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Agent skill

Chem Irc Verification

by learningmatter-mit in learningmatter-mit/AtomisticSkills

Verify non-periodic molecular TS connectivity with forward/reverse IRC using endpoint connectivity and RMSD checks.

MITAuto-check passed

Install Chem Irc Verification

skills CLI
$ npx skills add learningmatter-mit/AtomisticSkills --skill chem-irc-verification -a claude-code

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

GitHub CLI
$ gh skill install learningmatter-mit/AtomisticSkills chem-irc-verification --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/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/chem-irc-verification .claude/skills/chem-irc-verification && 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/

Facts

Skill name
chem-irc-verification
GitHub stars
176
Token cost
~972 tokens
SKILL.md length
288 words
Files
12 (incl. scripts)
Skills in repo
129
Repo updated
First seen
Licence
MIT

At a glance

Verify non-periodic molecular TS connectivity with forward/reverse IRC using endpoint connectivity and RMSD checks.

  • SKILL.md covers Scope, Tool, Arguments and Outputs, plus 4 more sections
  • Runs Shell and Python scripts from its folder

What it does

Chem Irc Verification is an agent skill from learningmatter-mit/AtomisticSkills. Verify non-periodic molecular TS connectivity with forward/reverse IRC using endpoint connectivity and RMSD checks.

Its SKILL.md is about 970 tokens, which your agent loads only when the skill is triggered. The skill folder holds 15 other files, including scripts (for example `examples/acetonitrile/README.md`, `examples/acetonitrile/output/irc_verification_results.json` and `examples/acetonitrile/run_example.sh`).

The repository describes itself as: Integrating AtomisticSkills into Agentic IDEs (Cursor, Claude Code, Codex, Google Antigravity, Hermes Agent, etc). The licence is MIT.

Example prompts

  • “/chem-irc-verification”

Requirements

  • Python 3
  • A Bash shell

What it can do on your machine

Read from SKILL.md and the folder at commit 6257444. 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

    Ships 1 file in scripts/ (Shell and Python), which the agent can run.

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    Links to these hosts (documentation or services it may open):

    • github.com

    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

Chem Irc Verification loads about 972 tokens when it runs. Until then it costs about 34 tokens; SKILL.md has 288 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~34
When it runs · the whole SKILL.md, loaded when a task matches
~972

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); the scripts in this folder are not scanned.

SKILL.md

The full file from learningmatter-mit/AtomisticSkills at commit 6257444, republished under its MIT licence (© learningmatter-mit). 288 words, ~972 tokens.

Download SKILL.mdSave it as .claude/skills/chem-irc-verification/SKILL.md (or your agent's skills folder). This skill also uses 11 other files; get the full folder from GitHub.
name
chem-irc-verification
description
Verify non-periodic molecular TS connectivity with forward/reverse IRC using endpoint connectivity and RMSD checks.
metadata.category
chemistry
metadata.venv
fairchem, mlip

IRC Verification with Sella

Verify that a saddle-point-optimized TS connects the intended reactant and product.

Scope

  • Domain: molecular chemistry only (non-periodic systems).
  • Trigger: user has optimized reactant/product + optimized TS and needs IRC endpoint verification.
  • Exclusions: periodic systems and barrier-only workflows.

Tool

verify_irc_sella.py

Runs forward/reverse IRC from the TS, optionally relaxes endpoints, then checks mapping quality.

Use with MACE
bash
${CLAUDE_SKILL_DIR}/../../venv/run mlip python ${CLAUDE_SKILL_DIR}/scripts/verify_irc_sella.py \
  --reactant reactant_optimized.xyz \
  --product product_optimized.xyz \
  --ts ts_optimized.xyz \
  --model_type mace \
  --model_name MACE-OFF23-small \
  --fmax 0.02 \
  --steps 1000 \
  --rmsd_threshold 0.20 \
  --relax_endpoints true \
  --endpoint_relax_fmax 0.02 \
  --output_dir results/irc
Use with FAIRChem (UMA)
bash
${CLAUDE_SKILL_DIR}/../../venv/run fairchem python ${CLAUDE_SKILL_DIR}/scripts/verify_irc_sella.py \
  --reactant reactant_optimized.xyz \
  --product product_optimized.xyz \
  --ts ts_optimized.xyz \
  --model_type fairchem \
  --model_name uma-s-1p1 \
  --task_name omol \
  --fmax 0.02 \
  --steps 1000 \
  --rmsd_threshold 0.20 \
  --relax_endpoints true \
  --endpoint_relax_fmax 0.02 \
  --output_dir results/irc

Arguments

  • --reactant: required optimized reactant geometry.
  • --product: required optimized product geometry.
  • --ts: required saddle-point-optimized TS geometry.
  • --model_type: required backend (mace or fairchem).
  • --model_name: optional model identifier/checkpoint.
  • --task_name: optional model head/task (for UMA molecular runs use omol).
  • --device: auto|cpu|cuda (default auto).
  • --fmax: IRC convergence threshold in eV/A (default 0.02).
  • --steps: maximum IRC steps per direction (default 1000).
  • --rmsd_threshold: endpoint RMSD threshold in A (default 0.20).
  • --relax_endpoints: true|false, relax IRC endpoints before matching (default true).
  • --endpoint_relax_fmax: force threshold for optional endpoint relaxation (default 0.02).
  • --output_dir: required output directory.

Outputs

  • irc_forward.traj, irc_reverse.traj: IRC trajectories.
  • irc_forward.log, irc_reverse.log: IRC logs.
  • irc_forward_endpoint.xyz, irc_reverse_endpoint.xyz: terminal endpoint geometries.
  • irc_verification_results.json: endpoint assignment and pass/fail summary.

irc_verification_results.json fields include:

  • selected endpoint assignment (endpoint_mapping)
  • per-pair metrics (connectivity_match, rmsd_angstrom, thresholds)
  • all candidate assignments with total RMSD
  • final decision (verification_passed)

Verification Criterion

Verification passes only if both mapped endpoint-target pairs satisfy:

  • same formula and atom order
  • connectivity graph match
  • Kabsch-aligned RMSD <= rmsd_threshold

Default criterion: both pairs must pass with rmsd_threshold = 0.20 A.

Model Guidance

  • Recommended for molecules:
    • MACE-OFF23-small / MACE-OFF23-medium
    • uma-s-1p1 with --task_name omol
  • Use the same backend/model/head as TS optimization to avoid model inconsistency.

Prerequisites And Constraints

  • Run in mlip (MACE) or fairchem (FairChem) depending on backend (venv/run <venv> ...).
  • Script enforces pbc=False for all inputs.
  • Reactant/product/TS must have identical composition and consistent atom ordering.

Examples

See examples/ directory for sample inputs and outputs.

Author: Juno Nam Contact: GitHub @recisic

© learningmatter-mit, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 11 other files (scripts) in skills/chem-irc-verification of learningmatter-mit/AtomisticSkills.

  • SKILL.md
  • examples/acetonitrile/README.md
  • examples/acetonitrile/output/irc_forward.traj
  • examples/acetonitrile/output/irc_forward_endpoint.xyz
  • examples/acetonitrile/output/irc_reverse.traj
  • examples/acetonitrile/output/irc_reverse_endpoint.xyz
  • examples/acetonitrile/output/irc_verification_results.json
  • examples/acetonitrile/product_optimized.xyz
  • examples/acetonitrile/reactant_optimized.xyz
  • examples/acetonitrile/run_example.sh
  • examples/acetonitrile/ts_optimized.xyz
  • scripts/verify_irc_sella.py

Open the folder on GitHubat commit 6257444

Compare with similar skills

Chem Irc Verification 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.

Chem Irc Verification compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Chem Irc Verification this skilllearningmatter-mit/AtomisticSkills176—~972Automated safety check: PassMIT
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Protocol Reversezhaoxuya520/reverse-skill40k2 repos~620Automated safety check: WarnMIT
macOS Reversezhaoxuya520/reverse-skill40k2 repos~366Automated safety check: PassMIT
Node Connectopenclaw/openclaw392k—~1.6kAutomated safety check: PassMIT
Protocol Reversesickn33/agentic-awesome-skills47k1 repos~689Automated safety check: PassMIT

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Questions about Chem Irc Verification

What does Chem Irc Verification do?

Verify non-periodic molecular TS connectivity with forward/reverse IRC using endpoint connectivity and RMSD checks. Chem Irc Verification is an agent skill from learningmatter-mit/AtomisticSkills. Verify non-periodic molecular TS connectivity with forward/reverse IRC using endpoint connectivity and RMSD checks.

How do I install Chem Irc Verification in Claude Code?

Run `npx skills add learningmatter-mit/AtomisticSkills --skill chem-irc-verification -a claude-code`. Or copy the skill folder (skills/chem-irc-verification in learningmatter-mit/AtomisticSkills) into .claude/skills/chem-irc-verification in your project. Claude Code loads it when a task matches its description.

How do I install Chem Irc Verification in Codex?

Run `npx skills add learningmatter-mit/AtomisticSkills --skill chem-irc-verification -a codex`. Or copy the skill folder (skills/chem-irc-verification in learningmatter-mit/AtomisticSkills) into .agents/skills/chem-irc-verification in your project. Codex loads it when a task matches its description.

Can I use Chem Irc Verification 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 learningmatter-mit/AtomisticSkills --skill chem-irc-verification -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/chem-irc-verification, .gemini/skills/chem-irc-verification, .github/skills/chem-irc-verification and .opencode/skills/chem-irc-verification in your project.

What does Chem Irc Verification need to run?

Going by SKILL.md and its folder, Chem Irc Verification needs a shell and Python for the scripts in its folder. Our summary lists: Python 3; A Bash shell.

Does Chem Irc Verification access the network?

SKILL.md names 1 domain. As links in the text: github.com. This is read from the text; nothing was executed.

Is Chem Irc Verification 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. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.

What licence does Chem Irc Verification use?

Chem Irc Verification is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Chem Irc Verification use?

About 972 tokens (SKILL.md is roughly 3.9k 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 Chem Irc Verification?

Skills that share tags, products or a category with Chem Irc Verification: Connect (ComposioHQ/awesome-claude-skills, 77k stars), Protocol Reverse (zhaoxuya520/reverse-skill, 40k stars), macOS Reverse (zhaoxuya520/reverse-skill, 40k stars) and Node Connect (openclaw/openclaw, 392k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Chem Irc Verification?

learningmatter-mit (a GitHub organization) maintains it in learningmatter-mit/AtomisticSkills, which has 176 GitHub stars. The repository holds 129 skills in this directory. The repository was last updated on October 7, 2026.

Source: learningmatter-mit/AtomisticSkills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.