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chem-irc-verification
Verify non-periodic molecular TS connectivity with forward/reverse IRC using endpoint connectivity and RMSD checks.
Übersicht
Verify non-periodic molecular TS connectivity with forward/reverse IRC using endpoint connectivity and RMSD checks.
Vollständige Dokumentation lesen
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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 (maceorfairchem).--model_name: optional model identifier/checkpoint.--task_name: optional model head/task (for UMA molecular runs useomol).--device:auto|cpu|cuda(defaultauto).--fmax: IRC convergence threshold in eV/A (default0.02).--steps: maximum IRC steps per direction (default1000).--rmsd_threshold: endpoint RMSD threshold in A (default0.20).--relax_endpoints:true|false, relax IRC endpoints before matching (defaulttrue).--endpoint_relax_fmax: force threshold for optional endpoint relaxation (default0.02).--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-mediumuma-s-1p1with--task_name omol
- Use the same backend/model/head as TS optimization to avoid model inconsistency.
Prerequisites And Constraints
- Activate
mace-agentorfairchem-agentdepending on backend. - Script enforces
pbc=Falsefor 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
Dateimetadaten
name: chem-irc-verification description: Verify non-periodic molecular TS connectivity with forward/reverse IRC using endpoint connectivity and RMSD checks. category: [chemistry]
Originaltext anzeigen
--- 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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Lizenz: 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
Tools sind Metadatenhinweise, keine getestete Kompatibilität. Prompts sind Vorschläge.
Mit einer kleinen Aufgabe beginnen
- 1Quelle lesen und Eingaben, Ergebnisse, Abhängigkeiten sowie Berechtigungen prüfen.
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Prüfe Abhängigkeiten, API-Schlüssel und externe Kosten in der Quelle. Öffentliche Repositories bedeuten nicht, dass alle Dienste kostenlos sind.
Quelle und Nutzungshinweise
Metadaten und Prüfungen dienen der Orientierung. Beliebtheit, Quellenerfassung und erfolgreiche Ausführung sind verschiedene Fakten.
- Quell-Repository
- learningmatter-mit/AtomisticSkills
- Lizenz
- MIT
- Version
- 1.0.0
- Letzter GitHub-Push
- 3. Sept. 2026
- Verzeichnis aktualisiert
- 6. Sept. 2026
Version aus den Verzeichnismetadaten; Releases der Quelle prüfen.
Qualität
66/100
Vielversprechend
Vertrauen
66/100
Nur Sandbox
Audit
77/100
Prüfung nötig
- 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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Weitere Details
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}Für Ersteller
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