Agent skill

Bader Charge Analysis

A skill your agent uses when the user asks about Bader charge analysis, charge transfer, oxidation states from DFT, or electron density partitioning.

AGPL-3.0Auto-check passed

Install Bader Charge Analysis

skills CLI

$ npx skills add Hello-QM/catgo-LRG --skill bader-charge-analysis -a claude-code

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

GitHub CLI

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

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 bader-charge-analysis -a codex

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

GitHub CLI

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

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

GitHub CLI

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

--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 bader-charge-analysis -a gemini-cli

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

GitHub CLI

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

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 bader-charge-analysis -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/charge-analysis .github/skills/bader-charge-analysis && 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 "bader-charge-analysis" agent skill from https://github.com/Hello-QM/catgo-LRG/tree/main/.claude/skills/charge-analysis into .github/skills/bader-charge-analysis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bader-charge-analysis", 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 bader-charge-analysis -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 bader-charge-analysis --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/charge-analysis .opencode/skills/bader-charge-analysis && 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 "bader-charge-analysis" agent skill from https://github.com/Hello-QM/catgo-LRG/tree/main/.claude/skills/charge-analysis into .opencode/skills/bader-charge-analysis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bader-charge-analysis", 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: bader-charge-analysis
GitHub stars: 205
Token cost: ~1.4k tokens
SKILL.md length: 353 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 about Bader charge analysis, charge transfer, oxidation states from DFT, or electron density partitioning.

Works in 3 steps: Single-point with charge output → Bader analysis post-processing → Get results
The user asks about Bader charge analysis
SKILL.md covers Overview, VASP Settings for Bader Analysis, MCP Workflow and Python API, plus 4 more sections
Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md

What it does

Bader Charge Analysis is an agent skill from Hello-QM/catgo-LRG. Use when the user asks about Bader charge analysis, charge transfer, oxidation states from DFT, or electron density partitioning.

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 about Bader charge analysis
Charge transfer
Oxidation states from DFT
Electron density partitioning

Example prompts

“/bader-charge-analysis”

Requirements

Python 3

Workflow steps

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

Single-point with charge output
Bader analysis post-processing
Get results

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 and python).
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

Bader Charge Analysis loads about 1.4k tokens when it runs. Until then it costs about 38 tokens; SKILL.md has 353 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~38
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). 353 words, ~1,419 tokens.

Download SKILL.mdSave it as .claude/skills/bader-charge-analysis/SKILL.md (or your agent's skills folder).

name: bader-charge-analysis
description: Use when the user asks about Bader charge analysis, charge transfer, oxidation states from DFT, or electron density partitioning.

Bader Charge Analysis

Overview

Bader analysis partitions the continuous electron density from DFT into atomic basins defined by zero-flux surfaces of the density gradient. This gives physically meaningful atomic charges and charge transfer values.

What Bader Charges Tell You

Charge transfer between adsorbate and surface
Oxidation states of atoms in a material
Electron donation/back-donation in catalytic bonds
Ionic vs covalent character of bonds

VASP Settings for Bader Analysis

Bader analysis requires fine-grid charge density output:

LAECHG = .TRUE.    # Write core charge density (AECCAR0, AECCAR2)
LCHARG = .TRUE.    # Write valence charge density (CHGCAR)
NGXF, NGYF, NGZF   # Fine FFT grid (2x default, e.g., NGXF=2*NGX)

The all-electron charge density is: AECCAR0 + AECCAR2, which is summed with the Bader code to avoid errors from pseudopotential smoothing.

MCP Workflow

Step 1: Single-point with charge output

json

{"tool": "catgo_workflow_engine", "arguments": {
  "action": "add_task", "workflow_id": "wf_bader",
  "task_type": "single_point",
  "params": {
    "software": "vasp",
    "ENCUT": 520,
    "LAECHG": true,
    "LCHARG": true,
    "PREC": "Accurate",
    "system_name": "charge density"
  }
}}

Step 2: Bader analysis post-processing

json

{"tool": "catgo_workflow_engine", "arguments": {
  "action": "add_task", "workflow_id": "wf_bader",
  "task_type": "charge_analysis",
  "depends_on": "task_sp",
  "params": {"method": "bader", "system_name": "Bader charges"}
}}

Step 3: Get results

json

{"tool": "catgo_workflow_engine", "arguments": {
  "action": "get_result", "workflow_id": "wf_bader", "task_id": "task_bader"
}}

json

{"tool": "catgo_analyze", "arguments": {
  "action": "charges", "workflow_id": "wf_bader", "task_id": "task_bader"
}}

Python API

Basic Bader Analysis

python

from catgo.workflow import Workflow

wf = Workflow("Bader charge - CO on Pt(111)")

inp = wf.add_task("structure_input", structure=co_pt_json)

# Relax first
opt = wf.add_task("geo_opt",
    structure=inp.output.structure,
    software="vasp", ENCUT=520)

# Single-point with charge density output
sp = wf.add_task("single_point",
    structure=opt.output.structure,
    software="vasp", ENCUT=520,
    LAECHG=True, LCHARG=True, PREC="Accurate")

# Bader post-processing
bader = wf.add_task("charge_analysis",
    chgcar=sp.output.chgcar,
    aeccar0=sp.output.aeccar0,
    aeccar2=sp.output.aeccar2,
    method="bader")

wf.submit()

Charge Transfer Analysis

python

# Compare charges before and after adsorption
wf = Workflow("Charge transfer analysis")

# Clean slab Bader
slab_sp = wf.add_task("single_point",
    structure=slab_opt.output.structure,
    software="vasp", ENCUT=520, LAECHG=True, LCHARG=True)
slab_bader = wf.add_task("charge_analysis",
    chgcar=slab_sp.output.chgcar,
    aeccar0=slab_sp.output.aeccar0,
    aeccar2=slab_sp.output.aeccar2)

# Slab+adsorbate Bader
ads_sp = wf.add_task("single_point",
    structure=ads_opt.output.structure,
    software="vasp", ENCUT=520, LAECHG=True, LCHARG=True)
ads_bader = wf.add_task("charge_analysis",
    chgcar=ads_sp.output.chgcar,
    aeccar0=ads_sp.output.aeccar0,
    aeccar2=ads_sp.output.aeccar2)

wf.submit()

# After completion:
# dq = q_ads(atom) - q_clean(atom) for each surface atom
# Positive dq = atom lost electrons; Negative dq = atom gained electrons

DAG Structure

structure --> geo_opt --> single_point(LAECHG) --> charge_analysis

Output Format

Bader analysis returns per-atom data:

Field	Description
`atom_index`	0-based atom index
`element`	Element symbol
`bader_charge`	Electrons in Bader basin
`valence_electrons`	POTCAR valence electron count
`net_charge`	valence_electrons - bader_charge (+ means cation)
`volume`	Bader basin volume (A^3)

Interpreting Results

Common Reference Charges (VASP PAW, valence electrons)

Element	ZVAL (valence e-)	Typical Net Charge Range
O	6	-0.8 to -1.4 (oxide)
Ti	4 or 10	+1.5 to +2.5 (TiO2)
Pt	10	-0.1 to +0.3 (metallic)
C	4	-0.5 to +1.0 (varies)
H	1	+0.4 to +0.6 (on O), -0.3 (on metal)

Show full SKILL.md (142 more words)Show less

Charge Transfer Upon Adsorption

dq_adsorbate = sum(net_charge of adsorbate atoms in slab+ads system)
             - sum(net_charge of same atoms in isolated adsorbate)

dq < 0: adsorbate gains electrons (acceptor, e.g., CO on Pt)
dq > 0: adsorbate loses electrons (donor, e.g., Na on surface)

Common Pitfalls

Always use LAECHG=.TRUE. to get all-electron charge density. Bader analysis on pseudocharge (CHGCAR alone) gives wrong atomic charges because core electrons are missing.
PREC=Accurate and a fine FFT grid improve Bader basin boundaries. Coarse grids can misassign charge near atomic boundaries.
Bader charges are NOT formal oxidation states. They are typically smaller in magnitude (e.g., Ti in TiO2 shows +2.3, not +4).
For charge transfer analysis, use the SAME computational settings for the reference and adsorbed systems.
The Bader program (Henkelman group) must be available on the HPC. CatGo calls it automatically during charge_analysis post-processing.
For spin-polarized systems, Bader can also partition spin density -- this gives magnetic moments per atom.

Files

Just SKILL.md in .claude/skills/charge-analysis of Hello-QM/catgo-LRG.

Open the folder on GitHubat commit fd6291b

Compare with similar skills

Bader Charge Analysis 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.

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Questions about Bader Charge Analysis

What does Bader Charge Analysis do?

A skill your agent uses when the user asks about Bader charge analysis, charge transfer, oxidation states from DFT, or electron density partitioning. Bader Charge Analysis is an agent skill from Hello-QM/catgo-LRG. Use when the user asks about Bader charge analysis, charge transfer, oxidation states from DFT, or electron density partitioning.

When should I use Bader Charge Analysis?

Bader Charge Analysis fits situations like: the user asks about Bader charge analysis; charge transfer; oxidation states from DFT; electron density partitioning.

How do I install Bader Charge Analysis in Claude Code?

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

How do I install Bader Charge Analysis in Codex?

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

Can I use Bader Charge Analysis 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 bader-charge-analysis -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/bader-charge-analysis, .gemini/skills/bader-charge-analysis, .github/skills/bader-charge-analysis and .opencode/skills/bader-charge-analysis in your project.

What does Bader Charge Analysis need to run?

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

Does Bader Charge Analysis 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 Bader Charge Analysis 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 Bader Charge Analysis use?

Bader Charge Analysis 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 Bader Charge Analysis use?

About 1.4k tokens (SKILL.md is roughly 5.7k 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 Bader Charge Analysis?

Skills that share tags, products or a category with Bader Charge Analysis: Intelligence Transfer (ruvnet/ruflo, 74k stars), Performing DNS Enumeration And Zone Transfer (mukul975/Anthropic-Cybersecurity-Skills, 34k stars), MoviePilot Failed Transfer Retry (jxxghp/MoviePilot, 12k stars) and Transfer Bridge (GarethManning/education-agent-skills, 840 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Bader Charge Analysis?

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 Bader Charge Analysis

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

Bader Charge Analysis

Overview

What Bader Charges Tell You

VASP Settings for Bader Analysis

MCP Workflow

Step 1: Single-point with charge output

Step 2: Bader analysis post-processing

Step 3: Get results

Python API

Basic Bader Analysis

Charge Transfer Analysis

DAG Structure

Output Format

Interpreting Results

Common Reference Charges (VASP PAW, valence electrons)

Charge Transfer Upon Adsorption

Common Pitfalls

Files

Compare with similar skills

Similar skills

More from Hello-QM/catgo-LRG

Questions about Bader Charge Analysis