Backend:
- Add POST /generate-extractor for AI code generation via Claude CLI
- Add POST /generate-extractor/stream for SSE streaming generation
- Add POST /validate-extractor with enhanced syntax checking
- Add POST /check-dependencies for import analysis
- Add POST /test-extractor for live OP2 file testing
- Add ClaudeCodeSession service for managing CLI sessions
Frontend:
- Add lib/api/claude.ts with typed API functions
- Enhance CodeEditorPanel with:
- Streaming generation with live preview
- Code snippets library (6 templates: displacement, stress, frequency, mass, energy, reaction)
- Test button for live OP2 validation
- Cancel button for stopping generation
- Dependency warnings display
- Integrate streaming and testing into NodeConfigPanelV2
Uses Claude CLI (--print mode) to leverage Pro/Max subscription without API costs.
Phase 1 - Foundation:
- Add NodeConfigPanelV2 using useSpecStore for AtomizerSpec v2.0 mode
- Deprecate AtomizerCanvas and useCanvasStore with migration docs
- Add VITE_USE_LEGACY_CANVAS env var for emergency fallback
- Enhance NodePalette with collapse support, filtering, exports
- Add drag-drop support to SpecRenderer with default node data
- Setup test infrastructure (Vitest + Playwright configs)
- Add useSpecStore unit tests (15 tests)
Phase 2 - File Structure & Model:
- Create FileStructurePanel with tree view of study files
- Add ModelNodeV2 with collapsible file dependencies
- Add tabbed left sidebar (Components/Files tabs)
- Add GET /api/files/structure/{study_id} backend endpoint
- Auto-expand 1_setup folders in file tree
- Show model file introspection with solver type and expressions
Technical:
- All TypeScript checks pass
- All 15 unit tests pass
- Production build successful
## Documentation Updates
- DASHBOARD.md: Updated to V3.0 with Canvas V3 features, file browser, introspection
- DASHBOARD_IMPLEMENTATION_STATUS.md: Marked Canvas V3 features as COMPLETE
- CANVAS.md: New comprehensive guide for Canvas Builder V3 with all features
- CLAUDE.md: Added dashboard quick reference and Canvas V3 features
## Canvas V3 Features Documented
- File Browser: Browse studies directory for model files
- Model Introspection: Auto-discover expressions, solver type, dependencies
- One-Click Add: Add expressions as design variables instantly
- Claude Bug Fixes: WebSocket reconnection, SQL errors resolved
- Health Check: /api/health endpoint for monitoring
## Backend Services
- NX introspection service with expression discovery
- File browser API with type filtering
- Claude session management improvements
- Context builder enhancements
## Frontend Components
- FileBrowser: Modal for file selection with search
- IntrospectionPanel: View discovered model information
- ExpressionSelector: Dropdown for design variable configuration
- Improved chat hooks with reconnection logic
## Plan Documents
- Added RALPH_LOOP_CANVAS_V2/V3 implementation records
- Added ATOMIZER_DASHBOARD_V2_MASTER_PLAN
- Added investigation and sync documentation
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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>
