Agent skill

Structure Enumeration

Generate candidate crystal structures by element substitution in prototype structures

Apache-2.0Auto-check passedResearch & Science

Install Structure Enumeration

skills CLI

$ npx skills add lamm-mit/scienceclaw --skill structure-enumeration -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI

$ gh skill install lamm-mit/scienceclaw structure-enumeration --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy

$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/structure-enumeration .claude/skills/structure-enumeration && rm -rf skills-src

Use ~/.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/

Paste into Claude Code

Install the "structure-enumeration" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/structure-enumeration into .claude/skills/structure-enumeration/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "structure-enumeration", 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

$skill-installer install https://github.com/lamm-mit/scienceclaw/tree/main/skills/structure-enumeration

Type 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.

skills CLI

$ npx skills add lamm-mit/scienceclaw --skill structure-enumeration -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install lamm-mit/scienceclaw structure-enumeration --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/structure-enumeration .agents/skills/structure-enumeration && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "structure-enumeration" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/structure-enumeration into .agents/skills/structure-enumeration/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "structure-enumeration", 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.

skills CLI

$ npx skills add lamm-mit/scienceclaw --skill structure-enumeration -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install lamm-mit/scienceclaw structure-enumeration --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/structure-enumeration .cursor/skills/structure-enumeration && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "structure-enumeration" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/structure-enumeration into .cursor/skills/structure-enumeration/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "structure-enumeration", 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

$ gemini skills install https://github.com/lamm-mit/scienceclaw.git --path skills/structure-enumeration

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add lamm-mit/scienceclaw --skill structure-enumeration -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install lamm-mit/scienceclaw structure-enumeration --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/structure-enumeration .gemini/skills/structure-enumeration && rm -rf skills-src

Use ~/.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/

Paste into Gemini CLI

Install the "structure-enumeration" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/structure-enumeration into .gemini/skills/structure-enumeration/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "structure-enumeration", 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.

GitHub CLI

$ gh skill install lamm-mit/scienceclaw structure-enumeration

Installs 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).

skills CLI

$ npx skills add lamm-mit/scienceclaw --skill structure-enumeration -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/structure-enumeration .github/skills/structure-enumeration && rm -rf skills-src

Use ~/.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/

Paste into GitHub Copilot

Install the "structure-enumeration" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/structure-enumeration into .github/skills/structure-enumeration/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "structure-enumeration", 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.

skills CLI

$ npx skills add lamm-mit/scienceclaw --skill structure-enumeration -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install lamm-mit/scienceclaw structure-enumeration --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/structure-enumeration .opencode/skills/structure-enumeration && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "structure-enumeration" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/structure-enumeration into .opencode/skills/structure-enumeration/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "structure-enumeration", 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: structure-enumeration
GitHub stars: 244
Token cost: ~1k tokens
SKILL.md length: 296 words
Files: 2 (incl. scripts)
Skills in repo: 85
Repo updated: Aug 21, 2026
First seen: Oct 7, 2026
Licence: Apache-2.0

At a glance

Generate candidate crystal structures by element substitution in prototype structures

Works in 5 steps: Loads each prototype structure (from MP,… → Identifies the metal site (heaviest… → For each target metal, substitutes the… → …
Tasks that involve Physical and earth sciences
SKILL.md covers Scripts, Parameters, Wyckoff Spec Format and How It Works, plus 1 more section
Runs Python scripts from its folder; calls python3

What it does

Structure Enumeration is an agent skill from lamm-mit/scienceclaw. Generate candidate crystal structures by element substitution in prototype structures

Its SKILL.md is about 1k tokens, which your agent loads only when the skill is triggered. The skill folder holds 2 other files, including scripts (for example `scripts/enumerate_structures.py`).

It sits in Research & Science, covering Physical and earth sciences. The licence is Apache-2.0.

When your agent uses it

Tasks that involve Physical and earth sciences

Example prompts

“/structure-enumeration”

Requirements

Python 3

Workflow steps

5 steps, taken from the first numbered list in SKILL.md.

Loads each prototype structure (from MP, local file, or Wyckoff construction)
Identifies the metal site (heaviest non-hydrogen element)
For each target metal, substitutes the metal site and writes a new CIF file
The original prototype is also saved (with _prototype suffix)
All CIF files are written to --output-dir

What it can do on your machine

Read from SKILL.md and the folder at commit ab9aba1. 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.
Shell commands in SKILL.md call:
- python3
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
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

Structure Enumeration loads about 1k tokens when it runs. Until then it costs about 27 tokens; SKILL.md has 296 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~27
When it runs · the whole SKILL.md, loaded when a task matches: ~1k

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 lamm-mit/scienceclaw at commit ab9aba1, republished under its Apache-2.0 licence (© lamm-mit). 296 words, ~1,018 tokens.

Download SKILL.mdSave it as .claude/skills/structure-enumeration/SKILL.md (or your agent's skills folder). This skill also uses 1 other file; get the full folder from GitHub.

name: structure-enumeration
description: Generate candidate crystal structures by element substitution in prototype structures

Structure Enumeration Skill

Generate candidate crystal structures by substituting elements in a prototype structure. Supports three prototype sources: Materials Project lookup, local CIF files, or building from spacegroup + Wyckoff positions.

Scripts

`enumerate_structures.py` — Substitute elements in a prototype

From Materials Project (for ambient-pressure phases):

bash

python3 {baseDir}/scripts/enumerate_structures.py \
  --prototypes LaH3,CaH2 \
  --metals Y,Ca,Sc,Ce \
  --format json

From Wyckoff positions (for high-pressure or hypothetical phases not in MP):

bash

python3 {baseDir}/scripts/enumerate_structures.py \
  --wyckoff '[{"name":"LaH10","spacegroup":225,"lattice":{"a":5.1},"species":["La","H","H"],"coords":[[0,0,0],[0.25,0.25,0.25],[0.118,0.118,0.118]]}]' \
  --metals Y,Ca,Sc,Ce \
  --format json

Multiple prototypes via Wyckoff:

bash

python3 {baseDir}/scripts/enumerate_structures.py \
  --wyckoff '[{"name":"LaH10","spacegroup":225,"lattice":{"a":5.1},"species":["La","H","H"],"coords":[[0,0,0],[0.25,0.25,0.25],[0.118,0.118,0.118]]},{"name":"CaH6","spacegroup":229,"lattice":{"a":3.54},"species":["Ca","H"],"coords":[[0,0,0],[0.25,0,0.5]]}]' \
  --metals Y,Sc,Ce,Ba \
  --format json

Parameters

Parameter	Description
`--prototypes`	Comma-separated formulas to fetch from Materials Project (e.g. `LaH3,CaH2`). Only works for phases in MP.
`--mp-ids`	Comma-separated Materials Project IDs (e.g. `mp-1234,mp-5678`)
`--prototype-files`	Comma-separated paths to local CIF/POSCAR files
`--wyckoff`	JSON array of prototype specs for building from spacegroup + Wyckoff positions (see format below). Use this for high-pressure phases not in MP.
`--metals`	Required. Comma-separated target metals for substitution (e.g. `Y,Ca,Sc,Ce`)
`--output-dir`	Directory for output CIF files (default: `~/.scienceclaw/enumerated_structures`)
`--format`	`summary` \| `json`
`--dry-run`	Show plan without generating structures

Wyckoff Spec Format

Each prototype is a JSON object with:

json

{
  "name": "LaH10",
  "spacegroup": 225,
  "lattice": {"a": 5.1},
  "species": ["La", "H", "H"],
  "coords": [[0,0,0], [0.25,0.25,0.25], [0.118,0.118,0.118]]
}

name: label for the prototype
spacegroup: international space group number
lattice: {"a": ...} for cubic, {"a": ..., "c": ...} for hexagonal
species: element at each Wyckoff site (first non-H element is the metal site for substitution)
coords: fractional coordinates for each Wyckoff site

Common superhydride prototypes

Prototype	SG	SG#	Lattice	Species	Coordinates
LaH10 (clathrate)	Fm-3m	225	a=5.1	La, H, H	[0,0,0], [0.25,0.25,0.25], [0.118,0.118,0.118]
CaH6 (sodalite)	Im-3m	229	a=3.54	Ca, H	[0,0,0], [0.25,0,0.5]
H3S	Im-3m	229	a=3.09	S, H	[0,0,0], [0.5,0,0.5]
YH9	P63/mmc	194	a=3.6, c=5.5	Y, H, H	[0,0,0.25], [0.167,0.333,0.25], [0.167,0.333,0.583]

How It Works

Loads each prototype structure (from MP, local file, or Wyckoff construction)
Identifies the metal site (heaviest non-hydrogen element)
For each target metal, substitutes the metal site and writes a new CIF file
The original prototype is also saved (with _prototype suffix)
All CIF files are written to --output-dir

Output (JSON)

json

{
  "status": "success",
  "output_dir": "/home/user/.scienceclaw/enumerated_structures",
  "prototypes_used": ["LaH10", "CaH6"],
  "metals": ["Y", "Ca", "Sc"],
  "total_generated": 6,
  "structures": [
    {
      "label": "YH10_from_LaH10",
      "formula": "YH10",
      "prototype": "LaH10",
      "metal": "Y",
      "n_atoms": 44,
      "cif_path": "/home/user/.scienceclaw/enumerated_structures/YH10_from_LaH10.cif"
    }
  ]
}

Files

SKILL.md and 1 other file (scripts) in skills/structure-enumeration of lamm-mit/scienceclaw.

SKILL.md
scripts/enumerate_structures.py

Open the folder on GitHubat commit ab9aba1

Compare with similar skills

Structure Enumeration 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.

Structure Enumeration compared with similar skills
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Questions about Structure Enumeration

What does Structure Enumeration do?

Generate candidate crystal structures by element substitution in prototype structures. Structure Enumeration is an agent skill from lamm-mit/scienceclaw.

When should I use Structure Enumeration?

Structure Enumeration fits situations like: tasks that involve Physical and earth sciences.

How do I install Structure Enumeration in Claude Code?

Run `npx skills add lamm-mit/scienceclaw --skill structure-enumeration -a claude-code`. Or copy the skill folder (skills/structure-enumeration in lamm-mit/scienceclaw) into .claude/skills/structure-enumeration in your project. Claude Code loads it when a task matches its description.

How do I install Structure Enumeration in Codex?

Run `npx skills add lamm-mit/scienceclaw --skill structure-enumeration -a codex`. Or copy the skill folder (skills/structure-enumeration in lamm-mit/scienceclaw) into .agents/skills/structure-enumeration in your project. Codex loads it when a task matches its description.

Can I use Structure Enumeration 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 lamm-mit/scienceclaw --skill structure-enumeration -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/structure-enumeration, .gemini/skills/structure-enumeration, .github/skills/structure-enumeration and .opencode/skills/structure-enumeration in your project.

What does Structure Enumeration need to run?

Going by SKILL.md and its folder, Structure Enumeration needs Python for the scripts in its folder and the command-line tools its instructions call (python3). Our summary lists: Python 3.

Does Structure Enumeration access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Structure Enumeration 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 Structure Enumeration use?

Structure Enumeration is published under the Apache-2.0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Structure Enumeration use?

About 1k tokens (SKILL.md is roughly 4.1k 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 Structure Enumeration?

Skills that share tags, products or a category with Structure Enumeration: 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 Structure Enumeration?

lamm-mit (a GitHub user) maintains it in lamm-mit/scienceclaw, which has 244 GitHub stars. The repository holds 85 skills in this directory. The repository was last updated on August 21, 2026.

Source: lamm-mit/scienceclaw on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.

Install Structure Enumeration

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

Workflow steps

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

Structure Enumeration Skill

Scripts

enumerate_structures.py — Substitute elements in a prototype

Parameters

Wyckoff Spec Format

Common superhydride prototypes

How It Works

Output (JSON)

Files

Compare with similar skills

Similar skills

More from lamm-mit/scienceclaw

Related

Questions about Structure Enumeration

`enumerate_structures.py` — Substitute elements in a prototype