Phase 1-7 of Canvas V4 Ralph Loop implementation:
Backend:
- Add /api/files routes for browsing model files
- Add /api/nx routes for NX model introspection
- Add NXIntrospector service to discover expressions and extractors
- Add health check with database status
Frontend:
- Add FileBrowser component for selecting .sim/.prt/.fem files
- Add IntrospectionPanel to discover expressions and extractors
- Update NodeConfigPanel with browse and introspect buttons
- Update schema with NODE_HANDLES for proper flow direction
- Update validation for correct DesignVar -> Model -> Solver flow
- Update useCanvasStore.addNode() to accept custom data
Flow correction: Design Variables now connect TO Model (as source),
not FROM Model. This matches the actual data flow in optimization.
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Bug Fixes:
- Fix Atomizer Assistant error with reconnect button and error state handling
- Enable connection/edge deletion with keyboard Delete/Backspace keys
- Fix drag & drop positioning using screenToFlowPosition correctly
- Fix loadFromConfig to create all node types and edges properly
UI/UX Improvements:
- Minimal responsive header with context breadcrumb
- Better contrast with white text on dark backgrounds
- Larger font sizes in NodePalette for readability
- Study-aware header showing selected study name
New Features:
- Enhanced ExecuteDialog with Create/Update mode toggle
- Select existing study to update or create new study
- Home page Canvas Builder button for quick access
- Home navigation button in CanvasView header
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Ignore .claude-mcp-*.json session config files
- Ignore .claude-prompt-*.md system prompt files
- These are ephemeral files created during chat sessions
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Ensure MCP config file is created before CLI calls
- Pass --mcp-config flag to Claude CLI for atomizer tools access
- Add mcp__atomizer-tools__* to allowed tools in user mode
- Enables canvas validate/execute/interpret intent tools
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add textarea input with Enter-to-send functionality to ChatPanel
- Pass sendMessage and isConnected props from AtomizerCanvas
- Add disabled states during thinking/disconnected states
- Use Lucide Send icon for submit button
- Show connection status with Sparkles welcome icon
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Phase 5 of Canvas Professional Upgrade:
- Create ExpressionSelector component with searchable dropdown
- Fetch expressions from NX introspection API
- Auto-populate label, units, and default min/max from expression value
- Add refresh button to reload expressions
- Integrate into NodeConfigPanel for DesignVar nodes
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Phase 4 of Canvas Professional Upgrade:
- Add /studies/{id}/nx/introspect endpoint for full model introspection
- Add /studies/{id}/nx/expressions endpoint for expression list
- Add caching to avoid re-running NX journal on each request
- Add frontend API client methods: introspectNxModel, getNxExpressions
- Use existing introspect_part.py extractor
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Phase 3 of Canvas Professional Upgrade:
- Fix ConfigImporter API endpoint URL (/api/optimization/studies/...)
- Add currentStudyId prop to auto-select study in importer
- Parse response correctly (data.config instead of raw response)
- Replace file upload emoji with FolderOpen Lucide icon
- Add "Load Study Config" button to Setup canvas tab header
- Show button only when canvas is empty
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Phase 2 of Canvas Professional Upgrade:
- Update AtomizerCanvas with Lucide icons (MessageCircle, Plug, X)
- Update CanvasView page with dark theme styling
- Replace emoji buttons with Lucide icons (ClipboardList, Download, Trash2)
- Update Setup canvas tab for full-width responsive layout
- Use calc(100vh-6rem) for proper canvas height
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Phase 1 of Canvas Professional Upgrade:
- Replace all emoji icons in nodes with Lucide components
- Update BaseNode to use iconColor prop instead of color/colorBg
- Update NodePalette with matching Lucide icons
- Update templates.ts with Lucide icon names (Box, Scale, BarChart3, etc.)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Canvas Builder Visual Updates:
- Update all Canvas components to use Atomaster dark theme
- BaseNode: dark background (bg-dark-800), white text, primary selection glow
- NodePalette: dark sidebar with hover states
- NodeConfigPanel: dark inputs, labels, and panel background
- ValidationPanel: semi-transparent error/warning panels with backdrop blur
- ChatPanel: dark message area with themed welcome state
- ExecuteDialog: dark modal with primary button styling
- ConfigImporter: dark tabs, inputs, and file upload zone
- TemplateSelector: dark cards with category pills and hover effects
Setup Page Integration:
- Add Configuration/Canvas Builder tab switcher
- Canvas tab renders AtomizerCanvas full-height
- Tabs styled to match Atomaster theme
Build: Passes TypeScript and Vite build
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add canvas.ts MCP tool with validate_canvas_intent, execute_canvas_intent, interpret_canvas_intent
- Add useCanvasChat.ts bridge hook connecting canvas to chat system
- Update context_builder.py with canvas tool instructions
- Add ExecuteDialog for study name input
- Add ChatPanel for canvas-integrated Claude responses
- Connect AtomizerCanvas to Claude via useCanvasChat
Canvas workflow now:
1. Build graph visually
2. Click Validate/Analyze/Execute
3. Claude processes intent via MCP tools
4. Response shown in integrated chat panel
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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>
- Update README.md with LLM assistant section
- Create optimization_memory JSONL structure
- Move implementation plans from skills/modules to docs/plans
- Verify all imports work correctly
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add neural optional group (torch, torch-geometric, tensorboard)
- Add gnn optional group (torch, torch-geometric)
- Add all optional group for convenience
- Remove mcp optional group (not implemented)
- Remove mcp_server from packages.find
- Update pytest coverage config
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Consolidate surrogates module to processors/surrogates/
- Move ensemble_surrogate.py to proper location
- Add deprecation shim for old import path
- Create tests/ directory with pytest structure
- Move test files from archive/test_scripts/
- Add conftest.py with shared fixtures
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Delete orphaned files: temp_compare.py, run_cleanup.py
- Delete stale cache files from archive/temp_outputs/
- Update .gitignore with .coverage.*, .obsidian/ entries
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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>
Self-Aware Turbo v3 optimization validated on M1 Mirror flat back:
- Best WS: 205.58 (12% better than previous best 218.26)
- 100% feasibility rate, 100% unique designs
- Uses 556 training samples from V5-V8 campaign data
Key innovations in V9:
- Adaptive exploration schedule (15% → 8% → 3%)
- Mass threshold at 118 kg (optimal sweet spot)
- 70% exploitation near best design
- Seeded with best known design from V7
- Ensemble surrogate with R²=0.99
Updated documentation:
- SYS_16: SAT protocol updated to v3.0 VALIDATED
- Cheatsheet: Added SAT v3 as recommended method
- Context: Updated protocol overview
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Added new PART 8: Self-Aware Turbo (SAT) - Validated Breakthrough
- Explains ensemble surrogate with epistemic uncertainty
- Documents OOD detection and adaptive exploration schedule
- Includes V9 results: WS=205.58 (best ever)
- Added SAT sound bites for podcast
- Updated document to 12 sections
Generated with Claude Code
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Key changes based on feedback:
- Reposition as "optimizer & NX configurator" not "LLM-first"
- Add Part 2: Study Characterization & Performance Learning
- Add Part 3: Protocol Evolution workflow (Research → Review → Approve)
- Add Part 4: MCP-first development approach with documentation hierarchy
- Emphasize simulation optimization over CAD/mesh concerns
- Add LAC knowledge accumulation for parameter-performance relationships
- Add privilege levels for protocol approval (user/power_user/admin)
- Update sound bites and core messaging
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Added GitHub remote URL (Anto01/Atomizer) to CLAUDE.md so it persists
across sessions. Also recorded in LAC user_preference.jsonl.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Expanded Key Directories section with full optimization_engine structure
- Added Import Migration section with new import paths
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Update feature_registry.json paths to new module locations (v0.3.0)
- Update cheatsheet with new import paths (v2.3)
- Mark migration plan as completed (v3.0)
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add TrialManager (trial_manager.py) for consistent trial_NNNN naming
- Add DashboardDB (dashboard_db.py) for Optuna-compatible database schema
- Update CLAUDE.md with trial management documentation
- Update ATOMIZER_CONTEXT.md with v1.8 trial system
- Update cheatsheet v2.2 with new utilities
- Update SYS_14 protocol to v2.3 with TrialManager integration
- Add LAC learnings for trial management patterns
- Add archive/README.md for deprecated code policy
Key principles:
- Trial numbers NEVER reset (monotonic)
- Folders NEVER get overwritten
- Database always synced with filesystem
- Surrogate predictions are NOT trials (only FEA results)
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Adds tests/debug_lateral_discrepancy.py to investigate differences between
Zernike OPD lateral displacement reporting and Simcenter post-processing.
Key findings documented:
- OPD reports sqrt(dx² + dy²) - combined XY magnitude
- Simcenter shows individual components (dx or dy)
- Both are correct, OPD magnitude is more meaningful for optics
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Replace Standard (Z-only) extraction with OPD method (X,Y,Z displacement)
- Add toggle buttons to switch between WFE, ΔX, ΔY, ΔZ views
- Show method comparison metrics (OPD vs Standard RMS difference)
- Display lateral displacement statistics (max/RMS)
- Fall back to Standard method if BDF geometry file not found
- Use ZernikeOPDExtractor for more accurate WFE computation (+8-11%)
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Major improvements to Zernike WFE visualization:
- Add ZernikeDashboardInsight: Unified dashboard with all orientations (40°, 60°, 90°)
on one page with light theme and executive summary
- Add OPD method toggle: Switch between Standard (Z-only) and OPD (X,Y,Z) methods
in ZernikeWFEInsight with interactive buttons
- Add lateral displacement maps: Visualize X,Y displacement for each orientation
- Add displacement component views: Toggle between WFE, ΔX, ΔY, ΔZ in relative views
- Add metrics comparison table showing both methods side-by-side
New extractors:
- extract_zernike_figure.py: ZernikeOPDExtractor using BDF geometry interpolation
- extract_zernike_opd.py: Parabola-based OPD with focal length
Key finding: OPD method gives 8-11% higher WFE values than Standard method
(more conservative/accurate for surfaces with lateral displacement under gravity)
Documentation updates:
- SYS_12: Added E22 ZernikeOPD as recommended method
- SYS_16: Added ZernikeDashboard, updated ZernikeWFE with OPD features
- Cheatsheet: Added Zernike method comparison table
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Dashboard integration for Study Insights module (SYS_16):
- Backend: New /api/insights/ routes for generating and viewing insights
- Frontend: New Insights.tsx page with Plotly visualization
- Navigation: Added Insights tab between Analysis and Results
Available insight types:
- Zernike WFE (wavefront error for mirrors)
- Stress Field (Von Mises stress contours)
- Modal Analysis (natural frequencies/mode shapes)
- Thermal Field (temperature distribution)
- Design Space (parameter-objective exploration)
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Remove old study folders that have been superseded or archived:
- bracket_pareto_3obj
- bracket_stiffness_optimization (V1-V3)
- bracket_stiffness_optimization_atomizerfield
- drone_gimbal_arm_optimization
- m1_mirror_adaptive_V11 through V15
- m1_mirror_zernike_optimization
- simple_beam_optimization
- training_data_export_test
- uav_arm_atomizerfield_test
These studies have been consolidated or are no longer needed.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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>
