex System Builder
learningmatter-mit/AtomisticSkills
Build a solvated, charge-neutralized protein-ligand complex for OpenMM molecular dynamics simulation.
Drug Pocket Detection
learningmatter-mit/AtomisticSkills
Identify and rank ligandable pockets on a protein structure or model using geometry (fpocket) or an ML predictor (P2Rank).
Chem Bond Dissociation
learningmatter-mit/AtomisticSkills
Calculate homolytic and heterolytic bond dissociation energies (BDEs) for all single bonds in a molecule using MLIPs with RDKit fragmentation.
Chem Conformer Search
learningmatter-mit/AtomisticSkills
Generate molecular conformers with RDKit ETKDG, relax with MLIPs, and rank by energy with Boltzmann weighting.
Chem DB Mof
learningmatter-mit/AtomisticSkills
Query multiple MOF databases (QMOF via MPContribs; ARC-MOF DB7/Majumdar et al.
Related
Categories
Questions about Mat DB Optimade
What does Mat DB Optimade do?
Query the Crystallography Open Database (COD) and other OPTIMADE-compliant databases for experimental crystal structures. Mat DB Optimade is an agent skill from learningmatter-mit/AtomisticSkills. Query the Crystallography Open Database (COD) and other OPTIMADE-compliant databases for experimental crystal structures.
When should I use Mat DB Optimade?
Mat DB Optimade fits situations like: tasks that involve Physical and earth sciences.
How do I install Mat DB Optimade in Claude Code?
Run `npx skills add learningmatter-mit/AtomisticSkills --skill mat-db-optimade -a claude-code`. Or copy the skill folder (skills/mat-db-optimade in learningmatter-mit/AtomisticSkills) into .claude/skills/mat-db-optimade in your project. Claude Code loads it when a task matches its description.
How do I install Mat DB Optimade in Codex?
Run `npx skills add learningmatter-mit/AtomisticSkills --skill mat-db-optimade -a codex`. Or copy the skill folder (skills/mat-db-optimade in learningmatter-mit/AtomisticSkills) into .agents/skills/mat-db-optimade in your project. Codex loads it when a task matches its description.
Can I use Mat DB Optimade 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 mat-db-optimade -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/mat-db-optimade, .gemini/skills/mat-db-optimade, .github/skills/mat-db-optimade and .opencode/skills/mat-db-optimade in your project.
What does Mat DB Optimade need to run?
Going by SKILL.md and its folder, Mat DB Optimade needs Python for the scripts in its folder. Our summary lists: Python 3.
Does Mat DB Optimade access the network?
SKILL.md names 2 domains. As links in the text: doi.org and github.com. This is read from the text; nothing was executed.
Is Mat DB Optimade 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 Mat DB Optimade use?
Mat DB Optimade 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 Mat DB Optimade use?
About 634 tokens (SKILL.md is roughly 2.5k 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 Mat DB Optimade?
Skills that share tags, products or a category with Mat DB Optimade: Cantera Ignition Delay (K-Dense-AI/scientific-agent-skills, 48k stars), Astropy (zLanqing/codex-claude-academic-skills, 4.6k stars), Pymatgen (zLanqing/codex-claude-academic-skills, 4.6k stars) and Weather (trpc-group/trpc-agent-go, 1.8k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Mat DB Optimade?
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.