9 Commits

Author SHA1 Message Date
73a7b9d9f1 feat: Add dashboard chat integration and MCP server
Major changes:
- Dashboard: WebSocket-based chat with session management
- Dashboard: New chat components (ChatPane, ChatInput, ModeToggle)
- Dashboard: Enhanced UI with parallel coordinates chart
- MCP Server: New atomizer-tools server for Claude integration
- Extractors: Enhanced Zernike OPD extractor
- Reports: Improved report generator

New studies (configs and scripts only):
- M1 Mirror: Cost reduction campaign studies
- Simple Beam, Simple Bracket, UAV Arm studies

Note: Large iteration data (2_iterations/, best_design_archive/)
excluded via .gitignore - kept on local Gitea only.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
2026-01-13 15:53:55 -05:00
b8a04c62b8 docs: Consolidate documentation and fix protocol numbering (partial)
Phase 2 of restructuring plan:
- Rename SYS_16_STUDY_INSIGHTS -> SYS_17_STUDY_INSIGHTS
- Rename SYS_17_CONTEXT_ENGINEERING -> SYS_18_CONTEXT_ENGINEERING
- Promote Bootstrap V3.0 (Context Engineering) as default
- Archive old Bootstrap V2.0
- Create knowledge_base/playbook.json for ACE framework
- Add OP_08 (Generate Report) to routing tables
- Add SYS_16-18 to protocol tables
- Update docs/protocols/README.md to version 1.1
- Update CLAUDE.md with new protocols
- Create docs/plans/RESTRUCTURING_PLAN.md for continuation

Remaining: Phase 2.8 (Cheatsheet), Phases 3-6

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
2026-01-07 08:52:07 -05:00
32caa5d05c feat: Implement Study Interview Mode as default study creation method
Study Interview Mode is now the DEFAULT for all study creation requests.
This intelligent Q&A system guides users through optimization setup with:

- 7-phase interview flow: introspection → objectives → constraints → design_variables → validation → review → complete
- Material-aware validation with 12 materials and fuzzy name matching
- Anti-pattern detection for 12 common mistakes (mass-no-constraint, stress-over-yield, etc.)
- Auto extractor mapping E1-E24 based on goal keywords
- State persistence with JSON serialization and backup rotation
- StudyBlueprint generation with full validation

Triggers: "create a study", "new study", "optimize this", any study creation intent
Skip with: "skip interview", "quick setup", "manual config"

Components:
- StudyInterviewEngine: Main orchestrator
- QuestionEngine: Conditional logic evaluation
- EngineeringValidator: MaterialsDatabase + AntiPatternDetector
- InterviewPresenter: Markdown formatting for Claude
- StudyBlueprint: Validated configuration output
- InterviewState: Persistent state management

All 129 tests passing.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
2026-01-03 11:06:07 -05:00
82f36689b7 feat: Pre-migration checkpoint - updated docs and utilities
Updates before optimization_engine migration:
- Updated migration plan to v2.1 with complete file inventory
- Added OP_07 disk optimization protocol
- Added SYS_16 self-aware turbo protocol
- Added study archiver and cleanup utilities
- Added ensemble surrogate module
- Updated NX solver and session manager
- Updated zernike HTML generator
- Added context engineering plan
- LAC session insights updates

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
2025-12-29 10:22:45 -05:00
f13563d7ab feat: Major update - Physics docs, Zernike OPD, insights, NX journals, tools
Documentation:
- Add docs/06_PHYSICS/ with Zernike fundamentals and OPD method docs
- Add docs/guides/CMA-ES_EXPLAINED.md optimization guide
- Update CLAUDE.md and ATOMIZER_CONTEXT.md with current architecture
- Update OP_01_CREATE_STUDY protocol

Planning:
- Add DYNAMIC_RESPONSE plans for random vibration/PSD support
- Add OPTIMIZATION_ENGINE_MIGRATION_PLAN for code reorganization

Insights System:
- Update design_space, modal_analysis, stress_field, thermal_field insights
- Improve error handling and data validation

NX Journals:
- Add analyze_wfe_zernike.py for Zernike WFE analysis
- Add capture_study_images.py for automated screenshots
- Add extract_expressions.py and introspect_part.py utilities
- Add user_generated_journals/journal_top_view_image_taking.py

Tests & Tools:
- Add comprehensive Zernike OPD test suite
- Add audit_v10 tests for WFE validation
- Add tools for Pareto graphs and mirror data extraction
- Add migrate_studies_to_topics.py utility

Knowledge Base:
- Initialize LAC (Learning Atomizer Core) with failure/success patterns

Dashboard:
- Update Setup.tsx and launch_dashboard.py
- Add restart-dev.bat helper script

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
2025-12-23 19:47:37 -05:00
274081d977 refactor: Engine updates and NX hooks improvements
optimization_engine:
- Updated nx_solver.py with improvements
- Enhanced solve_simulation.py
- Updated extractors/__init__.py
- Improved NX CAD hooks (expression_manager, feature_manager,
  geometry_query, model_introspection, part_manager)
- Enhanced NX CAE solver_manager hook

Documentation:
- Updated OP_01_CREATE_STUDY.md protocol
- Updated SYS_12_EXTRACTOR_LIBRARY.md

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
2025-12-20 13:47:21 -05:00
Antoine
01a7d7d121 docs: Complete M1 mirror optimization campaign V11-V15
## M1 Mirror Campaign Summary
- V11-V15 optimization campaign completed (~1,400 FEA evaluations)
- Best design: V14 Trial #725 with Weighted Sum = 121.72
- V15 NSGA-II confirmed V14 TPE found optimal solution
- Campaign improved from WS=129.33 (V11) to WS=121.72 (V14): -5.9%

## Key Results
- 40° tracking: 5.99 nm (target 4.0 nm)
- 60° tracking: 13.10 nm (target 10.0 nm)
- Manufacturing: 26.28 nm (target 20.0 nm)
- Targets not achievable within current design space

## Documentation Added
- V15 STUDY_REPORT.md: Detailed NSGA-II results analysis
- M1_MIRROR_CAMPAIGN_SUMMARY.md: Full V11-V15 campaign overview
- Updated CLAUDE.md, ATOMIZER_CONTEXT.md with NXSolver patterns
- Updated 01_CHEATSHEET.md with --resume guidance
- Updated OP_01_CREATE_STUDY.md with FEARunner template

## Studies Added
- m1_mirror_adaptive_V13: TPE validation (291 trials)
- m1_mirror_adaptive_V14: TPE intensive (785 trials, BEST)
- m1_mirror_adaptive_V15: NSGA-II exploration (126 new FEA)

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
2025-12-16 14:55:23 -05:00
Antoine
1bb201e0b7 feat: Add post-optimization tools and mandatory best design archiving
New Tools (tools/):
- analyze_study.py: Generate comprehensive optimization reports
- find_best_iteration.py: Find best iteration folder, optionally copy it
- archive_best_design.py: Archive best design to 3_results/best_design_archive/<timestamp>/

Protocol Updates:
- OP_02_RUN_OPTIMIZATION.md v1.1: Add mandatory archive_best_design step
  in Post-Run Actions. This MUST be done after every optimization run.

V14 Updates:
- run_optimization.py: Auto-archive best design at end of optimization
- optimization_config.json: Expand bounds for V14 continuation
  - lateral_outer_angle: min 13->11 deg (was at 4.7%)
  - lateral_inner_pivot: min 7->5 mm (was at 8.1%)
  - lateral_middle_pivot: max 23->27 mm (was at 99.4%)
  - whiffle_min: max 60->72 mm (was at 96.3%)

Usage:
  python tools/analyze_study.py m1_mirror_adaptive_V14
  python tools/find_best_iteration.py m1_mirror_adaptive_V14
  python tools/archive_best_design.py m1_mirror_adaptive_V14

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
2025-12-12 10:28:35 -05:00
Antoine
602560c46a feat: Add MLP surrogate with Turbo Mode for 100x faster optimization
Neural Acceleration (MLP Surrogate):
- Add run_nn_optimization.py with hybrid FEA/NN workflow
- MLP architecture: 4-layer (64->128->128->64) with BatchNorm/Dropout
- Three workflow modes:
  - --all: Sequential export->train->optimize->validate
  - --hybrid-loop: Iterative Train->NN->Validate->Retrain cycle
  - --turbo: Aggressive single-best validation (RECOMMENDED)
- Turbo mode: 5000 NN trials + 50 FEA validations in ~12 minutes
- Separate nn_study.db to avoid overloading dashboard

Performance Results (bracket_pareto_3obj study):
- NN prediction errors: mass 1-5%, stress 1-4%, stiffness 5-15%
- Found minimum mass designs at boundary (angle~30deg, thick~30mm)
- 100x speedup vs pure FEA exploration

Protocol Operating System:
- Add .claude/skills/ with Bootstrap, Cheatsheet, Context Loader
- Add docs/protocols/ with operations (OP_01-06) and system (SYS_10-14)
- Update SYS_14_NEURAL_ACCELERATION.md with MLP Turbo Mode docs

NX Automation:
- Add optimization_engine/hooks/ for NX CAD/CAE automation
- Add study_wizard.py for guided study creation
- Fix FEM mesh update: load idealized part before UpdateFemodel()

New Study:
- bracket_pareto_3obj: 3-objective Pareto (mass, stress, stiffness)
- 167 FEA trials + 5000 NN trials completed
- Demonstrates full hybrid workflow

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
2025-12-06 20:01:59 -05:00