What is chem-irc-verification?

A verification workflow that checks whether a molecular transition-state structure connects the intended reactant and product. It uses forward and reverse intrinsic reaction-coordinate (IRC) calculations and compares the resulting endpoints.

Use it to verify optimized, non-periodic molecular transition states with MACE or FAIRChem models and endpoint RMSD checks.

It detects transition states that look plausible but lead to the wrong molecules or fail to connect both sides of the reaction.

chem-irc-verification — Skill for Claude Code and Codex by learningmatter-mit: A verification workflow that checks whether a molecular trans

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

agentmods

npx agentmods add skills/learningmatter-mit/atomisticskills/chem-irc-verification

Any agent

npx skills add learningmatter-mit/AtomisticSkills --skill chem-irc-verification

Clone the repo

git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills

Made for: Claude Code, Codex.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

README.md

[![agentmods](https://agentmods.dev/badge/skills/learningmatter-mit/atomisticskills/chem-irc-verification.svg)](https://agentmods.dev/skills/learningmatter-mit/atomisticskills/chem-irc-verification)

Your own site

<a href="https://agentmods.dev/skills/learningmatter-mit/atomisticskills/chem-irc-verification"><img src="https://agentmods.dev/badge/skills/learningmatter-mit/atomisticskills/chem-irc-verification.svg" alt="Measured on agentmods" height="20"></a>

Per session 26 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 982 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 0 findings. Scan, not verified.

Origin original No closer match found in the catalogue.

Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

Model	Per session	Once invoked
Fable 5	$0.00026	$0.00982
Opus 5	$0.00013	$0.00491
Sonnet 5	$0.00005	$0.00196
Haiku 4.5	$0.00003	$0.00098

Measured 4d ago against content hash 304cdbdf19f6, method: parsed. Prices are Anthropic first-party input rates as of 2026-08-30, from the pricing page.

Security

Grade A, and why

chem-irc-verification scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 4d ago.

The scan reads SKILL.md. This mod also ships 2 executable files (examples/acetonitrile/run_example.sh, scripts/verify_irc_sella.py), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

.agents/skills/chem-irc-verification/SKILL.md · 118 lines

How it starts

The opening of the file, as written. The whole thing — 118 lines — stays where its author put it; the contents beside it link to each section on GitHub.

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

# Env: mace-agent
python .agents/skills/chem-irc-verification/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)

# Env: fairchem-agent
python .agents/skills/chem-irc-verification/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.

Read the full file on GitHub · 118 lines

Files

What ships with it

11 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

4d ago First seen · 118 lines · 26 tokens per session scan A 304cdbdf19f6

Subscribe to this mod's changes

chem-irc-verification is a skill published in the GitHub repository learningmatter-mit/AtomisticSkills (158 stars, last pushed yesterday), licensed MIT. It adds 26 tokens to every session and 982 once invoked, about $0.0001 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

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