neb-irc-activation-energy SKILL.md skillA
neb-irc-activation-energy from jaechang-hits/sciagent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add jaechang-hits/sciagent-skills/neb-irc-activation-energy@git:20260815.8ceaf44Pins git:20260815.8ceaf44 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- jaechang-hits/sciagent-skills
- Path
skills/scientific-computing/neb-irc-activation-energy/SKILL.md- Versions recorded
- 5
- Latest version
- git:20260815.01d627a, committed Aug 15, 2026
- First version recorded
- Aug 15, 2026
- Size
- 15,822 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
NEB-IRC activation energy pipeline for reaction barriers using GFN2-xTB and pysisyphus. Optimize reactant and product geometries, run CI-NEB path search, optimize the transition state with a Hessian, verify with IRC (one imaginary mode, endpoints matching reactant/product, single NEB maximum), and report the electronic and Gibbs barriers. Use when you need a transition state, reaction barrier, activation energy, minimum energy path, or intrinsic reaction coordinate. Covers reactant/product…
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# NEB-IRC activation energy pipeline ## Overview Computes a reaction activation energy end to end — optimize reactant and product, find the minimum energy path with climbing-image NEB, refine the transition state with a Hessian, and confirm it with IRC — using GFN2-xTB through pysisyphus. Outputs a verified TS geometry, the barrier (ΔE‡; ΔG‡ after thermal corrections), an IRC energy profile (`irc_energy_profile.png`), and an animated TS imaginary-mode viewer (`ts_imaginary_mode.html`). Verification is required, not optional: a converged TS is meaningless until its single imaginary mode and IRC endpoints are checked. ## When to Use - Finding the transition state for an elementary reaction step and its activation energy - Computing a reaction barrier (ΔE‡ or ΔG‡) to rank a series of related reactions - Running a climbing-image NEB / minimum energy path between a reactant and product - Verifying a candidate TS with IRC — does it connect the intended reactant and product? - Screening barriers at a cheap semi-empirical level before committing DFT time Reach for DFT on a multi-core node instead when you need quantitative agreement with …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/neb-irc-activation-energy@sha256:009d2bd80db7da53The line at the top of this page pins the label git:20260815.8ceaf44, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_urynkk6kdswwjq6t)
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Versions
The registry has recorded 5 versions of this file, all committed on Aug 15, 2026.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260815.01d627a latest | 2026-08-15 | 01d627a | 15,822 B | A | view · diff |
| git:20260815.88171ad | 2026-08-15 | 88171ad | 15,903 B | A | view · diff |
| git:20260815.8ceaf44 | 2026-08-15 | 8ceaf44 | 16,546 B | A | view · diff |
| git:20260815.d26e626 | 2026-08-15 | d26e626 | 16,579 B | A | view · diff |
| git:20260815.e698250 | 2026-08-15 | e698250 | 16,352 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (15822 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
jaechang-hits/sciagent-skills · 381 stars · license a license file GitHub does not identify · pushed 2026-10-16 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_urynkk6kdswwjq6t GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/neb-irc-activation-energy GET https://markdownregistry.com/api/v1/blob/009d2bd80db7da53749b8672bb2dc81ad2b835c31374426180f7cfdec61b4415
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.