Agent skill

Energy Diagram

A skill your agent uses when the user asks to generate a reaction energy diagram, free energy profile, potential energy surface plot, or pathway comparison diagram for catalysis or reaction…

AGPL-3.0Auto-check passedDevelopment

Install Energy Diagram

skills CLI

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

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

GitHub CLI

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

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 energy-diagram -a codex

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

GitHub CLI

$ gh skill install Hello-QM/catgo-LRG energy-diagram --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/energy-diagram .agents/skills/energy-diagram && 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 "energy-diagram" agent skill from https://github.com/Hello-QM/catgo-LRG/tree/main/.claude/skills/energy-diagram into .agents/skills/energy-diagram/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "energy-diagram", 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 energy-diagram -a cursor

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

GitHub CLI

$ gh skill install Hello-QM/catgo-LRG energy-diagram --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/energy-diagram .cursor/skills/energy-diagram && 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 "energy-diagram" agent skill from https://github.com/Hello-QM/catgo-LRG/tree/main/.claude/skills/energy-diagram into .cursor/skills/energy-diagram/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "energy-diagram", 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/energy-diagram

--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 energy-diagram -a gemini-cli

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

GitHub CLI

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

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 energy-diagram -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/energy-diagram .github/skills/energy-diagram && 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 "energy-diagram" agent skill from https://github.com/Hello-QM/catgo-LRG/tree/main/.claude/skills/energy-diagram into .github/skills/energy-diagram/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "energy-diagram", 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 energy-diagram -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 energy-diagram --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/energy-diagram .opencode/skills/energy-diagram && 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 "energy-diagram" agent skill from https://github.com/Hello-QM/catgo-LRG/tree/main/.claude/skills/energy-diagram into .opencode/skills/energy-diagram/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "energy-diagram", 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: energy-diagram
GitHub stars: 205
Token cost: ~1.8k tokens
SKILL.md length: 568 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 generate a reaction energy diagram, free energy profile, potential energy surface plot, or pathway comparison diagram for catalysis or reaction…

Works in 5 steps: Transition-state steps (is_ts: true)… → Energies should be Gibbs free energies… → When comparing pathways, use the same… → …
The user asks to generate a reaction energy diagram
SKILL.md covers Overview, MCP Tool:…, Parameters and Return Format, plus 3 more sections
Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md

What it does

Energy Diagram is an agent skill from Hello-QM/catgo-LRG. Use when the user asks to generate a reaction energy diagram, free energy profile, potential energy surface plot, or pathway comparison diagram for catalysis or reaction mechanism studies.

Its SKILL.md is about 1.8k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

It sits in Development, covering Diagrams. 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 generate a reaction energy diagram
Free energy profile
Potential energy surface plot
Pathway comparison diagram for catalysis

Example prompts

“/energy-diagram”

Requirements

Python 3

Workflow steps

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

Transition-state steps (is_ts: true) must be placed between two
Energies should be Gibbs free energies in eV, referenced to a common
When comparing pathways, use the same energy reference for all of
The anti-overlap algorithm adjusts annotation positions when
The returned traces use null-gap separation for disconnected

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

Energy Diagram loads about 1.8k tokens when it runs. Until then it costs about 51 tokens; SKILL.md has 568 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~51
When it runs · the whole SKILL.md, loaded when a task matches: ~1.8k

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). 568 words, ~1,807 tokens.

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

name: energy-diagram
description: Use when the user asks to generate a reaction energy diagram, free energy profile, potential energy surface plot, or pathway comparison diagram for catalysis or reaction mechanism studies.
tags: analysis, catalysis, energy-diagram, free-energy, pathway, Plotly

Energy Diagram Generation

Overview

Generates Plotly-compatible reaction energy pathway diagrams from computed intermediate and transition-state energies. The output includes horizontal line segments for intermediates, cubic-spline curves for transition states, and dashed connectors between consecutive steps.

Key applications:

Reaction mechanism comparison: Overlay multiple pathways on one diagram
Catalysis studies: Visualize OER, HER, CO2RR, NRR free energy profiles
Transition state analysis: Show activation barriers as TS arches
Publication figures: Export as SVG/PNG from the Plotly viewer

MCP Tool: catgo_catalysis_energy_diagram

In the full MCP server, use the catgo_catalysis_energy_diagram tool. In the workflow engine, the free_energy node generates energy diagrams automatically from upstream gibbs_energy nodes.

Generate a Simple Energy Diagram

json

{"tool": "catgo_catalysis_energy_diagram", "arguments": {
  "pathways": [
    {
      "name": "OER on RuO2(110)",
      "color": "#1f77b4",
      "steps": [
        {"label": "*", "energy": 0.0},
        {"label": "*OH", "energy": 0.85},
        {"label": "*O", "energy": 1.60},
        {"label": "*OOH", "energy": 3.20},
        {"label": "O2", "energy": 4.92}
      ]
    }
  ]
}}

Compare Multiple Pathways

json

{"tool": "catgo_catalysis_energy_diagram", "arguments": {
  "pathways": [
    {
      "name": "RuO2(110)",
      "color": "#1f77b4",
      "steps": [
        {"label": "*", "energy": 0.0},
        {"label": "*OH", "energy": 0.85},
        {"label": "*O", "energy": 1.60},
        {"label": "*OOH", "energy": 3.20},
        {"label": "O2", "energy": 4.92}
      ]
    },
    {
      "name": "IrO2(110)",
      "color": "#ff7f0e",
      "steps": [
        {"label": "*", "energy": 0.0},
        {"label": "*OH", "energy": 1.05},
        {"label": "*O", "energy": 1.95},
        {"label": "*OOH", "energy": 3.45},
        {"label": "O2", "energy": 4.92}
      ]
    }
  ]
}}

Include Transition States

Mark transition states with "is_ts": true. These appear as cubic-spline arches between the adjacent intermediates:

json

{"tool": "catgo_catalysis_energy_diagram", "arguments": {
  "pathways": [
    {
      "name": "CO oxidation on Pt(111)",
      "color": "#2ca02c",
      "steps": [
        {"label": "CO* + O*", "energy": 0.0},
        {"label": "TS", "energy": 0.85, "is_ts": true},
        {"label": "CO2(g)", "energy": -1.20}
      ]
    }
  ]
}}

Custom Layout Configuration

json

{"tool": "catgo_catalysis_energy_diagram", "arguments": {
  "pathways": [ ... ],
  "config": {
    "height": 500,
    "y_label": "Gibbs Free Energy (eV)",
    "x_label": "Reaction Coordinate",
    "energy_format": ".3f",
    "line_width": 4
  }
}}

Parameters

pathways (required)

Array of pathway objects. Each pathway contains:

Field	Type	Required	Description
name	string	no	Legend label for this pathway
color	string	no	Line color (CSS color, e.g., `"#1f77b4"`)
steps	list[dict]	yes	Ordered list of intermediates and TSs

Each step dict:

Field	Type	Required	Description
label	string	yes	State label (e.g., "*OH", "TS1")
energy	float	yes	Energy in eV
is_ts	bool	no	True for transition states (default false)

config (optional)

Parameter	Type	Default	Description
base_spacing	float	1.0	Base horizontal spacing between states
hline_ratio	float	0.3	Width of horizontal energy lines
ts_spacing_ratio	float	0.4	Width of TS spline curves
vline_ratio	float	0.3	Width of dashed connectors
line_width	float	3	Line thickness
energy_format	string	".2f"	Python format string for energy labels
height	int	450	Plot height in pixels
y_label	string	"Free Energy (eV)"	Y-axis title
x_label	string	"Reaction Coordinate"	X-axis title

Return Format

json

{
  "traces": [ ... ],
  "layout": { ... },
  "annotations": [ ... ]
}

The return value is directly compatible with Plotly: pass traces as the data array, merge annotations into layout.annotations, and render with Plotly.newPlot(div, traces, layout).

Workflow Integration: free_energy Node

In the CatGo workflow engine, the free_energy node automatically generates an energy diagram from upstream gibbs_energy nodes:

json

{"tool": "catgo_workflow", "arguments": {
  "action": "batch",
  "workflow_id": "wf_oer",
  "operations": [
    {"op": "add_node", "node_type": "free_energy", "label": "diagram",
     "params": {"input_mode": "auto"}},
    {"op": "connect", "from_id": "gibbs_oh", "to_id": "diagram",
     "from_handle": "gibbs", "to_handle": "gibbs"},
    {"op": "connect", "from_id": "gibbs_o", "to_id": "diagram",
     "from_handle": "gibbs", "to_handle": "gibbs"},
    {"op": "connect", "from_id": "gibbs_ooh", "to_id": "diagram",
     "from_handle": "gibbs", "to_handle": "gibbs"}
  ]
}}

The free_energy node collects Gibbs energies from all connected upstream nodes and arranges them into a pathway diagram automatically.

Show full SKILL.md (231 more words)Show less

Important: Use Gibbs Free Energies, NOT DFT Energies

All energy values passed to this tool must be Gibbs free energies (G), not raw DFT electronic energies (E_DFT). Each intermediate and gas-phase reference must go through the full chain: geo_opt --> freq --> gibbs_energy.

G = E_DFT + ZPE - TS

Using raw E_DFT omits zero-point energy (ZPE) and entropy (TS), which contribute 0.2-0.5 eV per intermediate. This makes the resulting diagram quantitatively wrong and can change which step is potential-determining.

For electrochemical reactions (OER, HER, CO2RR, NRR), also apply:

Atom balancing with gas-phase references (H2, H2O, CO2, N2, NH3)
pH correction: subtract 0.059 * pH eV per proton-transfer step at 298 K

Common Pitfalls

Transition-state steps (is_ts: true) must be placed between two non-TS steps in the pathway. A TS at the start or end of a pathway will cause errors because the spline needs adjacent energy values.
Energies should be Gibbs free energies in eV, referenced to a common zero (typically the clean slab + gas-phase references).
When comparing pathways, use the same energy reference for all of them. Shifting one pathway by a constant offset invalidates the comparison.
The anti-overlap algorithm adjusts annotation positions when multiple pathways have states at the same x-coordinate. For heavily overlapping pathways, increase base_spacing in the config.
The returned traces use null-gap separation for disconnected line segments. This is a standard Plotly pattern for drawing multiple segments in one trace.

Files

Just SKILL.md in .claude/skills/energy-diagram of Hello-QM/catgo-LRG.

Open the folder on GitHubat commit fd6291b

Compare with similar skills

Energy Diagram 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.

Energy Diagram compared with similar skills
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Fireworks Tech Graphtisfeng/Easydict	15k	1 repos	~1.4k	Automated safety check: Pass	MIT	5 days ago
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Questions about Energy Diagram

What does Energy Diagram do?

A skill your agent uses when the user asks to generate a reaction energy diagram, free energy profile, potential energy surface plot, or pathway comparison diagram for catalysis or reaction…. Energy Diagram is an agent skill from Hello-QM/catgo-LRG. Use when the user asks to generate a reaction energy diagram, free energy profile, potential energy surface plot, or pathway comparison diagram for catalysis or reaction mechanism studies.

When should I use Energy Diagram?

Energy Diagram fits situations like: the user asks to generate a reaction energy diagram; free energy profile; potential energy surface plot; pathway comparison diagram for catalysis.

How do I install Energy Diagram in Claude Code?

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

How do I install Energy Diagram in Codex?

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

Can I use Energy Diagram 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 energy-diagram -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/energy-diagram, .gemini/skills/energy-diagram, .github/skills/energy-diagram and .opencode/skills/energy-diagram in your project.

What does Energy Diagram need to run?

SKILL.md names no scripts, command-line tools or credentials: Energy Diagram is instructions for the agent only. Our summary lists: Python 3.

Does Energy Diagram 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 Energy Diagram 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 Energy Diagram use?

Energy Diagram 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 Energy Diagram use?

About 1.8k tokens (SKILL.md is roughly 7.2k 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 Energy Diagram?

Skills that share tags, products or a category with Energy Diagram: Archify Diagrams (tt-a1i/archify, 82k stars), JSON Canvas (heyitsnoah/claudesidian, 2.6k stars), Diagram Design (cathrynlavery/diagram-design, 49k stars) and Fireworks Tech Graph (tisfeng/Easydict, 15k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Energy Diagram?

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 Energy Diagram

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

Energy Diagram Generation

Overview

MCP Tool: catgo_catalysis_energy_diagram

Generate a Simple Energy Diagram

Compare Multiple Pathways

Include Transition States

Custom Layout Configuration

Parameters

pathways (required)

config (optional)

Return Format

Workflow Integration: free_energy Node

Important: Use Gibbs Free Energies, NOT DFT Energies

Common Pitfalls

Files

Compare with similar skills

Similar skills

More from Hello-QM/catgo-LRG

Related

Questions about Energy Diagram