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chem-irc-verification

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

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Prix non confirmé★ 161 Stars GitHubRegistre mis à jour · 6 sept. 2026agent-skill

Vue d’ensemble

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

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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.

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

Activate mace-agent or fairchem-agent depending on backend.
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

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Métadonnées du fichier

name: chem-irc-verification
description: Verify non-periodic molecular TS connectivity with forward/reverse IRC using endpoint connectivity and RMSD checks.
category: [chemistry]

Voir le texte original

---
name: chem-irc-verification
description: Verify non-periodic molecular TS connectivity with forward/reverse IRC using endpoint connectivity and RMSD checks.
category: [chemistry]
---

# 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
# 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)

```bash
# 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.

## 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

- Activate `mace-agent` or `fairchem-agent` depending on backend.
- 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](https://github.com/recisic)

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Licence: MIT

Dependency or permission surface needs review
Permission surface may require sandboxing
Quality score needs review
Permission surface needs review: secrets or environment access, shell or command execution
Stars/forks activity: 161 stars, 24 forks; issue activity unavailable in current metadata
Dependency/runtime risk: command execution surface, credential or environment access
Permission surface: secrets or environment access, shell or command execution

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Commencer par une petite tâche

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Source et conseils d’utilisation

Répertorié

Métadonnées et examens sont indicatifs. Popularité, découverte et exécution réussie sont des faits distincts.

Dépôt source: learningmatter-mit/AtomisticSkills
Licence: MIT
Version: 1.0.0
Dernier push GitHub: 3 sept. 2026
Registre mis à jour: 6 sept. 2026
Chemin des instructions: .agents/skills/chem-irc-verification/SKILL.md @ d1f7ecfda2cd

Version déclarée dans le registre ; vérifiez les versions de la source.

Qualité

66/100

Prometteur

Confiance

66/100

Sandbox uniquement

Audit

77/100

Revue nécessaire

Ouvrir l’audit complet Voir le rapport d’évaluation

Dependency or permission surface needs review
Permission surface may require sandboxing
Quality score needs review
Permission surface needs review: secrets or environment access, shell or command execution
Stars/forks activity: 161 stars, 24 forks; issue activity unavailable in current metadata
Dependency/runtime risk: command execution surface, credential or environment access
Permission surface: secrets or environment access, shell or command execution

Verified installs: —
Résultats: —

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Plus de détails

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    "receipt": "https://www.openagentskill.com/api/agent/receipt?task=Use%20chem-irc-verification%20in%20an%20agent%20workflow&agent=codex&max_risk=medium&format=text",
    "install": "https://www.openagentskill.com/api/skills/learningmatter-mit-chem-irc-verification/install",
    "manifest": "https://www.openagentskill.com/api/registry/manifest/learningmatter-mit-chem-irc-verification"
  }
}

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Créateur: learningmatter-mit
Source: learningmatter-mit/AtomisticSkills
Indexé par: Index communautaire OpenAgentSkill

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