Agent skill

Intercalation

A skill your agent uses when the user asks to intercalate atoms or ions between layers, insert lithium into a cathode, or place species in interlayer gaps of a layered material.

AGPL-3.0Auto-check passed

Install Intercalation

skills CLI

$ npx skills add Hello-QM/catgo-LRG --skill intercalation -a claude-code

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

GitHub CLI

$ gh skill install Hello-QM/catgo-LRG intercalation --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/Hello-QM/catgo-LRG.git skills-src && mkdir -p .claude/skills && cp -r skills-src/.claude/skills/structure-intercalation .claude/skills/intercalation && 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 "intercalation" agent skill from https://github.com/Hello-QM/catgo-LRG/tree/main/.claude/skills/structure-intercalation into .claude/skills/intercalation/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "intercalation", 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/Hello-QM/catgo-LRG/tree/main/.claude/skills/structure-intercalation

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 Hello-QM/catgo-LRG --skill intercalation -a codex

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

GitHub CLI

$ gh skill install Hello-QM/catgo-LRG intercalation --agent codex

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

Manual copy

$ git clone --depth 1 https://github.com/Hello-QM/catgo-LRG.git skills-src && mkdir -p .agents/skills && cp -r skills-src/.claude/skills/structure-intercalation .agents/skills/intercalation && 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 "intercalation" agent skill from https://github.com/Hello-QM/catgo-LRG/tree/main/.claude/skills/structure-intercalation into .agents/skills/intercalation/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "intercalation", 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 Hello-QM/catgo-LRG --skill intercalation -a cursor

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

GitHub CLI

$ gh skill install Hello-QM/catgo-LRG intercalation --agent cursor

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

Manual copy

$ git clone --depth 1 https://github.com/Hello-QM/catgo-LRG.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/.claude/skills/structure-intercalation .cursor/skills/intercalation && 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 "intercalation" agent skill from https://github.com/Hello-QM/catgo-LRG/tree/main/.claude/skills/structure-intercalation into .cursor/skills/intercalation/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "intercalation", 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/Hello-QM/catgo-LRG.git --path .claude/skills/structure-intercalation

--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 Hello-QM/catgo-LRG --skill intercalation -a gemini-cli

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

GitHub CLI

$ gh skill install Hello-QM/catgo-LRG intercalation --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/Hello-QM/catgo-LRG.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/.claude/skills/structure-intercalation .gemini/skills/intercalation && 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 "intercalation" agent skill from https://github.com/Hello-QM/catgo-LRG/tree/main/.claude/skills/structure-intercalation into .gemini/skills/intercalation/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "intercalation", 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 Hello-QM/catgo-LRG intercalation

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 Hello-QM/catgo-LRG --skill intercalation -a github-copilot

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

Manual copy

$ git clone --depth 1 https://github.com/Hello-QM/catgo-LRG.git skills-src && mkdir -p .github/skills && cp -r skills-src/.claude/skills/structure-intercalation .github/skills/intercalation && 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 "intercalation" agent skill from https://github.com/Hello-QM/catgo-LRG/tree/main/.claude/skills/structure-intercalation into .github/skills/intercalation/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "intercalation", 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 Hello-QM/catgo-LRG --skill intercalation -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 Hello-QM/catgo-LRG intercalation --agent opencode

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

Manual copy

$ git clone --depth 1 https://github.com/Hello-QM/catgo-LRG.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/.claude/skills/structure-intercalation .opencode/skills/intercalation && 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 "intercalation" agent skill from https://github.com/Hello-QM/catgo-LRG/tree/main/.claude/skills/structure-intercalation into .opencode/skills/intercalation/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "intercalation", 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: intercalation
GitHub stars: 205
Token cost: ~1.4k tokens
SKILL.md length: 494 words
Files: 1
Skills in repo: 75
Repo updated: Sep 22, 2026
First seen: Oct 7, 2026
Licence: AGPL-3.0

At a glance

A skill your agent uses when the user asks to intercalate atoms or ions between layers, insert lithium into a cathode, or place species in interlayer gaps of a layered material.

Works in 5 steps: Fetch the host structure → Create a supercell for dilute… → Intercalate Li → …
The user asks to intercalate atoms
SKILL.md covers Overview, MCP Tool: catgo_intercalation, Complete Workflow: Li… and Intercalation Voltage…, plus 3 more sections
Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md

What it does

Intercalation is an agent skill from Hello-QM/catgo-LRG. Use when the user asks to intercalate atoms or ions between layers, insert lithium into a cathode, or place species in interlayer gaps of a layered material.

Its SKILL.md is about 1.4k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

The repository describes itself as: AI-driven workbench for computational materials science — interactive 3D structure viewer, natural-language CatBot assistant, visual DAG workflow engine, HPC job submission… The licence is AGPL-3.0.

When your agent uses it

The user asks to intercalate atoms
Ions between layers
Insert lithium into a cathode
Place species in interlayer gaps of a layered material

Example prompts

“/intercalation”

Workflow steps

5 steps, taken from the step headings in SKILL.md.

Fetch the host structure
Create a supercell for dilute intercalation
Intercalate Li
Verify
Relax and compute intercalation voltage

What it can do on your machine

Read from SKILL.md and the folder at commit fd6291b. 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
No scripts in the folder and no shell commands in SKILL.md (its code samples are json).
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

Intercalation loads about 1.4k tokens when it runs. Until then it costs about 43 tokens; SKILL.md has 494 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~43
When it runs · the whole SKILL.md, loaded when a task matches: ~1.4k

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); files beside SKILL.md are not scanned.

SKILL.md

The full file from Hello-QM/catgo-LRG at commit fd6291b, republished under its AGPL-3.0 licence (© Hello-QM). 494 words, ~1,354 tokens.

Download SKILL.mdSave it as .claude/skills/intercalation/SKILL.md (or your agent's skills folder).

name: intercalation
description: Use when the user asks to intercalate atoms or ions between layers, insert lithium into a cathode, or place species in interlayer gaps of a layered material.

Intercalation

Overview

Intercalation inserts guest atoms or ions into the interlayer spaces of a layered host material. This is fundamental to battery electrode design, where ions shuttle between electrodes during charge/discharge cycles.

Common applications:

Li-ion batteries: Li intercalation in LiCoO2, LiFePO4, graphite
Na-ion batteries: Na intercalation in layered oxides, MXenes
Supercapacitors: ion insertion in MXenes, layered hydroxides
Catalysis: intercalated species modifying interlayer chemistry
2D materials: ion intercalation in MoS2, graphite for exfoliation

MCP Tool: catgo_intercalation

json

{"tool": "catgo_intercalation", "arguments": {
  "structure": "<current structure dict>",
  "species": "Li",
  "position": "auto",
  "n_intercalants": 1
}}

Parameter	Description	Default
`structure`	Layered host structure dict	(required)
`species`	Intercalant element symbol	(required)
`position`	Placement strategy	"auto"
`n_intercalants`	Number of intercalant atoms to insert	1

Position Modes

Mode	Description
`auto`	Finds the largest gap in z-fractional coordinates and inserts at the midpoint. Best default for layered materials.
`tetrahedral`	Places at approximate tetrahedral interstitial sites (frac coords ~0.25).
`octahedral`	Places at approximate octahedral interstitial sites (frac coords ~0.5).
`custom`	For manual positioning (specify coordinates separately).

Router: `/build/intercalation` (POST)

Complete Workflow: Li Intercalation in LiCoO2

Step 1: Fetch the host structure

json

{"tool": "catgo_fetch", "arguments": {
  "action": "crystal", "formula": "CoO2", "source": "mp"
}}

Or fetch the fully lithiated phase:

json

{"tool": "catgo_fetch", "arguments": {
  "action": "crystal", "formula": "LiCoO2", "source": "mp"
}}

Step 2: Create a supercell for dilute intercalation

json

{"tool": "catgo_structure", "arguments": {
  "action": "supercell",
  "scaling": [2, 2, 1]
}}

Step 3: Intercalate Li

json

{"tool": "catgo_intercalation", "arguments": {
  "species": "Li",
  "position": "auto",
  "n_intercalants": 1
}}

For higher concentrations, increase n_intercalants. Multiple intercalants are distributed across the interlayer plane.

Step 4: Verify

json

{"tool": "catgo_view", "arguments": {"action": "get_state"}}

Check: Li atom is between layers, not overlapping with host atoms, reasonable interlayer distance preserved.

Step 5: Relax and compute intercalation voltage

json

{"tool": "catgo_workflow_engine", "arguments": {
  "action": "create", "params": {"name": "Li-CoO2 intercalation"}
}}

json

{"tool": "catgo_workflow_engine", "arguments": {
  "action": "add_task", "params": {
    "workflow_id": "<wf_id>",
    "task_type": "geo_opt",
    "params": {"software": "vasp", "ENCUT": 520,
               "LDAU": true, "LDAUU": {"Co": 3.32},
               "system_name": "LixCoO2 relax"}
  }
}}

Intercalation Voltage Calculation

The average intercalation voltage is:

V = -(E[Li_x2 Host] - E[Li_x1 Host] - (x2 - x1) * E[Li_metal]) / ((x2 - x1) * F)

where F is the Faraday constant. In practice:

Relax the empty host (x = 0)
Relax the fully intercalated structure (x = 1)
Optionally relax intermediate compositions
Compute V from the energy difference

Common Intercalant Species

Species	Application	Typical Hosts
Li	Li-ion batteries	CoO2, FePO4, MnO2, graphite, TiS2
Na	Na-ion batteries	MnO2, V2O5, Prussian blue analogues
K	K-ion batteries	Graphite, MoS2
Mg	Mg batteries	V2O5, MoS2, TiS2
H	Proton intercalation	MnO2, WO3 (electrochromics)

Show full SKILL.md (190 more words)Show less

DFT Considerations

DFT+U: Required for transition metal oxides (Co, Mn, Fe, Ni). Common U values: Co (3.32 eV), Mn (3.9 eV), Fe (5.3 eV), Ni (6.2 eV).
Van der Waals: DFT-D3 corrections important for layered materials where interlayer bonding is weak.
Spin polarization: Always use ISPIN=2 for transition metal oxides.
K-points: Sufficient sampling in the layer plane; fewer points needed perpendicular to layers.

Common Pitfalls

The auto position mode finds the largest z-gap. For materials with multiple interlayer gaps of similar size, verify the intercalant ended up in the correct gap.
Always relax after intercalation. The host lattice expands to accommodate the guest species.
For concentrated intercalation (multiple atoms), ensure intercalants are not placed too close together. Check with catgo_view after insertion.
The host structure should be a bulk layered material, not a slab. Slabs have vacuum that will confuse the auto-positioning algorithm.
Transition metal oxidation states change upon intercalation (e.g., Co4+ to Co3+ when Li is inserted). This affects magnetic moments and DFT+U parameters.
For accurate voltage predictions, use the same ENCUT, k-points, and DFT+U parameters for all compositions in the voltage calculation.

Files

Just SKILL.md in .claude/skills/structure-intercalation of Hello-QM/catgo-LRG.

Open the folder on GitHubat commit fd6291b

Compare with similar skills

Intercalation 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.

Intercalation compared with similar skills
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Wrdn Effect Atom OptimisticUsefulSoftwareCo/executor	4.1k	—	~2.9k	Automated safety check: Notes	MIT	today
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Questions about Intercalation

What does Intercalation do?

A skill your agent uses when the user asks to intercalate atoms or ions between layers, insert lithium into a cathode, or place species in interlayer gaps of a layered material. Intercalation is an agent skill from Hello-QM/catgo-LRG. Use when the user asks to intercalate atoms or ions between layers, insert lithium into a cathode, or place species in interlayer gaps of a layered material.

When should I use Intercalation?

Intercalation fits situations like: the user asks to intercalate atoms; ions between layers; insert lithium into a cathode; place species in interlayer gaps of a layered material.

How do I install Intercalation in Claude Code?

Run `npx skills add Hello-QM/catgo-LRG --skill intercalation -a claude-code`. Or copy the skill folder (.claude/skills/structure-intercalation in Hello-QM/catgo-LRG) into .claude/skills/intercalation in your project. Claude Code loads it when a task matches its description.

How do I install Intercalation in Codex?

Run `npx skills add Hello-QM/catgo-LRG --skill intercalation -a codex`. Or copy the skill folder (.claude/skills/structure-intercalation in Hello-QM/catgo-LRG) into .agents/skills/intercalation in your project. Codex loads it when a task matches its description.

Can I use Intercalation 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 Hello-QM/catgo-LRG --skill intercalation -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/intercalation, .gemini/skills/intercalation, .github/skills/intercalation and .opencode/skills/intercalation in your project.

What does Intercalation need to run?

SKILL.md names no scripts, command-line tools or credentials: Intercalation is instructions for the agent only.

Does Intercalation 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 Intercalation 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. Review the folder before installing.

What licence does Intercalation use?

Intercalation is published under the AGPL-3.0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Intercalation use?

About 1.4k tokens (SKILL.md is roughly 5.4k 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 Intercalation?

Skills that share tags, products or a category with Intercalation: Compose Atoms (lobehub/lobehub, 83k stars), Atomic Chat MCP Tool for NanoClaw (nanocoai/nanoclaw, 31k stars), Performing Purple Team Atomic Testing (mukul975/Anthropic-Cybersecurity-Skills, 34k stars) and Wrdn Effect Atom Optimistic (UsefulSoftwareCo/executor, 4.1k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Intercalation?

Hello-QM (a GitHub user) maintains it in Hello-QM/catgo-LRG, which has 205 GitHub stars. The repository holds 75 skills in this directory. The repository was last updated on September 22, 2026.

Source: Hello-QM/catgo-LRG on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.

Install Intercalation

Facts

At a glance

What it does

When your agent uses it

Example prompts

Workflow steps

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

Intercalation

Overview

MCP Tool: catgo_intercalation

Position Modes

Router: /build/intercalation (POST)

Complete Workflow: Li Intercalation in LiCoO2

Step 1: Fetch the host structure

Step 2: Create a supercell for dilute intercalation

Step 3: Intercalate Li

Step 4: Verify

Step 5: Relax and compute intercalation voltage

Intercalation Voltage Calculation

Common Intercalant Species

DFT Considerations

Common Pitfalls

Files

Compare with similar skills

Similar skills

More from Hello-QM/catgo-LRG

Questions about Intercalation

Router: `/build/intercalation` (POST)