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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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Harga belum dikonfirmasi★ 161 Star GitHubDirektori diperbarui · 6 Sep 2026agent-skill

Ringkasan

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

Baca dokumentasi lengkap

Dokumentasi sumber, bukan instruksi untuk situs ini. Periksa izin sebelum menjalankan perintah.

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

Lihat sumber ↗

Metadata berkas

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

Lihat teks asli

---
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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Lisensi: MIT
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Lisensi: 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

Buka audit lengkap

Daftar alat adalah petunjuk metadata, bukan kompatibilitas teruji. Prompt adalah saran.

Mulai dengan tugas kecil

1Baca sumber dan pastikan masukan, keluaran, dependensi, serta izin.
2Minta rencana dari agent. Setujui pengaturan dan biaya sebelum uji terisolasi.
3Periksa hasil dan berkas yang berubah. Laporkan hanya yang dijalankan dan simpan revisi sumber.

Periksa dependensi, kunci API, dan biaya layanan pihak ketiga pada sumber. Repositori publik tidak berarti semua layanan gratis.

Sumber dan catatan penggunaan

Terindeks

Metadata dan tinjauan bersifat saran. Popularitas, penemuan sumber, dan keberhasilan eksekusi adalah fakta berbeda.

Repositori sumber: learningmatter-mit/AtomisticSkills
Lisensi: MIT
Versi: 1.0.0
Push GitHub terakhir: 3 Sep 2026
Direktori diperbarui: 6 Sep 2026
Jalur instruksi: .agents/skills/chem-irc-verification/SKILL.md @ d1f7ecfda2cd

Versi dilaporkan dalam metadata direktori; periksa rilis sumber.

Kualitas

66/100

Menjanjikan

Kepercayaan

66/100

Hanya sandbox

Audit

77/100

Perlu ditinjau

Buka audit lengkap Lihat laporan evaluasi

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: —
Hasil: —

Menyalin bukan memasang. Jumlah instalasi memerlukan laporan berhasil dan bukan jaminan kualitas menyeluruh.

Akses agent

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Detail lainnya

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    "resolve": "https://www.openagentskill.com/api/agent/resolve?task=Use%20chem-irc-verification%20in%20an%20agent%20workflow&agent=codex&max_risk=medium",
    "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"
  }
}

Untuk kreator

Sumber listing

Diindeks Registry

Dapat diklaim

Listing ini diindeks dari sumber publik dan belum ditandai resmi hingga klaim pemelihara disetujui.

Kreator: learningmatter-mit
Sumber: learningmatter-mit/AtomisticSkills
Diindeks oleh: Indeks komunitas OpenAgentSkill

Atribusi menautkan ke repositori publik atau profil kreator. Kreator dapat mengklaim listing untuk memperbarui sinyal kepemilikan.

Klaim skill ini

Klaim pemilik

Klaim listing skill ini

Listing Diindeks Registry ini dikaitkan dengan learningmatter-mit, tetapi belum ditandai resmi. Klaim untuk menambahkan sinyal pemilik terverifikasi dan membuat pembaruan peluncuran, pemasangan, serta audit berikutnya lebih tepercaya.

Kit berbagi

Kit backlink kreator

Tambahkan badge bukti ke README Anda

Tampilkan listing kanonis, sinyal kepercayaan dan audit saat ini, serta bukti Agent-Proven nyata di tempat pengembang mengevaluasi repositori.

[![Listed on OpenAgentSkill](https://www.openagentskill.com/api/badge/learningmatter-mit-chem-irc-verification?metric=listed&label=Listed)](https://www.openagentskill.com/skills/learningmatter-mit-chem-irc-verification?ref=github&utm_source=github&utm_medium=referral&utm_campaign=creator_badge)
[![OpenAgentSkill Trust](https://www.openagentskill.com/api/badge/learningmatter-mit-chem-irc-verification?metric=trust&label=Trust)](https://www.openagentskill.com/skills/learningmatter-mit-chem-irc-verification?ref=github&utm_source=github&utm_medium=referral&utm_campaign=creator_badge)
[![OpenAgentSkill Audit](https://www.openagentskill.com/api/badge/learningmatter-mit-chem-irc-verification?metric=audit&label=Audit)](https://www.openagentskill.com/skills/learningmatter-mit-chem-irc-verification/audit)
[![Agent Proven](https://www.openagentskill.com/api/badge/learningmatter-mit-chem-irc-verification?metric=proven&label=Agent%20Proven)](https://www.openagentskill.com/skills/learningmatter-mit-chem-irc-verification?ref=github&utm_source=github&utm_medium=referral&utm_campaign=creator_badge)

Pratinjau badge Buka audit Kit kreator

Sinyal komunitas

Bagikan apakah skill ini bermanfaat untuk alur kerja Agent Anda. Masukan gabungan meningkatkan peringkat dari waktu ke waktu.