{"slug":"learningmatter-mit-chem-dft-orca-optimization","name":"chem-dft-orca-optimization","description":"Run DFT geometry optimization (minimization or TS search) on a molecular structure using ORCA via SCINE/ReaDuct wrapper.","long_description":"---\nname: chem-dft-orca-optimization\ndescription: Run DFT geometry optimization (minimization or TS search) on a molecular structure using ORCA via SCINE/ReaDuct wrapper.\ncategory: [chemistry]\n---\n\n# DFT Geometry Optimization with ORCA\n\n## Goal\n\nOptimize the geometry of a molecular structure at the DFT level using the ORCA quantum chemistry program. Supports two modes: **minimization** (finding the nearest local minimum) and **transition state (TS) optimization** (single-ended saddle point search). The calculation uses the SCINE/ReaDuct wrapper for robust optimizer management.\n\n> [!IMPORTANT]\n> This skill provides **single-ended TS optimization** only. For reaction pathway methods (NEB, IRC), consider using the MLIP-based [NEB skill](../chem-neb-barrier/SKILL.md) or [IRC skill](../chem-irc-verification/SKILL.md) with MLIP pre-screening, then refine with DFT. For advanced ORCA features, use the [advanced ORCA skill](../chem-dft-orca-advanced-calculation/SKILL.md).\n\n## Background\n\nGeometry optimization iteratively adjusts nuclear positions to minimize (or, for TS search, to find a first-order saddle point of) the potential energy surface $E(\\mathbf{R})$. The SCINE/ReaDuct optimizer handles step control, coordinate transformations, and convergence criteria internally.\n\n- **Minimization** seeks a stationary point where $\\nabla E = 0$ and the Hessian has all positive eigenvalues.\n- **TS optimization** seeks a first-order saddle point where $\\nabla E = 0$ and the Hessian has exactly one negative eigenvalue.\n\n## 1. Prerequisites\n\n- **Conda environment:** `orca-agent` with `scine_utilities`, `scine_readuct`, and `ase` installed\n- **ORCA binary:** The environment variable `ORCA_BINARY_PATH` must point to the ORCA executable\n  ```bash\n  export ORCA_BINARY_PATH=/path/to/orca\n  ```\n- **Input structure:** A molecular structure file readable by ASE (`.xyz`, `.cif`, `.mol`, etc.)\n- For **TS optimization:** Provide a reasonable TS guess geometry. Poor initial guesses will likely fail to converge to the correct saddle point.\n\n## 2. Parameters\n\n| Parameter | Default | Description |\n|-----------|---------|-------------|\n| `--structure` | (required) | Path to input structure file |\n| `--opt_type` | `min` | `min` for minimization, `ts` for transition state search |\n| `--charge` | `0` | Molecular charge |\n| `--spin_multiplicity` | `1` | Spin multiplicity (2S+1) |\n| `--functional` | `PBE` | DFT functional (e.g. `PBE`, `B3LYP`, `wB97X-V`) |\n| `--basis_set` | `def2-SVP` | Basis set (e.g. `def2-SVP`, `def2-TZVP`) |\n| `--dispersion` | None | Dispersion correction (e.g. `D3BJ`, `D4`) |\n| `--solvation` | None | Implicit solvation model: `CPCM` or `SMD` |\n| `--solvent` | None | Solvent name; required if `--solvation` is set |\n| `--special_option` | `NOSOSCF` | ORCA special option passed to SCINE calculator. Set to empty string to disable. |\n| `--nprocs` | `1` | Number of CPU cores for ORCA |\n| `--convergence_max_iterations` | `200` | Maximum optimization steps |\n| `--calculate_final_hessian` | off | Compute Hessian at optimized geometry (for TS verification) |\n| `--calculator_settings` | None | Extra SCINE calculator settings as a JSON string (see below) |\n| `--optimizer_settings` | None | Extra ReaDuct optimizer kwargs as a JSON string (see below) |\n| `--output_dir` | auto | Output directory |\n\n## 3. Running an Optimization\n\n### Geometry minimization\n\n```bash\n# Env: orca-agent\npython .agent/skills/chem-dft-orca-optimization/scripts/run_optimization.py \\\n    --structure molecule.xyz \\\n    --functional B3LYP \\\n    --basis_set def2-TZVP \\\n    --dispersion D3BJ \\\n    --nprocs 4 \\\n    --output_dir research/my_project/optimization\n```\n\n### Transition state optimization\n\n```bash\n# Env: orca-agent\npython .agent/skills/chem-dft-orca-optimization/scripts/run_optimization.py \\\n    --structure ts_guess.xyz \\\n    --opt_type ts \\\n    --functional B3LYP \\\n    --basis_set def2-TZVP \\\n    --dispersion D3BJ \\\n    --calculate_final_hessian \\\n    --nprocs 4 \\\n    --output_dir research/my_project/ts_optimization\n```\n\n### With extra settings (calculator + optimizer)\n\nFor settings not exposed as dedicated flags, pass JSON strings. `--calculator_settings` applies to the SCINE/ORCA calculator, `--optimizer_settings` applies to the ReaDuct optimization task. SCINE is strict about types, so JSON ensures values are passed with the correct type (int, float, string).\n\n```bash\n# Env: orca-agent\npython .agent/skills/chem-dft-orca-optimization/scripts/run_optimization.py \\\n    --structure molecule.xyz \\\n    --functional B3LYP \\\n    --basis_set def2-TZVP \\\n    --calculator_settings '{\"max_scf_iterations\": 128}' \\\n    --optimizer_settings '{\"convergence_delta_value\": 1e-6}' \\\n    --output_dir research/my_project/opt_custom\n```\n\n### With implicit solvation\n\n```bash\n# Env: orca-agent\npython .agent/skills/chem-dft-orca-optimization/scripts/run_optimization.py \\\n    --structure molecule.xyz \\\n    --functional PBE0 \\\n    --basis_set def2-TZVP \\\n    --solvation SMD \\\n    --solvent water \\\n    --nprocs 4 \\\n    --output_dir research/my_project/opt_solvated\n```\n\n## 4. Output Files\n\n- `optimization_results.json`: Structured results containing:\n  - `converged`: Boolean indicating whether the optimization converged\n  - `final_energy_hartree`, `final_energy_eV`: Final electronic energy\n  - `final_max_force_eV_per_Ang`, `final_rms_force_eV_per_Ang`: Residual force information\n  - `opt_type`: Whether this was a minimization or TS search\n  - If `--calculate_final_hessian` was used: `hessian_eV_per_Ang2`, `hessian_wave_numbers_cm-1`, and `n_imaginary_modes`\n  - All input parameters for reproducibility\n- `initial_structure.xyz`: Copy of the input structure\n- `optimized_structure.xyz`: The optimized geometry\n\n## 5. Interpreting Results\n\n### Minimization\n- Check `converged: true` in the results JSON.\n- Residual forces should be small (max force < 0.01 eV/A for typical convergence).\n- If convergence fails, try increasing `--convergence_max_iterations` or improving the initial geometry.\n\n### TS Optimization\n- Convergence alone does not guarantee a valid TS. After convergence, verify the Hessian has exactly one imaginary frequency:\n  - **Recommended:** Use `--calculate_final_hessian` to compute the Hessian directly after optimization. The output will include `n_imaginary_modes` — expect exactly 1 for a valid TS.\n  - Alternatively, run a separate single-point Hessian with the [singlepoint skill](../chem-dft-orca-singlepoint/SKILL.md) using `--compute_hessian`.\n- Inspect the imaginary mode to confirm it corresponds to the expected reaction coordinate.\n- If the optimizer converges to a minimum instead of a saddle point, the initial guess was likely too far from the true TS.\n\n## 6. Constraints\n\n- **Non-periodic systems only:** ORCA does not handle periodic boundary conditions.\n- **Single-ended TS:** Only single-ended TS optimization is available. For double-ended methods (NEB), pre-screen with MLIPs.\n- **TS guess quality:** The TS optimizer requires a reasonable initial guess. Generate one using constrained scans, interpolation, or MLIP-based TS search methods.\n- **ORCA binary:** `ORCA_BINARY_PATH` must be set and point to a working ORCA installation.\n- **Environment:** All commands require the `orca-agent` conda environment.\n- **Solvation:** When using `--solvation`, you must also provide `--solvent`.\n\n## References\n\n- Neese, F., \"Software update: The ORCA program system—Version 5.0\", *WIREs Comput. Mol. Sci.*, 2022. [DOI](https://doi.org/10.1002/wcms.1606)\n- Unsleber, J.P. et al., \"SCINE—Software for Chemical Interaction Networks\", *J. Chem. Phys.*, 2024. [DOI](https://doi.org/10.1063/5.0206974)\n\n---\n\n**Author:** Miguel Steiner\n**Contact:** [GitHub @steinmig](https://github.com/steinmig)\n","tagline":"Run DFT geometry optimization (minimization or TS search) on a molecular structure using ORCA via SCINE/ReaDuct wrapper.","category":"[chemistry]","tags":["agent-skill"],"author":"learningmatter-mit","verified":false,"attribution":{"status":"registry_indexed","statusLabel":"Registry indexed","shortLabel":"REGISTRY INDEXED","sourceLabel":"github candidate review","sourceDetail":"learningmatter-mit/AtomisticSkills","creatorName":"learningmatter-mit","creatorUrl":"https://github.com/learningmatter-mit","sourceUrl":"https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-dft-orca-optimization","indexedBy":"OpenAgentSkill community index","claimUrl":"https://www.openagentskill.com/skills/learningmatter-mit-chem-dft-orca-optimization#claim-this-skill","claimCta":"Claim this skill","trustNote":"This listing was indexed from public sources and is not marked official until a maintainer claim is approved.","publicNote":"Attribution links to the public repository or creator profile. Creators can claim the listing to update ownership signals."},"stats":{"stars":161,"forks":24,"verified_installs":0,"successful_runs":0,"total_outcomes":0,"rating":0,"review_count":0,"quality_score":38.87},"quality":{"score":69,"tier":"promising","label":"Promising","summary":"Useful candidate, but compare it with alternatives before adopting.","signals":[{"label":"GitHub stars","value":"161","tone":"neutral"},{"label":"Freshness","value":"5d ago","tone":"positive"},{"label":"Install ready","value":"Yes","tone":"positive"},{"label":"License","value":"MIT","tone":"neutral"}],"warnings":["The SKILL.md excerpt is truncated, but the provided content is comprehensive and well-structured."]},"trust":{"version":"trust-score-v5","score":60,"base_score":68,"outcome_confidence":0,"tier":"review","label":"Sandbox only","summary":"Useful candidate with missing or mixed trust signals. Keep it in an isolated workspace until the outcome loop proves task fit.","recommendedAction":"Run only in a sandbox and compare close alternatives before using it for real work.","decision":{"install_policy":"human_review_before_install","auto_install_allowed":false,"human_review_required":true,"sandbox_first":true,"agent_action":"Compare alternatives before installing.","reasoning":["60/100 Trust Score v5","68/100 Trust Score v4 baseline","Needs more real agent outcomes before unattended install","Install path is available","Review before production"],"review_required_when":["The workspace contains production secrets, payments, private customer data, or irreversible actions.","The install command requests shell, network, credential, database, or broad filesystem access.","Outcome evidence is missing, recently failed, or required human review.","Production credentials, payments, or irreversible account changes without explicit human review","Sensitive private data before reviewing repository code, license, and permission surface","Automatic installation in a production workspace"]},"dimensions":[{"id":"github_adoption","label":"GitHub adoption","score":62,"weight":0.13,"status":"info","detail":"161 GitHub stars"},{"id":"repo_activity","label":"Stars/forks activity","score":57,"weight":0.08,"status":"warn","detail":"161 stars, 24 forks; issue activity unavailable in current metadata"},{"id":"maintenance","label":"Recent maintenance","score":100,"weight":0.14,"status":"pass","detail":"5d since push"},{"id":"license","label":"License clarity","score":86,"weight":0.09,"status":"pass","detail":"MIT"},{"id":"documentation","label":"README/SKILL.md completeness","score":86,"weight":0.14,"status":"pass","detail":"Metadata includes enough usage and workflow context"},{"id":"dependency_risk","label":"Dependency/runtime risk","score":54,"weight":0.12,"status":"warn","detail":"command execution surface, credential or environment access"},{"id":"installability","label":"Install availability","score":92,"weight":0.1,"status":"pass","detail":"npx skills add learningmatter-mit/AtomisticSkills --skill chem-dft-orca-optimization"},{"id":"install_safety","label":"Install command safety","score":92,"weight":0.1,"status":"pass","detail":"standard package or runtime install path"},{"id":"permission_surface","label":"Permission surface","score":36,"weight":0.07,"status":"fail","detail":"secrets or environment access, shell or command execution"},{"id":"repository","label":"Repository evidence","score":86,"weight":0.04,"status":"pass","detail":"https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-dft-orca-optimization"},{"id":"review_status","label":"Review status","score":66,"weight":0.05,"status":"info","detail":"AI review data available"},{"id":"agent_outcomes","label":"Agent Proven outcomes","score":54,"weight":0.13,"status":"info","detail":"No agent outcome data yet"}],"checks":[{"status":"info","label":"GitHub adoption","detail":"161 GitHub stars"},{"status":"warn","label":"Stars/forks activity","detail":"161 stars, 24 forks; issue activity unavailable in current metadata"},{"status":"pass","label":"Recent maintenance","detail":"5d since push"},{"status":"pass","label":"License clarity","detail":"MIT"},{"status":"pass","label":"README/SKILL.md completeness","detail":"Metadata includes enough usage and workflow context"},{"status":"warn","label":"Dependency/runtime risk","detail":"command execution surface, credential or environment access"},{"status":"pass","label":"Install availability","detail":"npx skills add learningmatter-mit/AtomisticSkills --skill chem-dft-orca-optimization"},{"status":"pass","label":"Install command safety","detail":"standard package or runtime install path"},{"status":"fail","label":"Permission surface","detail":"secrets or environment access, shell or command execution"},{"status":"pass","label":"Repository evidence","detail":"https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-dft-orca-optimization"},{"status":"info","label":"Review status","detail":"AI review data available"},{"status":"info","label":"Agent Proven outcomes","detail":"No agent outcome data yet"},{"status":"warn","label":"Ownership","detail":"No approved owner claim yet"},{"status":"info","label":"OpenAgentSkill usage","detail":"No local usage activity yet"},{"status":"info","label":"Agent outcomes","detail":"No agent outcome data yet"}],"strengths":["AI review approved","Install path is available","Repository evidence is available","Recently maintained repository","Install command has no obvious high-risk pattern","Outcome loop is ready but needs first real agent run"],"warnings":["The SKILL.md excerpt is truncated, but the provided content is comprehensive and well-structured.","Financial research output is not financial advice; require human review before any live investment decision.","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","No real agent outcome reports yet","Human review required before unattended installation"],"evidence":{"stars":"161 GitHub stars","repoActivity":"161 stars, 24 forks","lastPushed":"5d since push","license":"MIT","repository":"https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-dft-orca-optimization","install":"npx skills add learningmatter-mit/AtomisticSkills --skill chem-dft-orca-optimization","installSafety":"standard package or runtime install path","permissionSurface":"secrets or environment access, shell or command execution","documentation":"Strong README/SKILL.md context","agentOutcomes":"No agent outcome data yet","agentProvenScore":0,"outcomeConfidence":"0%","installPolicy":"human_review_before_install"},"installReadiness":{"ready":true,"command":"npx skills add learningmatter-mit/AtomisticSkills --skill chem-dft-orca-optimization","policy":"human_review_before_install","label":"Human review before install","notes":["Install path is available","Repository evidence is available","License is declared","No Agent Proven outcome evidence yet","5d since push","Financial domain: human review is required before use in a live investment workflow.","Trust Score v5 requires review or sandbox-only use before install."]},"agentCompatibility":["Codex","Claude Code","Cursor","OpenAgentSkill CLI"],"riskSummary":{"level":"medium","label":"Review before production","notes":["The SKILL.md excerpt is truncated, but the provided content is comprehensive and well-structured.","Financial research output is not financial advice; require human review before any live investment decision.","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"]},"outcomeEvidence":{"total":0,"successes":0,"failures":0,"notRelevant":0,"successRate":null,"installAttempts":0,"riskBlocked":0,"setupRequired":0,"installSuccessRate":null,"avgOutputQuality":null,"avgTimeToUsefulMs":null,"productionOutcomes":0,"humanReviewRequired":0,"recentSuccessRate":null,"recentFailureRate":null,"uniqueAgents":0,"agentProvenScore":0,"agentProvenLabel":"Needs first agent run","lastOutcomeAt":null,"label":"No agent outcome data yet"},"autoInstall":{"allowed":false,"sandboxRequired":true,"policy":"human_review_before_install","reason":"Compare alternatives before installing."},"outcome_loop":{"version":"openagentskill-agent-outcome-v4","required_after_install":true,"endpoint":"/api/agent/outcome","method":"POST","event_id_source":"feedback.event_id, install_receipt.resolve_event_id, or decision_packet.outcome_feedback.event_id","expected_outcomes":["success","failed","not_relevant","blocked_by_risk","setup_required"],"required_fields":["event_id","skill_slug","task"],"quality_fields":["task_success","output_quality","error_type","human_review_required","used_in_production","workspace","evidence_url","time_to_useful_ms","source_version"],"ranking_inputs_updated":["Trust Score v5 outcome confidence","Agent Proven Score","Resolve ranking task-fit evidence","Skill detail machine-readable metadata","Outcome leaderboard"]},"agent_contract":{"suited_tasks":["[chemistry]","agent-skill"],"suited_agents":["Codex","Claude Code","Cursor","OpenAgentSkill CLI"],"install_command":"npx skills add learningmatter-mit/AtomisticSkills --skill chem-dft-orca-optimization","trust_score":60,"trust_version":"trust-score-v5","risk_level":"medium","do_not_use_when":["Production credentials, payments, or irreversible account changes without explicit human review","Sensitive private data before reviewing repository code, license, and permission surface","Automatic installation in a production workspace","Autonomous investment, trading, tax, or suitability decisions without a qualified human review"],"before_install":["Read the audit page and machine-readable metadata.","Confirm the install command, license, and permission surface fit the workspace.","Get explicit human approval or choose an alternative before installing."],"after_run":["Report the outcome to /api/agent/outcome using the resolve event id.","Include output_quality, workspace, human_review_required, and evidence_url when available.","Re-resolve before broad production rollout."]},"bestFor":["[chemistry]","agent-skill"],"doNotUseFor":["Production credentials, payments, or irreversible account changes without explicit human review","Sensitive private data before reviewing repository code, license, and permission surface","Automatic installation in a production workspace","Autonomous investment, trading, tax, or suitability decisions without a qualified human review"],"knownRisks":["The SKILL.md excerpt is truncated, but the provided content is comprehensive and well-structured.","Financial research output is not financial advice; require human review before any live investment decision.","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"],"backward_compatible":{"trust_score_v4":{"version":"trust-score-v4","score":68,"tier":"review","label":"Manual review","summary":"Potentially useful, but at least one trust signal needs human inspection."}}},"trust_score_v5":{"version":"trust-score-v5","score":60,"base_score":68,"outcome_confidence":0,"tier":"review","label":"Sandbox only","summary":"Useful candidate with missing or mixed trust signals. Keep it in an isolated workspace until the outcome loop proves task fit.","recommendedAction":"Run only in a sandbox and compare close alternatives before using it for real work.","decision":{"install_policy":"human_review_before_install","auto_install_allowed":false,"human_review_required":true,"sandbox_first":true,"agent_action":"Compare alternatives before installing.","reasoning":["60/100 Trust Score v5","68/100 Trust Score v4 baseline","Needs more real agent outcomes before unattended install","Install path is available","Review before production"],"review_required_when":["The workspace contains production secrets, payments, private customer data, or irreversible actions.","The install command requests shell, network, credential, database, or broad filesystem access.","Outcome evidence is missing, recently failed, or required human review.","Production credentials, payments, or irreversible account changes without explicit human review","Sensitive private data before reviewing repository code, license, and permission surface","Automatic installation in a production workspace"]},"dimensions":[{"id":"github_adoption","label":"GitHub adoption","score":62,"weight":0.13,"status":"info","detail":"161 GitHub stars"},{"id":"repo_activity","label":"Stars/forks activity","score":57,"weight":0.08,"status":"warn","detail":"161 stars, 24 forks; issue activity unavailable in current metadata"},{"id":"maintenance","label":"Recent maintenance","score":100,"weight":0.14,"status":"pass","detail":"5d since push"},{"id":"license","label":"License clarity","score":86,"weight":0.09,"status":"pass","detail":"MIT"},{"id":"documentation","label":"README/SKILL.md completeness","score":86,"weight":0.14,"status":"pass","detail":"Metadata includes enough usage and workflow context"},{"id":"dependency_risk","label":"Dependency/runtime risk","score":54,"weight":0.12,"status":"warn","detail":"command execution surface, credential or environment access"},{"id":"installability","label":"Install availability","score":92,"weight":0.1,"status":"pass","detail":"npx skills add learningmatter-mit/AtomisticSkills --skill chem-dft-orca-optimization"},{"id":"install_safety","label":"Install command safety","score":92,"weight":0.1,"status":"pass","detail":"standard package or runtime install path"},{"id":"permission_surface","label":"Permission surface","score":36,"weight":0.07,"status":"fail","detail":"secrets or environment access, shell or command execution"},{"id":"repository","label":"Repository evidence","score":86,"weight":0.04,"status":"pass","detail":"https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-dft-orca-optimization"},{"id":"review_status","label":"Review status","score":66,"weight":0.05,"status":"info","detail":"AI review data available"},{"id":"agent_outcomes","label":"Agent Proven outcomes","score":54,"weight":0.13,"status":"info","detail":"No agent outcome data yet"}],"checks":[{"status":"info","label":"GitHub adoption","detail":"161 GitHub stars"},{"status":"warn","label":"Stars/forks activity","detail":"161 stars, 24 forks; issue activity unavailable in current metadata"},{"status":"pass","label":"Recent maintenance","detail":"5d since push"},{"status":"pass","label":"License clarity","detail":"MIT"},{"status":"pass","label":"README/SKILL.md completeness","detail":"Metadata includes enough usage and workflow context"},{"status":"warn","label":"Dependency/runtime risk","detail":"command execution surface, credential or environment access"},{"status":"pass","label":"Install availability","detail":"npx skills add learningmatter-mit/AtomisticSkills --skill chem-dft-orca-optimization"},{"status":"pass","label":"Install command safety","detail":"standard package or runtime install path"},{"status":"fail","label":"Permission surface","detail":"secrets or environment access, shell or command execution"},{"status":"pass","label":"Repository evidence","detail":"https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-dft-orca-optimization"},{"status":"info","label":"Review status","detail":"AI review data available"},{"status":"info","label":"Agent Proven outcomes","detail":"No agent outcome data yet"},{"status":"warn","label":"Ownership","detail":"No approved owner claim yet"},{"status":"info","label":"OpenAgentSkill usage","detail":"No local usage activity yet"},{"status":"info","label":"Agent outcomes","detail":"No agent outcome data yet"}],"strengths":["AI review approved","Install path is available","Repository evidence is available","Recently maintained repository","Install command has no obvious high-risk pattern","Outcome loop is ready but needs first real agent run"],"warnings":["The SKILL.md excerpt is truncated, but the provided content is comprehensive and well-structured.","Financial research output is not financial advice; require human review before any live investment decision.","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","No real agent outcome reports yet","Human review required before unattended installation"],"evidence":{"stars":"161 GitHub stars","repoActivity":"161 stars, 24 forks","lastPushed":"5d since push","license":"MIT","repository":"https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-dft-orca-optimization","install":"npx skills add learningmatter-mit/AtomisticSkills --skill chem-dft-orca-optimization","installSafety":"standard package or runtime install path","permissionSurface":"secrets or environment access, shell or command execution","documentation":"Strong README/SKILL.md context","agentOutcomes":"No agent outcome data yet","agentProvenScore":0,"outcomeConfidence":"0%","installPolicy":"human_review_before_install"},"installReadiness":{"ready":true,"command":"npx skills add learningmatter-mit/AtomisticSkills --skill chem-dft-orca-optimization","policy":"human_review_before_install","label":"Human review before install","notes":["Install path is available","Repository evidence is available","License is declared","No Agent Proven outcome evidence yet","5d since push","Financial domain: human review is required before use in a live investment workflow.","Trust Score v5 requires review or sandbox-only use before install."]},"agentCompatibility":["Codex","Claude Code","Cursor","OpenAgentSkill CLI"],"riskSummary":{"level":"medium","label":"Review before production","notes":["The SKILL.md excerpt is truncated, but the provided content is comprehensive and well-structured.","Financial research output is not financial advice; require human review before any live investment decision.","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"]},"outcomeEvidence":{"total":0,"successes":0,"failures":0,"notRelevant":0,"successRate":null,"installAttempts":0,"riskBlocked":0,"setupRequired":0,"installSuccessRate":null,"avgOutputQuality":null,"avgTimeToUsefulMs":null,"productionOutcomes":0,"humanReviewRequired":0,"recentSuccessRate":null,"recentFailureRate":null,"uniqueAgents":0,"agentProvenScore":0,"agentProvenLabel":"Needs first agent run","lastOutcomeAt":null,"label":"No agent outcome data yet"},"autoInstall":{"allowed":false,"sandboxRequired":true,"policy":"human_review_before_install","reason":"Compare alternatives before installing."},"outcome_loop":{"version":"openagentskill-agent-outcome-v4","required_after_install":true,"endpoint":"/api/agent/outcome","method":"POST","event_id_source":"feedback.event_id, install_receipt.resolve_event_id, or decision_packet.outcome_feedback.event_id","expected_outcomes":["success","failed","not_relevant","blocked_by_risk","setup_required"],"required_fields":["event_id","skill_slug","task"],"quality_fields":["task_success","output_quality","error_type","human_review_required","used_in_production","workspace","evidence_url","time_to_useful_ms","source_version"],"ranking_inputs_updated":["Trust Score v5 outcome confidence","Agent Proven Score","Resolve ranking task-fit evidence","Skill detail machine-readable metadata","Outcome leaderboard"]},"agent_contract":{"suited_tasks":["[chemistry]","agent-skill"],"suited_agents":["Codex","Claude Code","Cursor","OpenAgentSkill CLI"],"install_command":"npx skills add learningmatter-mit/AtomisticSkills --skill chem-dft-orca-optimization","trust_score":60,"trust_version":"trust-score-v5","risk_level":"medium","do_not_use_when":["Production credentials, payments, or irreversible account changes without explicit human review","Sensitive private data before reviewing repository code, license, and permission surface","Automatic installation in a production workspace","Autonomous investment, trading, tax, or suitability decisions without a qualified human review"],"before_install":["Read the audit page and machine-readable metadata.","Confirm the install command, license, and permission surface fit the workspace.","Get explicit human approval or choose an alternative before installing."],"after_run":["Report the outcome to /api/agent/outcome using the resolve event id.","Include output_quality, workspace, human_review_required, and evidence_url when available.","Re-resolve before broad production rollout."]},"bestFor":["[chemistry]","agent-skill"],"doNotUseFor":["Production credentials, payments, or irreversible account changes without explicit human review","Sensitive private data before reviewing repository code, license, and permission surface","Automatic installation in a production workspace","Autonomous investment, trading, tax, or suitability decisions without a qualified human review"],"knownRisks":["The SKILL.md excerpt is truncated, but the provided content is comprehensive and well-structured.","Financial research output is not financial advice; require human review before any live investment decision.","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"],"backward_compatible":{"trust_score_v4":{"version":"trust-score-v4","score":68,"tier":"review","label":"Manual review","summary":"Potentially useful, but at least one trust signal needs human inspection."}}},"trust_score_v4":{"version":"trust-score-v4","score":68,"tier":"review","label":"Manual review","summary":"Potentially useful, but at least one trust signal needs human inspection.","recommendedAction":"Inspect the repository, license, and recent activity before connecting it to agent workflows.","dimensions":[{"id":"github_adoption","label":"GitHub adoption","score":62,"weight":0.13,"status":"info","detail":"161 GitHub stars"},{"id":"repo_activity","label":"Stars/forks activity","score":57,"weight":0.08,"status":"warn","detail":"161 stars, 24 forks; issue activity unavailable in current metadata"},{"id":"maintenance","label":"Recent maintenance","score":100,"weight":0.14,"status":"pass","detail":"5d since push"},{"id":"license","label":"License clarity","score":86,"weight":0.09,"status":"pass","detail":"MIT"},{"id":"documentation","label":"README/SKILL.md completeness","score":86,"weight":0.14,"status":"pass","detail":"Metadata includes enough usage and workflow context"},{"id":"dependency_risk","label":"Dependency/runtime risk","score":54,"weight":0.12,"status":"warn","detail":"command execution surface, credential or environment access"},{"id":"installability","label":"Install availability","score":92,"weight":0.1,"status":"pass","detail":"npx skills add learningmatter-mit/AtomisticSkills --skill chem-dft-orca-optimization"},{"id":"install_safety","label":"Install command safety","score":92,"weight":0.1,"status":"pass","detail":"standard package or runtime install path"},{"id":"permission_surface","label":"Permission surface","score":36,"weight":0.07,"status":"fail","detail":"secrets or environment access, shell or command execution"},{"id":"repository","label":"Repository evidence","score":86,"weight":0.04,"status":"pass","detail":"https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-dft-orca-optimization"},{"id":"review_status","label":"Review status","score":66,"weight":0.05,"status":"info","detail":"AI review data available"},{"id":"agent_outcomes","label":"Agent Proven outcomes","score":54,"weight":0.13,"status":"info","detail":"No agent outcome data yet"}],"checks":[{"status":"info","label":"GitHub adoption","detail":"161 GitHub stars"},{"status":"warn","label":"Stars/forks activity","detail":"161 stars, 24 forks; issue activity unavailable in current metadata"},{"status":"pass","label":"Recent maintenance","detail":"5d since push"},{"status":"pass","label":"License clarity","detail":"MIT"},{"status":"pass","label":"README/SKILL.md completeness","detail":"Metadata includes enough usage and workflow context"},{"status":"warn","label":"Dependency/runtime risk","detail":"command execution surface, credential or environment access"},{"status":"pass","label":"Install availability","detail":"npx skills add learningmatter-mit/AtomisticSkills --skill chem-dft-orca-optimization"},{"status":"pass","label":"Install command safety","detail":"standard package or runtime install path"},{"status":"fail","label":"Permission surface","detail":"secrets or environment access, shell or command execution"},{"status":"pass","label":"Repository evidence","detail":"https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-dft-orca-optimization"},{"status":"info","label":"Review status","detail":"AI review data available"},{"status":"info","label":"Agent Proven outcomes","detail":"No agent outcome data yet"},{"status":"warn","label":"Ownership","detail":"No approved owner claim yet"},{"status":"info","label":"OpenAgentSkill usage","detail":"No local usage activity yet"},{"status":"info","label":"Agent outcomes","detail":"No agent outcome data yet"}],"strengths":["AI review approved","Install path is available","Repository evidence is available","Recently maintained repository","Install command has no obvious high-risk pattern"],"warnings":["The SKILL.md excerpt is truncated, but the provided content is comprehensive and well-structured.","Financial research output is not financial advice; require human review before any live investment decision.","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"],"evidence":{"stars":"161 GitHub stars","repoActivity":"161 stars, 24 forks","lastPushed":"5d since push","license":"MIT","repository":"https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-dft-orca-optimization","install":"npx skills add learningmatter-mit/AtomisticSkills --skill chem-dft-orca-optimization","installSafety":"standard package or runtime install path","permissionSurface":"secrets or environment access, shell or command execution","documentation":"Strong README/SKILL.md context","agentOutcomes":"No agent outcome data yet"},"installReadiness":{"ready":true,"command":"npx skills add learningmatter-mit/AtomisticSkills --skill chem-dft-orca-optimization","policy":"human_review_before_install","label":"Human review before install","notes":["Install path is available","Repository evidence is available","License is declared","No Agent Proven outcome evidence yet","5d since push","Financial domain: human review is required before use in a live investment workflow."]},"agentCompatibility":["Codex","Claude Code","Cursor","OpenAgentSkill CLI"],"riskSummary":{"level":"medium","label":"Review before production","notes":["The SKILL.md excerpt is truncated, but the provided content is comprehensive and well-structured.","Financial research output is not financial advice; require human review before any live investment decision.","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"]},"outcomeEvidence":{"total":0,"successes":0,"failures":0,"notRelevant":0,"successRate":null,"installAttempts":0,"riskBlocked":0,"setupRequired":0,"installSuccessRate":null,"avgOutputQuality":null,"avgTimeToUsefulMs":null,"productionOutcomes":0,"humanReviewRequired":0,"recentSuccessRate":null,"recentFailureRate":null,"uniqueAgents":0,"agentProvenScore":0,"agentProvenLabel":"Needs first agent run","lastOutcomeAt":null,"label":"No agent outcome data yet"},"autoInstall":{"allowed":false,"sandboxRequired":true,"policy":"human_review_before_install","reason":"Human review or sandbox validation is required before automatic installation."},"bestFor":["[chemistry]","agent-skill"],"doNotUseFor":["Production credentials, payments, or irreversible account changes without explicit human review","Sensitive private data before reviewing repository code, license, and permission surface","Automatic installation in a production workspace","Autonomous investment, trading, tax, or suitability decisions without a qualified human review"],"knownRisks":["The SKILL.md excerpt is truncated, but the provided content is comprehensive and well-structured.","Financial research output is not financial advice; require human review before any live investment decision.","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"]},"agent_proven":{"version":"agent-proven-v1","score":0,"tier":"unproven","label":"Needs first agent run","summary":"No agent outcome reports yet. Use Resolve, run one narrow sandbox task, then report the result.","metrics":{"totalOutcomes":0,"successfulOutcomes":0,"failedOutcomes":0,"installAttempts":0,"installSuccessRate":null,"successRate":null,"recentSuccessRate":null,"recentFailureRate":null,"riskBlocked":0,"setupRequired":0,"notRelevant":0,"avgOutputQuality":null,"avgTimeToUsefulMs":null,"productionOutcomes":0,"humanReviewRequired":0,"uniqueAgents":0,"lastOutcomeAt":null},"signals":[],"penalties":["No real agent outcome evidence yet"]},"outcome_stats":null,"safety":{"score":36,"level":"avoid_auto_install","label":"Avoid automatic install","safety_tier":{"tier":"blocked","label":"Blocked for auto-install","badge":"BLOCKED","summary":"This skill should not be selected by an agent without explicit human security review.","recommended_action":"Do not auto-install. Inspect the source, dependencies, and permission surface first.","auto_install_policy":"block","reasons":["Metadata combines secrets access with shell or command execution","High-risk permission hints: Shell or command execution, Secrets or environment access"]},"auto_install_allowed":false,"human_review_required":true,"blocked":true,"audit_risk":"needs_review","permission_hints":[{"id":"shell","label":"Shell or command execution","reason":"Skill metadata references terminal, CLI, shell, subprocess, or command execution workflows.","severity":"high"},{"id":"network","label":"Network access","reason":"Skill likely fetches remote pages, APIs, repositories, or external services.","severity":"medium"},{"id":"filesystem","label":"Filesystem access","reason":"Skill may read or write project files, documents, generated artifacts, or local workspace state.","severity":"medium"},{"id":"secrets","label":"Secrets or environment access","reason":"Skill metadata references credentials, tokens, environment variables, or secret-bearing workflows.","severity":"high"}],"policy_warnings":["High-risk permission hints: Shell or command execution, Secrets or environment access","Dependency or permission surface needs review"],"constraints_applied":{"max_risk":"medium","needs_install_command":true,"min_stars":0}},"safety_gate":{"tier":"blocked","label":"Blocked for auto-install","badge":"BLOCKED","auto_install_policy":"block","auto_install_allowed":false,"blocked":true,"human_review_required":true,"recommended_action":"Do not auto-install. Inspect the source, dependencies, and permission surface first.","reasons":["Metadata combines secrets access with shell or command execution","High-risk permission hints: Shell or command execution, Secrets or environment access"]},"eval":{"version":"openagentskill-skill-eval-v1","status":"failed","score":65,"risk_level":"high","decision":{"recommendation":"do_not_auto_install","reason":"Agent safety gate: This skill should not be selected by an agent without explicit human security review.","auto_install_allowed":false,"policy":"block","human_review_required":true},"blockers":["Agent safety gate: This skill should not be selected by an agent without explicit human security review.","Permission surface: secrets or environment access, shell or command execution"],"warnings":["Trust score: Potentially useful, but at least one trust signal needs human inspection.","Audit score: Needs review","High-risk permission hints: Shell or command execution, Secrets or environment access","Dependency or permission surface needs review","Permission surface may require sandboxing","Financial research output is not financial advice; require human review before any live investment decision","The SKILL.md excerpt is truncated, but the provided content is comprehensive and well-structured.","The skill depends on external software (ORCA, SCINE) and a specific conda environment, which may limit portability but is clearly documented.","Financial research output is not financial advice; require human review before any live investment decision.","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"],"validation_plan":["Inspect repository, README/SKILL.md, license, and recent commits before production use.","Install in an isolated workspace or sandbox with no production secrets available.","Run the smallest representative task and record files touched, commands run, network access, and outputs.","Compare the selected skill against at least one alternative when the eval status is review or failed.","Promote only after the agent reports a successful verification result and unresolved warnings are accepted."],"checks":[{"id":"task_fit","label":"Task fit","status":"pass","score":84,"required_for_auto_install":true,"detail":"Task wording matches this skill metadata.","evidence":["Evaluate chem-dft-orca-optimization before installing it in an agent workflow","[chemistry]","GitHub automation workflows; Claude Code teams; builders willing to evaluate younger projects"]},{"id":"install_path","label":"Install path","status":"pass","score":92,"required_for_auto_install":true,"detail":"Install handoff is available.","evidence":["npx skills add learningmatter-mit/AtomisticSkills --skill chem-dft-orca-optimization"]},{"id":"install_safety","label":"Install command safety","status":"pass","score":92,"required_for_auto_install":true,"detail":"standard package or runtime install path","evidence":["npx skills add learningmatter-mit/AtomisticSkills --skill chem-dft-orca-optimization"]},{"id":"trust_score","label":"Trust score","status":"warn","score":68,"required_for_auto_install":true,"detail":"Potentially useful, but at least one trust signal needs human inspection.","evidence":["Manual review","161 GitHub stars","MIT"]},{"id":"audit_score","label":"Audit score","status":"warn","score":76,"required_for_auto_install":true,"detail":"Needs review","evidence":["Dependency or permission surface needs review"]},{"id":"agent_safety_gate","label":"Agent safety gate","status":"fail","score":36,"required_for_auto_install":true,"detail":"This skill should not be selected by an agent without explicit human security review.","evidence":["Do not auto-install. Inspect the source, dependencies, and permission surface first.","Metadata combines secrets access with shell or command execution"]},{"id":"readme_skillmd_completeness","label":"README/SKILL.md completeness","status":"pass","score":86,"required_for_auto_install":false,"detail":"Metadata includes enough usage and workflow context","evidence":["Strong README/SKILL.md context"]},{"id":"license_clarity","label":"License clarity","status":"pass","score":86,"required_for_auto_install":true,"detail":"MIT","evidence":["MIT"]},{"id":"recent_maintenance","label":"Recent maintenance","status":"pass","score":100,"required_for_auto_install":false,"detail":"5d since push","evidence":["5d since push"]},{"id":"permission_surface","label":"Permission surface","status":"fail","score":36,"required_for_auto_install":true,"detail":"secrets or environment access, shell or command execution","evidence":["Shell or command execution: high","Network access: medium","Filesystem access: medium"]},{"id":"alternatives","label":"Alternatives available","status":"info","score":55,"required_for_auto_install":false,"detail":"No close alternatives were found in the current shortlist.","evidence":[]}],"endpoints":{"web":"https://www.openagentskill.com/skills/learningmatter-mit-chem-dft-orca-optimization/evals","api":"/api/agent/evals?slug=learningmatter-mit-chem-dft-orca-optimization","text":"/api/agent/evals?slug=learningmatter-mit-chem-dft-orca-optimization&format=text"}},"agent_readable_metadata":{"version":"openagentskill-agent-metadata-v2","skill":{"slug":"learningmatter-mit-chem-dft-orca-optimization","name":"chem-dft-orca-optimization","description":"Run DFT geometry optimization (minimization or TS search) on a molecular structure using ORCA via SCINE/ReaDuct wrapper.","category":"[chemistry]","url":"https://www.openagentskill.com/skills/learningmatter-mit-chem-dft-orca-optimization","repository":"https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-dft-orca-optimization","github_repo":"learningmatter-mit/AtomisticSkills"},"suited_tasks":["GitHub automation workflows","Claude Code teams","builders willing to evaluate younger projects","Inspect repository metadata","Compare code changes","Write concise engineering summaries","Navigate local resources","Run repeatable desktop actions"],"suited_agents":["Codex","Claude Code","Cursor","OpenAgentSkill CLI","CLI"],"install":{"command":"npx skills add learningmatter-mit/AtomisticSkills --skill chem-dft-orca-optimization","ready":true,"targets":[{"id":"openagentskill-cli","label":"CLI","kind":"command","value":"npx --yes https://github.com/Leon-Drq/openagentskill/releases/download/cli-v0.3.0/openagentskill-0.3.0.tgz add learningmatter-mit-chem-dft-orca-optimization"},{"id":"codex","label":"Codex","kind":"agent-prompt","value":"Install the \"chem-dft-orca-optimization\" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-dft-orca-optimization. Read its SKILL.md or equivalent instructions first, install only the files needed for this workspace, and summarize any required setup before using it. Skill purpose: Run DFT geometry optimization (minimization or TS search) on a molecular structure using ORCA via SCINE/ReaDuct wrapper. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"learningmatter-mit-chem-dft-orca-optimization\",\"task\":\"Install chem-dft-orca-optimization\",\"agent\":\"codex\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."},{"id":"claude-code","label":"Claude Code","kind":"agent-prompt","value":"Add \"chem-dft-orca-optimization\" as a Claude Code skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-dft-orca-optimization. Inspect the skill instructions, place the reusable skill files in the appropriate local skills location for this project, and report the activation steps. Skill purpose: Run DFT geometry optimization (minimization or TS search) on a molecular structure using ORCA via SCINE/ReaDuct wrapper. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"learningmatter-mit-chem-dft-orca-optimization\",\"task\":\"Install chem-dft-orca-optimization\",\"agent\":\"claude-code\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."},{"id":"cursor","label":"Cursor","kind":"agent-prompt","value":"Turn \"chem-dft-orca-optimization\" from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-dft-orca-optimization into a reusable Cursor project rule or agent instruction. Preserve the core workflow, adapt paths to this repo, and keep the rule scoped to tasks where it is relevant. Skill purpose: Run DFT geometry optimization (minimization or TS search) on a molecular structure using ORCA via SCINE/ReaDuct wrapper. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"learningmatter-mit-chem-dft-orca-optimization\",\"task\":\"Install chem-dft-orca-optimization\",\"agent\":\"cursor\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."}],"handoff_url":"https://www.openagentskill.com/api/skills/learningmatter-mit-chem-dft-orca-optimization/install","manifest_url":"https://www.openagentskill.com/api/registry/manifest/learningmatter-mit-chem-dft-orca-optimization"},"trust":{"score":68,"label":"Manual review","version":"trust-score-v4","install_policy":"human_review_before_install","evidence":{"stars":"161 GitHub stars","repoActivity":"161 stars, 24 forks","lastPushed":"5d since push","license":"MIT","repository":"https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-dft-orca-optimization","install":"npx skills add learningmatter-mit/AtomisticSkills --skill chem-dft-orca-optimization","installSafety":"standard package or runtime install path","permissionSurface":"secrets or environment access, shell or command execution","documentation":"Strong README/SKILL.md context","agentOutcomes":"No agent outcome data yet"},"outcome_evidence":{"total":0,"successes":0,"failures":0,"not_relevant":0,"success_rate":null,"recent_success_rate":null,"recent_failure_rate":null,"install_attempts":0,"install_success_rate":null,"risk_blocked":0,"setup_required":0,"avg_output_quality":null,"production_outcomes":0,"last_outcome_at":null,"label":"No agent outcome data yet"},"auto_install":{"allowed":false,"sandbox_required":true,"reason":"Human review or sandbox validation is required before automatic installation."},"best_for":["[chemistry]","agent-skill"],"known_risks":["The SKILL.md excerpt is truncated, but the provided content is comprehensive and well-structured.","Financial research output is not financial advice; require human review before any live investment decision.","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"]},"agent_proven":{"version":"agent-proven-v1","score":0,"tier":"unproven","label":"Needs first agent run","summary":"No agent outcome reports yet. Use Resolve, run one narrow sandbox task, then report the result.","metrics":{"totalOutcomes":0,"successfulOutcomes":0,"failedOutcomes":0,"installAttempts":0,"installSuccessRate":null,"successRate":null,"recentSuccessRate":null,"recentFailureRate":null,"riskBlocked":0,"setupRequired":0,"notRelevant":0,"avgOutputQuality":null,"avgTimeToUsefulMs":null,"productionOutcomes":0,"humanReviewRequired":0,"uniqueAgents":0,"lastOutcomeAt":null},"signals":[],"penalties":["No real agent outcome evidence yet"]},"audit":{"score":76,"risk_level":"needs_review","risk_label":"Needs review","warnings":["Dependency or permission surface needs review","Permission surface may require sandboxing","Financial research output is not financial advice; require human review before any live investment decision","The SKILL.md excerpt is truncated, but the provided content is comprehensive and well-structured.","The skill depends on external software (ORCA, SCINE) and a specific conda environment, which may limit portability but is clearly documented.","Financial research output is not financial advice; require human review before any live investment decision.","Quality score needs review","Permission surface needs review: secrets or environment access, shell or command execution"]},"safety_gate":{"tier":"blocked","label":"Blocked for auto-install","auto_install_policy":"block","auto_install_allowed":false,"human_review_required":true,"blocked":true,"recommended_action":"Do not auto-install. Inspect the source, dependencies, and permission surface first."},"quality":{"score":69,"label":"Promising"},"supply":{"track":"Coding and developer agents","scenario":"GitHub automation","maintenance":"5d since push","risk":"Needs review"},"alternative_skills":[],"do_not_use_when":["teams that need a vendor-supported SLA","production agents without a repository review","The SKILL.md excerpt is truncated, but the provided content is comprehensive and well-structured.","No OpenAgentSkill engagement data yet","High-risk permission hints: Shell or command execution, Secrets or environment access","Dependency or permission surface needs review","Permission surface may require sandboxing","Financial research output is not financial advice; require human review before any live investment decision"],"agent_contract":{"task_input":"Use chem-dft-orca-optimization in an agent workflow","recommended_action":"Do not auto-install. Inspect the source, dependencies, and permission surface first.","install_policy":"block","minimum_review_before_use":["Trust: 68/100 Manual review","Audit: 76/100 Needs review","Safety: 36/100 Avoid automatic install","Review repository, license, install command, and permission surface before production use."],"expected_agent_output":{"selected_skill":"learningmatter-mit-chem-dft-orca-optimization (chem-dft-orca-optimization)","install_command":"npx skills add learningmatter-mit/AtomisticSkills --skill chem-dft-orca-optimization","risk_summary":"Needs review; Blocked for auto-install; Review before production","verification_result":"Report the smallest successful task, files touched, warnings, and any missing setup."}},"outcome_feedback":{"endpoint":"https://www.openagentskill.com/api/agent/outcome","method":"POST","requires_resolve_event_id":true,"event_id_source":"Use install_receipt.outcome_feedback.event_id or feedback.event_id returned by /api/agent/resolve for the current task.","expected_outcomes":["success","failed","not_relevant","blocked_by_risk","setup_required"],"payload_template":{"event_id":"<install_receipt.outcome_feedback.event_id or feedback.event_id from /api/agent/resolve>","skill_slug":"learningmatter-mit-chem-dft-orca-optimization","task":"Use chem-dft-orca-optimization in an agent workflow","agent":"codex","outcome":"success","install_used":true,"risk_blocked":false,"setup_required":false,"task_success":true,"output_quality":4,"error_type":null,"human_review_required":false,"workspace":"sandbox","time_to_useful_ms":120000,"notes":"Report the smallest successful task, setup friction, files touched, and risk notes."}},"endpoints":{"web":"https://www.openagentskill.com/skills/learningmatter-mit-chem-dft-orca-optimization","api":"https://www.openagentskill.com/api/agent/skills/learningmatter-mit-chem-dft-orca-optimization","audit":"https://www.openagentskill.com/skills/learningmatter-mit-chem-dft-orca-optimization/audit","eval":"https://www.openagentskill.com/api/agent/evals?slug=learningmatter-mit-chem-dft-orca-optimization&task=Use%20chem-dft-orca-optimization%20in%20an%20agent%20workflow&max_risk=medium","resolve":"https://www.openagentskill.com/api/agent/resolve?task=Use%20chem-dft-orca-optimization%20in%20an%20agent%20workflow&agent=codex&max_risk=medium","receipt":"https://www.openagentskill.com/api/agent/receipt?task=Use%20chem-dft-orca-optimization%20in%20an%20agent%20workflow&agent=codex&max_risk=medium&format=text","install":"https://www.openagentskill.com/api/skills/learningmatter-mit-chem-dft-orca-optimization/install","manifest":"https://www.openagentskill.com/api/registry/manifest/learningmatter-mit-chem-dft-orca-optimization"}},"machine_metadata":{"version":"openagentskill-agent-metadata-v2","skill":{"slug":"learningmatter-mit-chem-dft-orca-optimization","name":"chem-dft-orca-optimization","description":"Run DFT geometry optimization (minimization or TS search) on a molecular structure using ORCA via SCINE/ReaDuct wrapper.","category":"[chemistry]","url":"https://www.openagentskill.com/skills/learningmatter-mit-chem-dft-orca-optimization","repository":"https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-dft-orca-optimization","github_repo":"learningmatter-mit/AtomisticSkills"},"suited_tasks":["GitHub automation workflows","Claude Code teams","builders willing to evaluate younger projects","Inspect repository metadata","Compare code changes","Write concise engineering summaries","Navigate local resources","Run repeatable desktop actions"],"suited_agents":["Codex","Claude Code","Cursor","OpenAgentSkill CLI","CLI"],"install":{"command":"npx skills add learningmatter-mit/AtomisticSkills --skill chem-dft-orca-optimization","ready":true,"targets":[{"id":"openagentskill-cli","label":"CLI","kind":"command","value":"npx --yes https://github.com/Leon-Drq/openagentskill/releases/download/cli-v0.3.0/openagentskill-0.3.0.tgz add learningmatter-mit-chem-dft-orca-optimization"},{"id":"codex","label":"Codex","kind":"agent-prompt","value":"Install the \"chem-dft-orca-optimization\" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-dft-orca-optimization. Read its SKILL.md or equivalent instructions first, install only the files needed for this workspace, and summarize any required setup before using it. Skill purpose: Run DFT geometry optimization (minimization or TS search) on a molecular structure using ORCA via SCINE/ReaDuct wrapper. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"learningmatter-mit-chem-dft-orca-optimization\",\"task\":\"Install chem-dft-orca-optimization\",\"agent\":\"codex\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."},{"id":"claude-code","label":"Claude Code","kind":"agent-prompt","value":"Add \"chem-dft-orca-optimization\" as a Claude Code skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-dft-orca-optimization. Inspect the skill instructions, place the reusable skill files in the appropriate local skills location for this project, and report the activation steps. Skill purpose: Run DFT geometry optimization (minimization or TS search) on a molecular structure using ORCA via SCINE/ReaDuct wrapper. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"learningmatter-mit-chem-dft-orca-optimization\",\"task\":\"Install chem-dft-orca-optimization\",\"agent\":\"claude-code\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."},{"id":"cursor","label":"Cursor","kind":"agent-prompt","value":"Turn \"chem-dft-orca-optimization\" from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-dft-orca-optimization into a reusable Cursor project rule or agent instruction. Preserve the core workflow, adapt paths to this repo, and keep the rule scoped to tasks where it is relevant. Skill purpose: Run DFT geometry optimization (minimization or TS search) on a molecular structure using ORCA via SCINE/ReaDuct wrapper. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"learningmatter-mit-chem-dft-orca-optimization\",\"task\":\"Install chem-dft-orca-optimization\",\"agent\":\"cursor\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."}],"handoff_url":"https://www.openagentskill.com/api/skills/learningmatter-mit-chem-dft-orca-optimization/install","manifest_url":"https://www.openagentskill.com/api/registry/manifest/learningmatter-mit-chem-dft-orca-optimization"},"trust":{"score":68,"label":"Manual review","version":"trust-score-v4","install_policy":"human_review_before_install","evidence":{"stars":"161 GitHub stars","repoActivity":"161 stars, 24 forks","lastPushed":"5d since push","license":"MIT","repository":"https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-dft-orca-optimization","install":"npx skills add learningmatter-mit/AtomisticSkills --skill chem-dft-orca-optimization","installSafety":"standard package or runtime install path","permissionSurface":"secrets or environment access, shell or command execution","documentation":"Strong README/SKILL.md context","agentOutcomes":"No agent outcome data yet"},"outcome_evidence":{"total":0,"successes":0,"failures":0,"not_relevant":0,"success_rate":null,"recent_success_rate":null,"recent_failure_rate":null,"install_attempts":0,"install_success_rate":null,"risk_blocked":0,"setup_required":0,"avg_output_quality":null,"production_outcomes":0,"last_outcome_at":null,"label":"No agent outcome data yet"},"auto_install":{"allowed":false,"sandbox_required":true,"reason":"Human review or sandbox validation is required before automatic installation."},"best_for":["[chemistry]","agent-skill"],"known_risks":["The SKILL.md excerpt is truncated, but the provided content is comprehensive and well-structured.","Financial research output is not financial advice; require human review before any live investment decision.","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"]},"agent_proven":{"version":"agent-proven-v1","score":0,"tier":"unproven","label":"Needs first agent run","summary":"No agent outcome reports yet. Use Resolve, run one narrow sandbox task, then report the result.","metrics":{"totalOutcomes":0,"successfulOutcomes":0,"failedOutcomes":0,"installAttempts":0,"installSuccessRate":null,"successRate":null,"recentSuccessRate":null,"recentFailureRate":null,"riskBlocked":0,"setupRequired":0,"notRelevant":0,"avgOutputQuality":null,"avgTimeToUsefulMs":null,"productionOutcomes":0,"humanReviewRequired":0,"uniqueAgents":0,"lastOutcomeAt":null},"signals":[],"penalties":["No real agent outcome evidence yet"]},"audit":{"score":76,"risk_level":"needs_review","risk_label":"Needs review","warnings":["Dependency or permission surface needs review","Permission surface may require sandboxing","Financial research output is not financial advice; require human review before any live investment decision","The SKILL.md excerpt is truncated, but the provided content is comprehensive and well-structured.","The skill depends on external software (ORCA, SCINE) and a specific conda environment, which may limit portability but is clearly documented.","Financial research output is not financial advice; require human review before any live investment decision.","Quality score needs review","Permission surface needs review: secrets or environment access, shell or command execution"]},"safety_gate":{"tier":"blocked","label":"Blocked for auto-install","auto_install_policy":"block","auto_install_allowed":false,"human_review_required":true,"blocked":true,"recommended_action":"Do not auto-install. Inspect the source, dependencies, and permission surface first."},"quality":{"score":69,"label":"Promising"},"supply":{"track":"Coding and developer agents","scenario":"GitHub automation","maintenance":"5d since push","risk":"Needs review"},"alternative_skills":[],"do_not_use_when":["teams that need a vendor-supported SLA","production agents without a repository review","The SKILL.md excerpt is truncated, but the provided content is comprehensive and well-structured.","No OpenAgentSkill engagement data yet","High-risk permission hints: Shell or command execution, Secrets or environment access","Dependency or permission surface needs review","Permission surface may require sandboxing","Financial research output is not financial advice; require human review before any live investment decision"],"agent_contract":{"task_input":"Use chem-dft-orca-optimization in an agent workflow","recommended_action":"Do not auto-install. Inspect the source, dependencies, and permission surface first.","install_policy":"block","minimum_review_before_use":["Trust: 68/100 Manual review","Audit: 76/100 Needs review","Safety: 36/100 Avoid automatic install","Review repository, license, install command, and permission surface before production use."],"expected_agent_output":{"selected_skill":"learningmatter-mit-chem-dft-orca-optimization (chem-dft-orca-optimization)","install_command":"npx skills add learningmatter-mit/AtomisticSkills --skill chem-dft-orca-optimization","risk_summary":"Needs review; Blocked for auto-install; Review before production","verification_result":"Report the smallest successful task, files touched, warnings, and any missing setup."}},"outcome_feedback":{"endpoint":"https://www.openagentskill.com/api/agent/outcome","method":"POST","requires_resolve_event_id":true,"event_id_source":"Use install_receipt.outcome_feedback.event_id or feedback.event_id returned by /api/agent/resolve for the current task.","expected_outcomes":["success","failed","not_relevant","blocked_by_risk","setup_required"],"payload_template":{"event_id":"<install_receipt.outcome_feedback.event_id or feedback.event_id from /api/agent/resolve>","skill_slug":"learningmatter-mit-chem-dft-orca-optimization","task":"Use chem-dft-orca-optimization in an agent workflow","agent":"codex","outcome":"success","install_used":true,"risk_blocked":false,"setup_required":false,"task_success":true,"output_quality":4,"error_type":null,"human_review_required":false,"workspace":"sandbox","time_to_useful_ms":120000,"notes":"Report the smallest successful task, setup friction, files touched, and risk notes."}},"endpoints":{"web":"https://www.openagentskill.com/skills/learningmatter-mit-chem-dft-orca-optimization","api":"https://www.openagentskill.com/api/agent/skills/learningmatter-mit-chem-dft-orca-optimization","audit":"https://www.openagentskill.com/skills/learningmatter-mit-chem-dft-orca-optimization/audit","eval":"https://www.openagentskill.com/api/agent/evals?slug=learningmatter-mit-chem-dft-orca-optimization&task=Use%20chem-dft-orca-optimization%20in%20an%20agent%20workflow&max_risk=medium","resolve":"https://www.openagentskill.com/api/agent/resolve?task=Use%20chem-dft-orca-optimization%20in%20an%20agent%20workflow&agent=codex&max_risk=medium","receipt":"https://www.openagentskill.com/api/agent/receipt?task=Use%20chem-dft-orca-optimization%20in%20an%20agent%20workflow&agent=codex&max_risk=medium&format=text","install":"https://www.openagentskill.com/api/skills/learningmatter-mit-chem-dft-orca-optimization/install","manifest":"https://www.openagentskill.com/api/registry/manifest/learningmatter-mit-chem-dft-orca-optimization"}},"supply_profile":{"track":{"slug":"coding","label":"Coding and developer agents","shortLabel":"Coding","description":"Code review, repo analysis, testing, CI, GitHub, DevOps, and developer workflow skills."},"scenario":{"label":"GitHub automation","description":"I need my agent to triage GitHub issues, review pull requests, and summarize repository changes.","useCases":[{"slug":"github-automation","title":"GitHub automation"},{"slug":"local-desktop","title":"Local desktop"},{"slug":"browser-automation","title":"Browser automation"}]},"applicableAgents":["Claude Code","CLI","Codex","Cursor"],"install":{"ready":true,"command":"npx skills add learningmatter-mit/AtomisticSkills --skill chem-dft-orca-optimization","primaryTarget":"CLI","targetCount":4},"githubQuality":{"stars":161,"starsLabel":"161","forks":24,"license":"MIT","qualityScore":69,"trustScore":68,"auditScore":76},"maintenance":{"status":"fresh","label":"5d since push","daysSincePush":5,"lastPushedAt":"2026-09-03T06:44:16+00:00"},"risk":{"level":"needs_review","label":"Needs review","requiresReview":true,"notes":["Dependency or permission surface needs review","Permission surface may require sandboxing","Financial research output is not financial advice; require human review before any live investment decision","The SKILL.md excerpt is truncated, but the provided content is comprehensive and well-structured.","The skill depends on external software (ORCA, SCINE) and a specific conda environment, which may limit portability but is clearly documented."]},"coverageTags":["Coding","GitHub automation","[chemistry]","agent-skill"]},"audit":{"audit_score":76,"risk_level":"needs_review","risk_label":"Needs review","quality_score":69,"trust_score":68,"maintenance_score":100,"security_score":73,"install_score":92,"warnings":["Dependency or permission surface needs review","Permission surface may require sandboxing","Financial research output is not financial advice; require human review before any live investment decision","The SKILL.md excerpt is truncated, but the provided content is comprehensive and well-structured.","The skill depends on external software (ORCA, SCINE) and a specific conda environment, which may limit portability but is clearly documented.","Financial research output is not financial advice; require human review before any live investment decision.","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"]},"quality_signals":{"model":"v2","star_score":15.47,"usage_score":0,"review_score":5.4,"metadata_score":3,"freshness_score":15},"platforms":["Claude Code"],"use_cases":[{"slug":"github-automation","title":"GitHub automation","url":"https://www.openagentskill.com/use-cases/github-automation"},{"slug":"local-desktop","title":"Local desktop","url":"https://www.openagentskill.com/use-cases/local-desktop"},{"slug":"browser-automation","title":"Browser automation","url":"https://www.openagentskill.com/use-cases/browser-automation"},{"slug":"research-agents","title":"Research agents","url":"https://www.openagentskill.com/use-cases/research-agents"}],"stacks":[{"slug":"browser-qa-agent","title":"Browser QA agent","url":"https://www.openagentskill.com/collections/browser-qa-agent"},{"slug":"research-report-agent","title":"Research report agent","url":"https://www.openagentskill.com/collections/research-report-agent"},{"slug":"content-growth-agent","title":"Content growth agent","url":"https://www.openagentskill.com/collections/content-growth-agent"}],"install":"npx skills add learningmatter-mit/AtomisticSkills --skill chem-dft-orca-optimization","install_targets":[{"id":"openagentskill-cli","label":"CLI","title":"OpenAgentSkill CLI","kind":"command","value":"npx --yes https://github.com/Leon-Drq/openagentskill/releases/download/cli-v0.3.0/openagentskill-0.3.0.tgz add learningmatter-mit-chem-dft-orca-optimization","description":"Resolve policy, run the source installer safely, and report a verified install receipt.","copyLabel":"Copy command"},{"id":"codex","label":"Codex","title":"Codex install prompt","kind":"agent-prompt","value":"Install the \"chem-dft-orca-optimization\" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-dft-orca-optimization. Read its SKILL.md or equivalent instructions first, install only the files needed for this workspace, and summarize any required setup before using it. Skill purpose: Run DFT geometry optimization (minimization or TS search) on a molecular structure using ORCA via SCINE/ReaDuct wrapper. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"learningmatter-mit-chem-dft-orca-optimization\",\"task\":\"Install chem-dft-orca-optimization\",\"agent\":\"codex\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes.","description":"Give Codex a repo-aware install prompt when the skill is not available through a local CLI.","copyLabel":"Copy prompt"},{"id":"claude-code","label":"Claude Code","title":"Claude Code skill prompt","kind":"agent-prompt","value":"Add \"chem-dft-orca-optimization\" as a Claude Code skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-dft-orca-optimization. Inspect the skill instructions, place the reusable skill files in the appropriate local skills location for this project, and report the activation steps. Skill purpose: Run DFT geometry optimization (minimization or TS search) on a molecular structure using ORCA via SCINE/ReaDuct wrapper. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"learningmatter-mit-chem-dft-orca-optimization\",\"task\":\"Install chem-dft-orca-optimization\",\"agent\":\"claude-code\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes.","description":"Use this prompt to ask Claude Code to add the skill and explain the local activation steps.","copyLabel":"Copy prompt"},{"id":"cursor","label":"Cursor","title":"Cursor rule prompt","kind":"agent-prompt","value":"Turn \"chem-dft-orca-optimization\" from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-dft-orca-optimization into a reusable Cursor project rule or agent instruction. Preserve the core workflow, adapt paths to this repo, and keep the rule scoped to tasks where it is relevant. Skill purpose: Run DFT geometry optimization (minimization or TS search) on a molecular structure using ORCA via SCINE/ReaDuct wrapper. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"learningmatter-mit-chem-dft-orca-optimization\",\"task\":\"Install chem-dft-orca-optimization\",\"agent\":\"cursor\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes.","description":"Use this when installing as Cursor project rules or reusable agent instructions.","copyLabel":"Copy prompt"}],"repository":"https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-dft-orca-optimization","github_repo":"learningmatter-mit/AtomisticSkills","version":"1.0.0","license":"MIT","urls":{"web":"https://www.openagentskill.com/skills/learningmatter-mit-chem-dft-orca-optimization","repository":"https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-dft-orca-optimization","api":"/api/agent/skills/learningmatter-mit-chem-dft-orca-optimization","install_api":"/api/skills/learningmatter-mit-chem-dft-orca-optimization/install"},"meta":{"created_at":"2026-09-06T11:56:05.232891+00:00","updated_at":"2026-09-06T11:56:05.384107+00:00","agent_friendly":true}}