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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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Precio sin confirmar★ 161 Estrellas de GitHubRegistro actualizado · 6 sept 2026agent-skill

Resumen

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

Leer documentación completa

Documentación de origen, no instrucciones para este sitio. Revisa los permisos antes de ejecutar comandos.

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

Metadatos del archivo
name: chem-irc-verification
description: Verify non-periodic molecular TS connectivity with forward/reverse IRC using endpoint connectivity and RMSD checks.
category: [chemistry]
Ver texto 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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Licencia: 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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Fuente y notas de uso

Indexado

Los metadatos y revisiones son orientativos. Popularidad, descubrimiento y ejecución correcta son hechos distintos.

Repositorio fuente
learningmatter-mit/AtomisticSkills
Licencia
MIT
Versión
1.0.0
Último push de GitHub
3 sept 2026
Registro actualizado
6 sept 2026

Versión declarada en el registro; consulta las versiones de la fuente.

Calidad

66/100

Prometedor

Confianza

66/100

Solo sandbox

Auditoría

77/100

Requiere revisión

  • 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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    "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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