# Gaussian Elf

> Generate electron-localization-function (ELF) cube files, a VMD three-dimensional isosurface image, and two-dimensional Multiwfn/Matplotlib plane maps from Gaussian formatted checkpoint (.fch) files. Use for Gaussian FCH ELF analysis and plots.

- **Type:** Skill
- **Install:** `agentstack add skill-nanhuai-x-gaussian-molecule-workflow-gaussian-elf`
- **Verified:** Yes — security-reviewed for prompt injection and unsafe behavior
- **Seller:** [Nanhuai-X](https://agentstack.voostack.com/s/nanhuai-x)
- **Installs:** 0
- **Category:** [Content & Media](https://agentstack.voostack.com/c/content-and-media)
- **Latest version:** 0.1.0
- **License:** MIT
- **Upstream author:** [Nanhuai-X](https://github.com/Nanhuai-X)
- **Source:** https://github.com/Nanhuai-X/gaussian-molecule-workflow/tree/main/skills/gaussian-elf

## Install

```sh
agentstack add skill-nanhuai-x-gaussian-molecule-workflow-gaussian-elf
```

Requires the [AgentStack CLI](https://agentstack.voostack.com/docs/cli). Works with Claude Code, Cursor, and any MCP-compatible agent.

## About

# Gaussian ELF analysis

Use this skill for `.fch` files when the desired outputs are an ELF volume and standard two-dimensional ELF maps.

## Preconditions

- Use `fch/.fch` as input and `output//` as the final destination.
- Locate Multiwfn with `MULTIWFN_BIN`, then `PATH`, then a path supplied by the user. VMD/Pillow are required when the 3D image is requested.
- NumPy and Matplotlib are required for the 2D maps; Pillow is required for PNG verification/conversion.
- Do not alter the user's repository or global `settings.ini`.

## Workflow

Run the bundled ELF exporter from the analysis folder:

```powershell
python /scripts/run_elf.py --input fch --output output
```

Use the bundled `assets/elf.txt`; do not depend on the original project layout.

1. Make an isolated temporary directory for each molecule and log Multiwfn output to `output//`.
2. Run the established Multiwfn ELF export sequence. Confirm a newly generated `elf.cub`, then place it at `_ELF.cub`.
3. Create a temporary copy of the Multiwfn `settings.ini` if silent DISLIN PNG output or a custom `graph2Dsize` is required. Point the run at that temporary configuration and remove it after successful collection; never permanently edit `settings.ini`.
4. Generate the default XY maps: color-filled and shaded with projection. Save them as `_ELF_fill_xy.png` and `_ELF_shaded+proj_xy.png`.
5. If VMD is requested, render the cube as `_ELF.png`. Confirm that the cube, 3D PNG, and default 2D PNG files are new and readable. Keep style, plane, offset, and plot size in the molecule log.

## Variants and failures

- Accept explicit `xy`, `xz`, `yz`, or a three-atom plane, plus offset and style parameters; retain the two default XY images unless the user asks otherwise.
- If `plane.txt` or a required PNG is not produced, stop, preserve the log, and report the exact missing-output issue. Do not reuse a previous plane file or image.
- Summarize one ELF cube, one optional VMD 3D PNG, and the requested 2D PNG maps per molecule and keep terminal output quiet during long runs.

## Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

- **Author:** [Nanhuai-X](https://github.com/Nanhuai-X)
- **Source:** [Nanhuai-X/gaussian-molecule-workflow](https://github.com/Nanhuai-X/gaussian-molecule-workflow)
- **License:** MIT

Install and usage instructions live in the source repository linked above.

## Pricing

- **Free** — Free

## Security capabilities

Automated source analysis of v0.1.0 — what this tool can access:

- **Network access:** no
- **Filesystem access:** no
- **Shell / process execution:** no
- **Environment & secrets:** no
- **Dynamic code execution:** no

*"Yes" means the capability is present in the source — more access means more to trust, not that it is unsafe.*


## Versions

- **0.1.0** — security scan: passed — Imported from the upstream source.

## Links

- Listing page: https://agentstack.voostack.com/l/skill-nanhuai-x-gaussian-molecule-workflow-gaussian-elf
- Seller: https://agentstack.voostack.com/s/nanhuai-x
- Browse the marketplace: https://agentstack.voostack.com/browse

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