fix: mass extraction NaN in Hydrotech Beam DOE — two bugs

Bug 1 — Journal (solve_simulation.py simple workflow):
  Expression lookup for p173 fails silently for derived/measurement
  expressions, so _temp_mass.txt was never written. Added MeasureManager
  fallback via extract_part_mass() (already used in assembly workflow).

Bug 2 — Extractor (extract_mass_from_expression.py):
  Journal writes 'p173=<value>' format but extractor tried float() on
  the whole content including 'p173='. Added key=value parsing.

Defense in depth — nx_interface.py:
  Added stdout parsing fallback: if _temp_mass.txt still missing, parse
  mass from journal output captured via solver.py stdout passthrough.

Files changed:
  - optimization_engine/nx/solve_simulation.py — MeasureManager fallback
  - optimization_engine/extractors/extract_mass_from_expression.py — key=value parse
  - optimization_engine/nx/solver.py — include stdout in result dict
  - projects/hydrotech-beam/studies/01_doe_landscape/nx_interface.py — stdout fallback

Tags: hydrotech-beam, mass-extraction

.claude/skills/01_CHEATSHEET.md

@@ -1,7 +1,7 @@
 ---
 skill_id: SKILL_001
-version: 2.4
-last_updated: 2025-12-31
+version: 2.5
+last_updated: 2026-01-22
 type: reference
 code_dependencies:
   - optimization_engine/extractors/__init__.py
@@ -14,8 +14,8 @@ requires_skills:
 
 # Atomizer Quick Reference Cheatsheet
 
-**Version**: 2.4
-**Updated**: 2025-12-31
+**Version**: 2.5
+**Updated**: 2026-01-22
 **Purpose**: Rapid lookup for common operations. "I want X → Use Y"
 
 ---
@@ -37,6 +37,8 @@ requires_skills:
 | **Use SAT (Self-Aware Turbo)** | **SYS_16** | SAT v3 for high-efficiency neural-accelerated optimization |
 | Generate physics insight | SYS_17 | `python -m optimization_engine.insights generate <study>` |
 | **Manage knowledge/playbook** | **SYS_18** | `from optimization_engine.context import AtomizerPlaybook` |
+| **Automate dev tasks** | **DevLoop** | `python tools/devloop_cli.py start "task"` |
+| **Test dashboard UI** | **DevLoop** | `python tools/devloop_cli.py browser --level full` |
 
 ---
 
@@ -678,6 +680,67 @@ feedback.process_trial_result(
 
 ---
 
+## DevLoop Quick Reference
+
+Closed-loop development system using AI agents + Playwright testing.
+
+### CLI Commands
+
+| Task | Command |
+|------|---------|
+| Full dev cycle | `python tools/devloop_cli.py start "Create new study"` |
+| Plan only | `python tools/devloop_cli.py plan "Fix validation"` |
+| Implement plan | `python tools/devloop_cli.py implement` |
+| Test study files | `python tools/devloop_cli.py test --study support_arm` |
+| Analyze failures | `python tools/devloop_cli.py analyze` |
+| Browser smoke test | `python tools/devloop_cli.py browser` |
+| Browser full tests | `python tools/devloop_cli.py browser --level full` |
+| Check status | `python tools/devloop_cli.py status` |
+| Quick test | `python tools/devloop_cli.py quick` |
+
+### Browser Test Levels
+
+| Level | Description | Tests |
+|-------|-------------|-------|
+| `quick` | Smoke test (page loads) | 1 |
+| `home` | Home page verification | 2 |
+| `full` | All UI + study tests | 5+ |
+| `study` | Canvas/dashboard for specific study | 3 |
+
+### State Files (`.devloop/`)
+
+| File | Purpose |
+|------|---------|
+| `current_plan.json` | Current implementation plan |
+| `test_results.json` | Filesystem/API test results |
+| `browser_test_results.json` | Playwright test results |
+| `analysis.json` | Failure analysis |
+
+### Prerequisites
+
+```bash
+# Start backend
+cd atomizer-dashboard/backend && python -m uvicorn api.main:app --reload --port 8000
+
+# Start frontend
+cd atomizer-dashboard/frontend && npm run dev
+
+# Install Playwright (once)
+cd atomizer-dashboard/frontend && npx playwright install chromium
+```
+
+### Standalone Playwright Tests
+
+```bash
+cd atomizer-dashboard/frontend
+npm run test:e2e          # Run all E2E tests
+npm run test:e2e:ui       # Playwright UI mode
+```
+
+**Full documentation**: `docs/guides/DEVLOOP.md`
+
+---
+
 ## Report Generation Quick Reference (OP_08)
 
 Generate comprehensive study reports from optimization data.

.claude/skills/modules/study-readme-generator.md

@@ -0,0 +1,206 @@
+# Study README Generator Skill
+
+**Skill ID**: STUDY_README_GENERATOR  
+**Version**: 1.0  
+**Purpose**: Generate intelligent, context-aware README.md files for optimization studies
+
+## When to Use
+
+This skill is invoked automatically during the study intake workflow when:
+1. A study moves from `introspected` to `configured` status
+2. User explicitly requests README generation
+3. Finalizing a study from the inbox
+
+## Input Context
+
+The README generator receives:
+
+```json
+{
+  "study_name": "bracket_mass_opt_v1",
+  "topic": "Brackets",
+  "description": "User's description from intake form",
+  "spec": { /* Full AtomizerSpec v2.0 */ },
+  "introspection": {
+    "expressions": [...],
+    "mass_kg": 1.234,
+    "solver_type": "NX_Nastran"
+  },
+  "context_files": {
+    "goals.md": "User's goals markdown content",
+    "notes.txt": "Any additional notes"
+  }
+}
+```
+
+## Output Format
+
+Generate a README.md with these sections:
+
+### 1. Title & Overview
+```markdown
+# {Study Name}
+
+**Topic**: {Topic}  
+**Created**: {Date}  
+**Status**: {Status}
+
+{One paragraph executive summary of the optimization goal}
+```
+
+### 2. Engineering Problem
+```markdown
+## Engineering Problem
+
+{Describe the physical problem being solved}
+
+### Model Description
+- **Geometry**: {Describe the part/assembly}
+- **Material**: {If known from introspection}
+- **Baseline Mass**: {mass_kg} kg
+
+### Loading Conditions
+{Describe loads and boundary conditions if available}
+```
+
+### 3. Optimization Formulation
+```markdown
+## Optimization Formulation
+
+### Design Variables ({count})
+| Variable | Expression | Range | Units |
+|----------|------------|-------|-------|
+| {name} | {expr_name} | [{min}, {max}] | {units} |
+
+### Objectives ({count})
+| Objective | Direction | Weight | Source |
+|-----------|-----------|--------|--------|
+| {name} | {direction} | {weight} | {extractor} |
+
+### Constraints ({count})
+| Constraint | Condition | Threshold | Type |
+|------------|-----------|-----------|------|
+| {name} | {operator} | {threshold} | {type} |
+```
+
+### 4. Methodology
+```markdown
+## Methodology
+
+### Algorithm
+- **Primary**: {algorithm_type}
+- **Max Trials**: {max_trials}
+- **Surrogate**: {if enabled}
+
+### Physics Extraction
+{Describe extractors used}
+
+### Convergence Criteria
+{Describe stopping conditions}
+```
+
+### 5. Expected Outcomes
+```markdown
+## Expected Outcomes
+
+Based on the optimization setup:
+- Expected improvement: {estimate if baseline available}
+- Key trade-offs: {identify from objectives/constraints}
+- Risk factors: {any warnings from validation}
+```
+
+## Generation Guidelines
+
+1. **Be Specific**: Use actual values from the spec, not placeholders
+2. **Be Concise**: Engineers don't want to read novels
+3. **Be Accurate**: Only state facts that can be verified from input
+4. **Be Helpful**: Include insights that aid understanding
+5. **No Fluff**: Avoid marketing language or excessive praise
+
+## Claude Prompt Template
+
+```
+You are generating a README.md for an FEA optimization study. 
+
+CONTEXT:
+{json_context}
+
+RULES:
+1. Use the actual data provided - never use placeholder values
+2. Write in technical engineering language appropriate for structural engineers
+3. Keep each section concise but complete
+4. If information is missing, note it as "TBD" or skip the section
+5. Include physical units wherever applicable
+6. Format tables properly with alignment
+
+Generate the README.md content:
+```
+
+## Example Output
+
+```markdown
+# Bracket Mass Optimization V1
+
+**Topic**: Simple_Bracket  
+**Created**: 2026-01-22  
+**Status**: Configured
+
+Optimize the mass of a structural L-bracket while maintaining stress below yield and displacement within tolerance.
+
+## Engineering Problem
+
+### Model Description
+- **Geometry**: L-shaped mounting bracket with web and flange
+- **Material**: Steel (assumed based on typical applications)
+- **Baseline Mass**: 0.847 kg
+
+### Loading Conditions
+Static loading with force applied at mounting holes. Fixed constraints at base.
+
+## Optimization Formulation
+
+### Design Variables (3)
+| Variable | Expression | Range | Units |
+|----------|------------|-------|-------|
+| Web Thickness | web_thickness | [2.0, 10.0] | mm |
+| Flange Width | flange_width | [15.0, 40.0] | mm |
+| Fillet Radius | fillet_radius | [2.0, 8.0] | mm |
+
+### Objectives (1)
+| Objective | Direction | Weight | Source |
+|-----------|-----------|--------|--------|
+| Total Mass | minimize | 1.0 | mass_extractor |
+
+### Constraints (1)
+| Constraint | Condition | Threshold | Type |
+|------------|-----------|-----------|------|
+| Max Stress | <= | 250 MPa | hard |
+
+## Methodology
+
+### Algorithm
+- **Primary**: TPE (Tree-structured Parzen Estimator)
+- **Max Trials**: 100
+- **Surrogate**: Disabled
+
+### Physics Extraction
+- Mass: Extracted from NX expression `total_mass`
+- Stress: Von Mises stress from SOL101 static analysis
+
+### Convergence Criteria
+- Max trials: 100
+- Early stopping: 20 trials without improvement
+
+## Expected Outcomes
+
+Based on the optimization setup:
+- Expected improvement: 15-30% mass reduction (typical for thickness optimization)
+- Key trade-offs: Mass vs. stress margin
+- Risk factors: None identified
+```
+
+## Integration Points
+
+- **Backend**: `api/services/claude_readme.py` calls Claude API with this prompt
+- **Endpoint**: `POST /api/intake/{study_name}/readme`
+- **Trigger**: Automatic on status transition to `configured`

.devloop/browser_test_results.json

@@ -0,0 +1,33 @@
+{
+  "timestamp": "2026-01-22T18:13:30.884945",
+  "scenarios": [
+    {
+      "scenario_id": "browser_home_stats",
+      "scenario_name": "Home page shows statistics",
+      "passed": true,
+      "duration_ms": 1413.166,
+      "error": null,
+      "details": {
+        "navigated_to": "http://localhost:3003/",
+        "found_selector": "text=Total Trials"
+      }
+    },
+    {
+      "scenario_id": "browser_expand_folder",
+      "scenario_name": "Topic folder expands on click",
+      "passed": true,
+      "duration_ms": 2785.3219999999997,
+      "error": null,
+      "details": {
+        "navigated_to": "http://localhost:3003/",
+        "found_selector": "span:has-text('completed'), span:has-text('running'), span:has-text('paused')",
+        "clicked": "button:has-text('trials')"
+      }
+    }
+  ],
+  "summary": {
+    "passed": 2,
+    "failed": 0,
+    "total": 2
+  }
+}

.devloop/current_plan.json

@@ -0,0 +1,16 @@
+{
+  "objective": "Implement Dashboard Intake & AtomizerSpec Integration: Phase 1 - Create backend intake API routes (create, introspect, list, topics endpoints) and spec_manager service. The spec_models.py and JSON schema have already been updated with SpecStatus, IntrospectionData, BaselineData, and ExpressionInfo models. Now need to create: 1) backend/api/services/spec_manager.py for centralized spec CRUD, 2) backend/api/routes/intake.py with endpoints for creating inbox folders, running introspection, listing inbox contents, and listing topics, 3) Register the intake router in main.py. Reference the plan at docs/plans/DASHBOARD_INTAKE_ATOMIZERSPEC_INTEGRATION.md",
+  "approach": "Fallback plan - manual implementation",
+  "tasks": [
+    {
+      "id": "task_001",
+      "description": "Implement: Implement Dashboard Intake & AtomizerSpec Integration: Phase 1 - Create backend intake API routes (create, introspect, list, topics endpoints) and spec_manager service. The spec_models.py and JSON schema have already been updated with SpecStatus, IntrospectionData, BaselineData, and ExpressionInfo models. Now need to create: 1) backend/api/services/spec_manager.py for centralized spec CRUD, 2) backend/api/routes/intake.py with endpoints for creating inbox folders, running introspection, listing inbox contents, and listing topics, 3) Register the intake router in main.py. Reference the plan at docs/plans/DASHBOARD_INTAKE_ATOMIZERSPEC_INTEGRATION.md",
+      "file": "TBD",
+      "priority": "high"
+    }
+  ],
+  "test_scenarios": [],
+  "acceptance_criteria": [
+    "Implement Dashboard Intake & AtomizerSpec Integration: Phase 1 - Create backend intake API routes (create, introspect, list, topics endpoints) and spec_manager service. The spec_models.py and JSON schema have already been updated with SpecStatus, IntrospectionData, BaselineData, and ExpressionInfo models. Now need to create: 1) backend/api/services/spec_manager.py for centralized spec CRUD, 2) backend/api/routes/intake.py with endpoints for creating inbox folders, running introspection, listing inbox contents, and listing topics, 3) Register the intake router in main.py. Reference the plan at docs/plans/DASHBOARD_INTAKE_ATOMIZERSPEC_INTEGRATION.md"
+  ]
+}

.devloop/test_results.json

@@ -0,0 +1,64 @@
+{
+  "timestamp": "2026-01-22T21:10:54.742272",
+  "scenarios": [
+    {
+      "scenario_id": "test_study_dir",
+      "scenario_name": "Study directory exists: stage_3_arm",
+      "passed": true,
+      "duration_ms": 0.0,
+      "error": null,
+      "details": {
+        "path": "C:\\Users\\antoi\\Atomizer\\studies\\Stage3\\stage_3_arm",
+        "exists": true
+      }
+    },
+    {
+      "scenario_id": "test_spec",
+      "scenario_name": "AtomizerSpec is valid JSON",
+      "passed": true,
+      "duration_ms": 1.045,
+      "error": null,
+      "details": {
+        "valid_json": true
+      }
+    },
+    {
+      "scenario_id": "test_readme",
+      "scenario_name": "README exists",
+      "passed": true,
+      "duration_ms": 0.0,
+      "error": null,
+      "details": {
+        "path": "C:\\Users\\antoi\\Atomizer\\studies\\Stage3\\stage_3_arm\\README.md",
+        "exists": true
+      }
+    },
+    {
+      "scenario_id": "test_run_script",
+      "scenario_name": "run_optimization.py exists",
+      "passed": true,
+      "duration_ms": 0.0,
+      "error": null,
+      "details": {
+        "path": "C:\\Users\\antoi\\Atomizer\\studies\\Stage3\\stage_3_arm\\run_optimization.py",
+        "exists": true
+      }
+    },
+    {
+      "scenario_id": "test_model_dir",
+      "scenario_name": "Model directory exists",
+      "passed": true,
+      "duration_ms": 0.0,
+      "error": null,
+      "details": {
+        "path": "C:\\Users\\antoi\\Atomizer\\studies\\Stage3\\stage_3_arm\\1_setup\\model",
+        "exists": true
+      }
+    }
+  ],
+  "summary": {
+    "passed": 5,
+    "failed": 0,
+    "total": 5
+  }
+}

.gitignore

@@ -15,6 +15,11 @@ lib64/
 parts/
 sdist/
 var/
+
+# NOTE: This repo includes a React frontend that legitimately uses src/lib/.
+# The broad Python ignore `lib/` would ignore that. Re-include it:
+!atomizer-dashboard/frontend/src/lib/
+!atomizer-dashboard/frontend/src/lib/**
 wheels/
 *.egg-info/
 .installed.cfg
@@ -122,5 +127,14 @@ backend_stderr.log
 # Auto-generated documentation (regenerate with: python -m optimization_engine.auto_doc all)
 docs/generated/
 
+# NX model introspection caches (generated)
+**/_introspection_*.json
+**/_introspection_cache.json
+**/_temp_introspection.json
+**/params.exp
+
+# Insight outputs (generated)
+**/3_insights/
+
 # Malformed filenames (Windows path used as filename)
 C:*

.mcp.json

@@ -7,6 +7,10 @@
         "ATOMIZER_MODE": "user",
         "ATOMIZER_ROOT": "C:/Users/antoi/Atomizer"
       }
+    },
+    "nxopen-docs": {
+      "command": "C:/Users/antoi/CADtomaste/Atomaste-NXOpen-MCP/.venv/Scripts/python.exe",
+      "args": ["-m", "nxopen_mcp.server", "--data-dir", "C:/Users/antoi/CADtomaste/Atomaste-NXOpen-MCP/data"]
     }
   }
 }

DEVELOPMENT.md

@@ -1,619 +0,0 @@
-# Atomizer Development Guide
-
-**Last Updated**: 2025-11-21
-**Current Phase**: Phase 3.2 - Integration Sprint + Documentation
-**Status**: 🟢 Core Complete (100%) | ✅ Protocols 10/11/13 Active (100%) | 🎯 Dashboard Live (95%) | 📚 Documentation Reorganized
-
-📘 **Quick Links**:
-- [Protocol Specifications](docs/PROTOCOLS.md) - All active protocols consolidated
-- [Documentation Index](docs/00_INDEX.md) - Complete documentation navigation
-- [README](README.md) - Project overview and quick start
-
----
-
-## Table of Contents
-
-1. [Current Phase](#current-phase)
-2. [Completed Features](#completed-features)
-3. [Active Development](#active-development)
-4. [Known Issues](#known-issues)
-5. [Testing Status](#testing-status)
-6. [Phase-by-Phase Progress](#phase-by-phase-progress)
-
----
-
-## Current Phase
-
-### Phase 3.2: Integration Sprint (🎯 TOP PRIORITY)
-
-**Goal**: Connect LLM intelligence components to production workflow
-
-**Timeline**: 2-4 weeks (Started 2025-11-17)
-
-**Status**: LLM components built and tested individually (85% complete). Need to wire them into production runner.
-
-📋 **Detailed Plan**: [docs/PHASE_3_2_INTEGRATION_PLAN.md](docs/PHASE_3_2_INTEGRATION_PLAN.md)
-
-**Critical Path**:
-
-#### Week 1: Make LLM Mode Accessible (16 hours)
-- [ ] **1.1** Create unified entry point `optimization_engine/run_optimization.py` (4h)
-  - Add `--llm` flag for natural language mode
-  - Add `--request` parameter for natural language input
-  - Support both LLM and traditional JSON modes
-  - Preserve backward compatibility
-
-- [ ] **1.2** Wire LLMOptimizationRunner to production (8h)
-  - Connect LLMWorkflowAnalyzer to entry point
-  - Bridge LLMOptimizationRunner → OptimizationRunner
-  - Pass model updater and simulation runner callables
-  - Integrate with existing hook system
-
-- [ ] **1.3** Create minimal example (2h)
-  - Create `examples/llm_mode_demo.py`
-  - Show natural language → optimization results
-  - Compare traditional (100 lines) vs LLM (3 lines)
-
-- [ ] **1.4** End-to-end integration test (2h)
-  - Test with simple_beam_optimization study
-  - Verify extractors generated correctly
-  - Validate output matches manual mode
-
-#### Week 2: Robustness & Safety (16 hours)
-- [ ] **2.1** Code validation pipeline (6h)
-  - Create `optimization_engine/code_validator.py`
-  - Implement syntax validation (ast.parse)
-  - Implement security scanning (whitelist imports)
-  - Implement test execution on example OP2
-  - Add retry with LLM feedback on failure
-
-- [ ] **2.2** Graceful fallback mechanisms (4h)
-  - Wrap all LLM calls in try/except
-  - Provide clear error messages
-  - Offer fallback to manual mode
-  - Never crash on LLM failure
-
-- [ ] **2.3** LLM audit trail (3h)
-  - Create `optimization_engine/llm_audit.py`
-  - Log all LLM requests and responses
-  - Log generated code with prompts
-  - Create `llm_audit.json` in study output
-
-- [ ] **2.4** Failure scenario testing (3h)
-  - Test invalid natural language request
-  - Test LLM unavailable
-  - Test generated code syntax errors
-  - Test validation failures
-
-#### Week 3: Learning System (12 hours)
-- [ ] **3.1** Knowledge base implementation (4h)
-  - Create `optimization_engine/knowledge_base.py`
-  - Implement `save_session()` - Save successful workflows
-  - Implement `search_templates()` - Find similar patterns
-  - Add confidence scoring
-
-- [ ] **3.2** Template extraction (4h)
-  - Extract reusable patterns from generated code
-  - Parameterize variable parts
-  - Save templates with usage examples
-  - Implement template application to new requests
-
-- [ ] **3.3** ResearchAgent integration (4h)
-  - Complete ResearchAgent implementation
-  - Integrate into ExtractorOrchestrator error handling
-  - Add user example collection workflow
-  - Save learned knowledge to knowledge base
-
-#### Week 4: Documentation & Discoverability (8 hours)
-- [ ] **4.1** Update README (2h)
-  - Add "🤖 LLM-Powered Mode" section
-  - Show example command with natural language
-  - Link to detailed docs
-
-- [ ] **4.2** Create LLM mode documentation (3h)
-  - Create `docs/LLM_MODE.md`
-  - Explain how LLM mode works
-  - Provide usage examples
-  - Add troubleshooting guide
-
-- [ ] **4.3** Create demo video/GIF (1h)
-  - Record terminal session
-  - Show before/after (100 lines → 3 lines)
-  - Create animated GIF for README
-
-- [ ] **4.4** Update all planning docs (2h)
-  - Update DEVELOPMENT.md status
-  - Update DEVELOPMENT_GUIDANCE.md (80-90% → 90-95%)
-  - Mark Phase 3.2 as ✅ Complete
-
----
-
-## Completed Features
-
-### ✅ Live Dashboard System (Completed 2025-11-21)
-
-#### Backend (FastAPI + WebSocket)
-- [x] **FastAPI Backend** ([atomizer-dashboard/backend/](atomizer-dashboard/backend/))
-  - REST API endpoints for study management
-  - WebSocket streaming with file watching (Watchdog)
-  - Real-time updates (<100ms latency)
-  - CORS configured for local development
-
-- [x] **REST API Endpoints** ([backend/api/routes/optimization.py](atomizer-dashboard/backend/api/routes/optimization.py))
-  - `GET /api/optimization/studies` - List all studies
-  - `GET /api/optimization/studies/{id}/status` - Get study status
-  - `GET /api/optimization/studies/{id}/history` - Get trial history
-  - `GET /api/optimization/studies/{id}/pruning` - Get pruning diagnostics
-
-- [x] **WebSocket Streaming** ([backend/api/websocket/optimization_stream.py](atomizer-dashboard/backend/api/websocket/optimization_stream.py))
-  - File watching on `optimization_history_incremental.json`
-  - Real-time trial updates via WebSocket
-  - Pruning alerts and progress updates
-  - Automatic observer lifecycle management
-
-#### Frontend (HTML + Chart.js)
-- [x] **Enhanced Live Dashboard** ([atomizer-dashboard/dashboard-enhanced.html](atomizer-dashboard/dashboard-enhanced.html))
-  - Real-time WebSocket updates
-  - Interactive convergence chart (Chart.js)
-  - Parameter space scatter plot
-  - Pruning alerts (toast notifications)
-  - Data export (JSON/CSV)
-  - Study auto-discovery and selection
-  - Metric dashboard (trials, best value, pruned count)
-
-#### React Frontend (In Progress)
-- [x] **Project Configuration** ([atomizer-dashboard/frontend/](atomizer-dashboard/frontend/))
-  - React 18 + Vite 5 + TypeScript 5.2
-  - TailwindCSS 3.3 for styling
-  - Recharts 2.10 for charts
-  - Complete build configuration
-
-- [x] **TypeScript Types** ([frontend/src/types/](atomizer-dashboard/frontend/src/types/))
-  - Complete type definitions for API data
-  - WebSocket message types
-  - Chart data structures
-
-- [x] **Custom Hooks** ([frontend/src/hooks/useWebSocket.ts](atomizer-dashboard/frontend/src/hooks/useWebSocket.ts))
-  - WebSocket connection management
-  - Auto-reconnection with exponential backoff
-  - Type-safe message routing
-
-- [x] **Reusable Components** ([frontend/src/components/](atomizer-dashboard/frontend/src/components/))
-  - Card, MetricCard, Badge, StudyCard components
-  - TailwindCSS styling with dark theme
-
-- [ ] **Dashboard Page** (Pending manual completion)
-  - Need to run `npm install`
-  - Create main.tsx, App.tsx, Dashboard.tsx
-  - Integrate Recharts for charts
-  - Test end-to-end
-
-#### Documentation
-- [x] **Dashboard Master Plan** ([docs/DASHBOARD_MASTER_PLAN.md](docs/DASHBOARD_MASTER_PLAN.md))
-  - Complete 3-page architecture (Configurator, Live Dashboard, Results Viewer)
-  - Tech stack recommendations
-  - Implementation phases
-
-- [x] **Implementation Status** ([docs/DASHBOARD_IMPLEMENTATION_STATUS.md](docs/DASHBOARD_IMPLEMENTATION_STATUS.md))
-  - Current progress tracking
-  - Testing instructions
-  - Next steps
-
-- [x] **React Implementation Guide** ([docs/DASHBOARD_REACT_IMPLEMENTATION.md](docs/DASHBOARD_REACT_IMPLEMENTATION.md))
-  - Complete templates for remaining components
-  - Recharts integration examples
-  - Troubleshooting guide
-
-- [x] **Session Summary** ([docs/DASHBOARD_SESSION_SUMMARY.md](docs/DASHBOARD_SESSION_SUMMARY.md))
-  - Features demonstrated
-  - How to use the dashboard
-  - Architecture explanation
-
-### ✅ Phase 1: Plugin System & Infrastructure (Completed 2025-01-16)
-
-#### Core Architecture
-- [x] **Hook Manager** ([optimization_engine/plugins/hook_manager.py](optimization_engine/plugins/hook_manager.py))
-  - Hook registration with priority-based execution
-  - Auto-discovery from plugin directories
-  - Context passing to all hooks
-  - Execution history tracking
-
-- [x] **Lifecycle Hooks**
-  - `pre_solve`: Execute before solver launch
-  - `post_solve`: Execute after solve, before extraction
-  - `post_extraction`: Execute after result extraction
-
-#### Logging Infrastructure
-- [x] **Detailed Trial Logs** ([detailed_logger.py](optimization_engine/plugins/pre_solve/detailed_logger.py))
-  - Per-trial log files in `optimization_results/trial_logs/`
-  - Complete iteration trace with timestamps
-  - Design variables, configuration, timeline
-  - Extracted results and constraint evaluations
-
-- [x] **High-Level Optimization Log** ([optimization_logger.py](optimization_engine/plugins/pre_solve/optimization_logger.py))
-  - `optimization.log` file tracking overall progress
-  - Configuration summary header
-  - Compact START/COMPLETE entries per trial
-  - Easy to scan format for monitoring
-
-- [x] **Result Appenders**
-  - [log_solve_complete.py](optimization_engine/plugins/post_solve/log_solve_complete.py) - Appends solve completion to trial logs
-  - [log_results.py](optimization_engine/plugins/post_extraction/log_results.py) - Appends extracted results to trial logs
-  - [optimization_logger_results.py](optimization_engine/plugins/post_extraction/optimization_logger_results.py) - Appends results to optimization.log
-
-#### Project Organization
-- [x] **Studies Structure** ([studies/](studies/))
-  - Standardized folder layout with `model/`, `optimization_results/`, `analysis/`
-  - Comprehensive documentation in [studies/README.md](studies/README.md)
-  - Example study: [bracket_stress_minimization/](studies/bracket_stress_minimization/)
-  - Template structure for future studies
-
-- [x] **Path Resolution** ([atomizer_paths.py](atomizer_paths.py))
-  - Intelligent project root detection using marker files
-  - Helper functions: `root()`, `optimization_engine()`, `studies()`, `tests()`
-  - `ensure_imports()` for robust module imports
-  - Works regardless of script location
-
-#### Testing
-- [x] **Hook Validation Test** ([test_hooks_with_bracket.py](tests/test_hooks_with_bracket.py))
-  - Verifies hook loading and execution
-  - Tests 3 trials with dummy data
-  - Checks hook execution history
-
-- [x] **Integration Tests**
-  - [run_5trial_test.py](tests/run_5trial_test.py) - Quick 5-trial optimization
-  - [test_journal_optimization.py](tests/test_journal_optimization.py) - Full optimization test
-
-#### Runner Enhancements
-- [x] **Context Passing** ([runner.py:332,365,412](optimization_engine/runner.py))
-  - `output_dir` passed to all hook contexts
-  - Trial number, design variables, extracted results
-  - Configuration dictionary available to hooks
-
-### ✅ Core Engine (Pre-Phase 1)
-- [x] Optuna integration with TPE sampler
-- [x] Multi-objective optimization support
-- [x] NX journal execution ([nx_solver.py](optimization_engine/nx_solver.py))
-- [x] Expression updates ([nx_updater.py](optimization_engine/nx_updater.py))
-- [x] OP2 result extraction (stress, displacement)
-- [x] Study management with resume capability
-- [x] Web dashboard (real-time monitoring)
-- [x] Precision control (4-decimal rounding)
-
----
-
-## Active Development
-
-### In Progress - Dashboard (High Priority)
-- [x] Backend API complete (FastAPI + WebSocket)
-- [x] HTML dashboard with Chart.js complete
-- [x] React project structure and configuration complete
-- [ ] **Complete React frontend** (Awaiting manual npm install)
-  - [ ] Run `npm install` in frontend directory
-  - [ ] Create main.tsx and App.tsx
-  - [ ] Create Dashboard.tsx with Recharts
-  - [ ] Test end-to-end with live optimization
-
-### Up Next - Dashboard (Next Session)
-- [ ] Study Configurator page (React)
-- [ ] Results Report Viewer page (React)
-- [ ] LLM chat interface integration (future)
-- [ ] Docker deployment configuration
-
-### In Progress - Phase 3.2 Integration
-- [ ] Feature registry creation (Phase 2, Week 1)
-- [ ] Claude skill definition (Phase 2, Week 1)
-
-### Up Next (Phase 2, Week 2)
-- [ ] Natural language parser
-- [ ] Intent classification system
-- [ ] Entity extraction for optimization parameters
-- [ ] Conversational workflow manager
-
-### Backlog (Phase 3+)
-- [ ] Custom function generator (RSS, weighted objectives)
-- [ ] Journal script generator
-- [ ] Code validation pipeline
-- [ ] Result analyzer with statistical analysis
-- [ ] Surrogate quality checker
-- [ ] HTML/PDF report generator
-
----
-
-## Known Issues
-
-### Critical
-- None currently
-
-### Minor
-- [ ] `.claude/settings.local.json` modified during development (contains user-specific settings)
-- [ ] Some old bash background processes still running from previous tests
-
-### Documentation
-- [ ] Need to add examples of custom hooks to studies/README.md
-- [ ] Missing API documentation for hook_manager methods
-- [ ] No developer guide for creating new plugins
-
----
-
-## Testing Status
-
-### Automated Tests
-- ✅ **Hook system** - `test_hooks_with_bracket.py` passing
-- ✅ **5-trial integration** - `run_5trial_test.py` working
-- ✅ **Full optimization** - `test_journal_optimization.py` functional
-- ⏳ **Unit tests** - Need to create for individual modules
-- ⏳ **CI/CD pipeline** - Not yet set up
-
-### Manual Testing
-- ✅ Bracket optimization (50 trials)
-- ✅ Log file generation in correct locations
-- ✅ Hook execution at all lifecycle points
-- ✅ Path resolution across different script locations
-- ✅ **Dashboard backend** - REST API and WebSocket tested successfully
-- ✅ **HTML dashboard** - Live updates working with Chart.js
-- ⏳ **React dashboard** - Pending npm install and completion
-- ⏳ Resume functionality with config validation
-
-### Test Coverage
-- Hook manager: ~80% (core functionality tested)
-- Logging plugins: 100% (tested via integration tests)
-- Path resolution: 100% (tested in all scripts)
-- Result extractors: ~70% (basic tests exist)
-- **Dashboard backend**: ~90% (REST endpoints and WebSocket tested)
-- **Dashboard frontend**: ~60% (HTML version tested, React pending)
-- Overall: ~65% estimated
-
----
-
-## Phase-by-Phase Progress
-
-### Phase 1: Plugin System ✅ (100% Complete)
-
-**Completed** (2025-01-16):
-- [x] Hook system for optimization lifecycle
-- [x] Plugin auto-discovery and registration
-- [x] Hook manager with priority-based execution
-- [x] Detailed per-trial logs (`trial_logs/`)
-- [x] High-level optimization log (`optimization.log`)
-- [x] Context passing system for hooks
-- [x] Studies folder structure
-- [x] Comprehensive studies documentation
-- [x] Model file organization (`model/` folder)
-- [x] Intelligent path resolution
-- [x] Test suite for hook system
-
-**Deferred to Future Phases**:
-- Feature registry → Phase 2 (with LLM interface)
-- `pre_mesh` and `post_mesh` hooks → Future (not needed for current workflow)
-- Custom objective/constraint registration → Phase 3 (Code Generation)
-
----
-
-### Phase 2: LLM Integration 🟡 (0% Complete)
-
-**Target**: 2 weeks (Started 2025-01-16)
-
-#### Week 1 Todos (Feature Registry & Claude Skill)
-- [ ] Create `optimization_engine/feature_registry.json`
-- [ ] Extract all current capabilities
-- [ ] Draft `.claude/skills/atomizer.md`
-- [ ] Test LLM's ability to navigate codebase
-
-#### Week 2 Todos (Natural Language Interface)
-- [ ] Implement intent classifier
-- [ ] Build entity extractor
-- [ ] Create workflow manager
-- [ ] Test end-to-end: "Create a stress minimization study"
-
-**Success Criteria**:
-- [ ] LLM can create optimization from natural language in <5 turns
-- [ ] 90% of user requests understood correctly
-- [ ] Zero manual JSON editing required
-
----
-
-### Phase 3: Code Generation ⏳ (Not Started)
-
-**Target**: 3 weeks
-
-**Key Deliverables**:
-- [ ] Custom function generator
-  - [ ] RSS (Root Sum Square) template
-  - [ ] Weighted objectives template
-  - [ ] Custom constraints template
-- [ ] Journal script generator
-- [ ] Code validation pipeline
-- [ ] Safe execution environment
-
-**Success Criteria**:
-- [ ] LLM generates 10+ custom functions with zero errors
-- [ ] All generated code passes safety validation
-- [ ] Users save 50% time vs. manual coding
-
----
-
-### Phase 4: Analysis & Decision Support ⏳ (Not Started)
-
-**Target**: 3 weeks
-
-**Key Deliverables**:
-- [ ] Result analyzer (convergence, sensitivity, outliers)
-- [ ] Surrogate model quality checker (R², CV score, confidence intervals)
-- [ ] Decision assistant (trade-offs, what-if analysis, recommendations)
-
-**Success Criteria**:
-- [ ] Surrogate quality detection 95% accurate
-- [ ] Recommendations lead to 30% faster convergence
-- [ ] Users report higher confidence in results
-
----
-
-### Phase 5: Automated Reporting ⏳ (Not Started)
-
-**Target**: 2 weeks
-
-**Key Deliverables**:
-- [ ] Report generator with Jinja2 templates
-- [ ] Multi-format export (HTML, PDF, Markdown, JSON)
-- [ ] LLM-written narrative explanations
-
-**Success Criteria**:
-- [ ] Reports generated in <30 seconds
-- [ ] Narrative quality rated 4/5 by engineers
-- [ ] 80% of reports used without manual editing
-
----
-
-### Phase 6: NX MCP Enhancement ⏳ (Not Started)
-
-**Target**: 4 weeks
-
-**Key Deliverables**:
-- [ ] NX documentation MCP server
-- [ ] Advanced NX operations library
-- [ ] Feature bank with 50+ pre-built operations
-
-**Success Criteria**:
-- [ ] NX MCP answers 95% of API questions correctly
-- [ ] Feature bank covers 80% of common workflows
-- [ ] Users write 50% less manual journal code
-
----
-
-### Phase 7: Self-Improving System ⏳ (Not Started)
-
-**Target**: 4 weeks
-
-**Key Deliverables**:
-- [ ] Feature learning system
-- [ ] Best practices database
-- [ ] Continuous documentation generation
-
-**Success Criteria**:
-- [ ] 20+ user-contributed features in library
-- [ ] Pattern recognition identifies 10+ best practices
-- [ ] Documentation auto-updates with zero manual effort
-
----
-
-## Development Commands
-
-### Running Dashboard
-```bash
-# Start backend server
-cd atomizer-dashboard/backend
-python -m uvicorn api.main:app --reload --host 0.0.0.0 --port 8000
-
-# Access HTML dashboard (current)
-# Open browser: http://localhost:8000
-
-# Start React frontend (when ready)
-cd atomizer-dashboard/frontend
-npm install  # First time only
-npm run dev  # Starts on http://localhost:3000
-```
-
-### Running Tests
-```bash
-# Hook validation (3 trials, fast)
-python tests/test_hooks_with_bracket.py
-
-# Quick integration test (5 trials)
-python tests/run_5trial_test.py
-
-# Full optimization test
-python tests/test_journal_optimization.py
-```
-
-### Code Quality
-```bash
-# Run linter (when available)
-# pylint optimization_engine/
-
-# Run type checker (when available)
-# mypy optimization_engine/
-
-# Run all tests (when test suite is complete)
-# pytest tests/
-```
-
-### Git Workflow
-```bash
-# Stage all changes
-git add .
-
-# Commit with conventional commits format
-git commit -m "feat: description"  # New feature
-git commit -m "fix: description"   # Bug fix
-git commit -m "docs: description"  # Documentation
-git commit -m "test: description"  # Tests
-git commit -m "refactor: description"  # Code refactoring
-
-# Push to GitHub
-git push origin main
-```
-
----
-
-## Documentation
-
-### For Developers
-- [DEVELOPMENT_ROADMAP.md](DEVELOPMENT_ROADMAP.md) - Strategic vision and phases
-- [studies/README.md](studies/README.md) - Studies folder organization
-- [CHANGELOG.md](CHANGELOG.md) - Version history
-
-### Dashboard Documentation
-- [docs/DASHBOARD_MASTER_PLAN.md](docs/DASHBOARD_MASTER_PLAN.md) - Complete architecture blueprint
-- [docs/DASHBOARD_IMPLEMENTATION_STATUS.md](docs/DASHBOARD_IMPLEMENTATION_STATUS.md) - Current progress
-- [docs/DASHBOARD_REACT_IMPLEMENTATION.md](docs/DASHBOARD_REACT_IMPLEMENTATION.md) - React implementation guide
-- [docs/DASHBOARD_SESSION_SUMMARY.md](docs/DASHBOARD_SESSION_SUMMARY.md) - Session summary
-- [atomizer-dashboard/README.md](atomizer-dashboard/README.md) - Dashboard quick start
-- [atomizer-dashboard/backend/README.md](atomizer-dashboard/backend/README.md) - Backend API docs
-- [atomizer-dashboard/frontend/README.md](atomizer-dashboard/frontend/README.md) - Frontend setup guide
-
-### For Users
-- [README.md](README.md) - Project overview and quick start
-- [docs/INDEX.md](docs/INDEX.md) - Complete documentation index
-- [docs/](docs/) - Additional documentation
-
----
-
-## Notes
-
-### Architecture Decisions
-- **Hook system**: Chose priority-based execution to allow precise control of plugin order
-- **Path resolution**: Used marker files instead of environment variables for simplicity
-- **Logging**: Two-tier system (detailed trial logs + high-level optimization.log) for different use cases
-
-### Performance Considerations
-- Hook execution adds <1s overhead per trial (acceptable for FEA simulations)
-- Path resolution caching could improve startup time (future optimization)
-- Log file sizes grow linearly with trials (~10KB per trial)
-
-### Future Considerations
-- Consider moving to structured logging (JSON) for easier parsing
-- May need database for storing hook execution history (currently in-memory)
-- Dashboard integration will require WebSocket for real-time log streaming
-
----
-
-**Last Updated**: 2025-11-21
-**Maintained by**: Antoine Polvé (antoine@atomaste.com)
-**Repository**: [GitHub - Atomizer](https://github.com/yourusername/Atomizer)
-
----
-
-## Recent Updates (November 21, 2025)
-
-### Dashboard System Implementation ✅
-- **Backend**: FastAPI + WebSocket with real-time file watching complete
-- **HTML Dashboard**: Functional dashboard with Chart.js, data export, pruning alerts
-- **React Setup**: Complete project configuration, types, hooks, components
-- **Documentation**: 5 comprehensive markdown documents covering architecture, implementation, and usage
-
-### Next Immediate Steps
-1. Run `npm install` in `atomizer-dashboard/frontend`
-2. Create `main.tsx`, `App.tsx`, and `Dashboard.tsx` using provided templates
-3. Test React dashboard with live optimization
-4. Build Study Configurator page (next major feature)

INSTALL_INSTRUCTIONS.md

@@ -1,63 +0,0 @@
-# Atomizer Installation Guide
-
-## Step 1: Install Miniconda (Recommended)
-
-1. Download Miniconda from: https://docs.conda.io/en/latest/miniconda.html
-   - Choose: **Miniconda3 Windows 64-bit**
-
-2. Run the installer:
-   - Check "Add Miniconda3 to my PATH environment variable"
-   - Check "Register Miniconda3 as my default Python"
-
-3. Restart your terminal/VSCode after installation
-
-## Step 2: Create Atomizer Environment
-
-Open **Anaconda Prompt** (or any terminal after restart) and run:
-
-```bash
-cd C:\Users\Antoine\Atomizer
-conda env create -f environment.yml
-conda activate atomizer
-```
-
-## Step 3: Install PyTorch with GPU Support (Optional but Recommended)
-
-If you have an NVIDIA GPU:
-
-```bash
-conda activate atomizer
-pip install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu121
-pip install torch-geometric
-```
-
-## Step 4: Verify Installation
-
-```bash
-conda activate atomizer
-python -c "import torch; import optuna; import pyNastran; print('All imports OK!')"
-python -c "import torch; print(f'CUDA available: {torch.cuda.is_available()}')"
-```
-
-## Step 5: Train Neural Network
-
-```bash
-conda activate atomizer
-cd C:\Users\Antoine\Atomizer\atomizer-field
-python train_parametric.py --train_dir ../atomizer_field_training_data/bracket_stiffness_optimization_atomizerfield --epochs 100 --output_dir runs/bracket_model
-```
-
-## Quick Commands Reference
-
-```bash
-# Activate environment (do this every time you open a new terminal)
-conda activate atomizer
-
-# Train neural network
-cd C:\Users\Antoine\Atomizer\atomizer-field
-python train_parametric.py --train_dir ../atomizer_field_training_data/bracket_stiffness_optimization_atomizerfield --epochs 100
-
-# Run optimization with neural acceleration
-cd C:\Users\Antoine\Atomizer\studies\bracket_stiffness_optimization_atomizerfield
-python run_optimization.py --run --trials 100 --enable-nn
-```

PROJECT_STATUS.md

@@ -0,0 +1,111 @@
+# PROJECT_STATUS.md
+
+> **Bridge document for Mario (Clawdbot) ↔ Claude Code coordination**
+> 
+> Both AIs should read this at session start. Update when priorities change.
+
+*Last updated: 2026-01-27 by Mario*
+
+---
+
+## Current Focus
+
+**Phase**: Foundation (Phase 1)
+**Sprint**: 2026-01-27 to 2026-02-03
+
+### This Week's Priorities
+
+**Now (Sprint 1.5): Draft + Publish (S2)**
+1. 🔴 Implement DraftManager (local autosave draft per study)
+2. 🔴 Add Draft vs Published banner + Publish button
+3. 🔴 Restore/discard draft prompt on load
+
+**Next (Sprint 2): Create Wizard v1 shell**
+4. 🟡 /create route + stepper
+5. 🟡 Files step (dependency tree + _i.prt warnings)
+6. 🟡 Introspection step (expressions + DV selection)
+
+### Completed recently
+- Spec/Canvas wiring sync foundation (converters, connect/delete wiring, output picker, panel rewiring, edge projection)
+
+### Blocked
+- None (but local npm install on this server fails due to peer deps; run builds/tests on Windows dev env)
+
+---
+
+## Active Decisions
+
+| Decision | Summary | Date |
+|----------|---------|------|
+| Full Partnership | Mario = PM, reviewer, architect. Antoine = developer, NX. | 2026-01-27 |
+| Dashboard on Windows | Keep simple for now, hybrid architecture later | 2026-01-27 |
+| Adopt Clawdbot Patterns | MEMORY.md, QUICK_REF.md, simplified CLAUDE.md | 2026-01-27 |
+
+---
+
+## For Claude Code
+
+When starting a session:
+
+1. ✅ Read CLAUDE.md (system instructions)
+2. ✅ Read PROJECT_STATUS.md (this file — current priorities)
+3. ✅ Read `knowledge_base/lac/session_insights/failure.jsonl` (critical lessons)
+4. 🔲 After session: Commit any new LAC insights to Git
+
+### LAC Commit Protocol (NEW)
+
+After each significant session, commit LAC changes:
+
+```bash
+cd Atomizer
+git add knowledge_base/lac/
+git commit -m "lac: Session insights from YYYY-MM-DD"
+git push origin main && git push github main
+```
+
+This ensures Mario can see what Claude Code learned.
+
+---
+
+## For Mario (Clawdbot)
+
+When checking on Atomizer:
+
+1. Pull latest from Gitea: `cd /home/papa/repos/Atomizer && git pull`
+2. Check `knowledge_base/lac/session_insights/` for new learnings
+3. Update tracking files in `/home/papa/clawd/memory/atomizer/`
+4. Update this file if priorities change
+
+### Heartbeat Check (Add to HEARTBEAT.md)
+
+```markdown
+### Atomizer Check (weekly)
+- git pull Atomizer repo
+- Check for new LAC insights
+- Review recent commits
+- Update roadmap if needed
+```
+
+---
+
+## Recent Activity
+
+| Date | Activity | Who |
+|------|----------|-----|
+| 2026-01-27 | Created master plan in PKM | Mario |
+| 2026-01-27 | Created tracking files | Mario |
+| 2026-01-27 | ACKed Atomizer project | Mario |
+| 2026-01-27 | Canvas V3.1 improvements | Claude Code (prior) |
+
+---
+
+## Links
+
+- **Master Plan**: `/home/papa/obsidian-vault/2-Projects/Atomizer-AtomasteAI/Development/ATOMIZER-NEXT-LEVEL-MASTERPLAN.md`
+- **Mario's Tracking**: `/home/papa/clawd/memory/atomizer/`
+- **LAC Insights**: `knowledge_base/lac/session_insights/`
+- **Full Roadmap**: See Master Plan in PKM
+
+---
+
+*This file lives in the repo. Both AIs can read it. Only update when priorities change.*

atomizer-dashboard/backend/api/main.py

@@ -13,7 +13,19 @@ import sys
 # Add parent directory to path to import optimization_engine
 sys.path.append(str(Path(__file__).parent.parent.parent.parent))
 
-from api.routes import optimization, claude, terminal, insights, context, files, nx, claude_code, spec
+from api.routes import (
+    optimization,
+    claude,
+    terminal,
+    insights,
+    context,
+    files,
+    nx,
+    claude_code,
+    spec,
+    devloop,
+    intake,
+)
 from api.websocket import optimization_stream
 
 
@@ -23,6 +35,7 @@ async def lifespan(app: FastAPI):
     """Manage application lifespan - start/stop session manager"""
     # Startup
     from api.routes.claude import get_session_manager
+
     manager = get_session_manager()
     await manager.start()
     print("Session manager started")
@@ -63,6 +76,9 @@ app.include_router(nx.router, prefix="/api/nx", tags=["nx"])
 app.include_router(claude_code.router, prefix="/api", tags=["claude-code"])
 app.include_router(spec.router, prefix="/api", tags=["spec"])
 app.include_router(spec.validate_router, prefix="/api", tags=["spec"])
+app.include_router(devloop.router, prefix="/api", tags=["devloop"])
+app.include_router(intake.router, prefix="/api", tags=["intake"])
+
 
 @app.get("/")
 async def root():
@@ -70,11 +86,13 @@ async def root():
     dashboard_path = Path(__file__).parent.parent.parent / "dashboard-enhanced.html"
     return FileResponse(dashboard_path)
 
+
 @app.get("/health")
 async def health_check():
     """Health check endpoint with database status"""
     try:
         from api.services.conversation_store import ConversationStore
+
         store = ConversationStore()
         # Test database by creating/getting a health check session
         store.get_session("health_check")
@@ -87,12 +105,8 @@ async def health_check():
         "database": db_status,
     }
 
+
 if __name__ == "__main__":
     import uvicorn
-    uvicorn.run(
-        "main:app",
-        host="0.0.0.0",
-        port=8000,
-        reload=True,
-        log_level="info"
-    )
+
+    uvicorn.run("main:app", host="0.0.0.0", port=8000, reload=True, log_level="info")

atomizer-dashboard/backend/api/routes/devloop.py

@@ -0,0 +1,416 @@
+"""
+DevLoop API Endpoints - Closed-loop development orchestration.
+
+Provides REST API and WebSocket for:
+- Starting/stopping development cycles
+- Monitoring progress
+- Executing single phases
+- Viewing history and learnings
+"""
+
+from fastapi import APIRouter, HTTPException, WebSocket, WebSocketDisconnect, BackgroundTasks
+from pydantic import BaseModel, Field
+from typing import Any, Dict, List, Optional
+import asyncio
+import json
+import sys
+from pathlib import Path
+from datetime import datetime
+
+# Add project root to path
+sys.path.append(str(Path(__file__).parent.parent.parent.parent.parent))
+
+router = APIRouter(prefix="/devloop", tags=["devloop"])
+
+# Global orchestrator instance
+_orchestrator = None
+_active_cycle = None
+_websocket_clients: List[WebSocket] = []
+
+
+def get_orchestrator():
+    """Get or create the DevLoop orchestrator."""
+    global _orchestrator
+    if _orchestrator is None:
+        from optimization_engine.devloop import DevLoopOrchestrator
+
+        _orchestrator = DevLoopOrchestrator(
+            {
+                "dashboard_url": "http://localhost:8000",
+                "websocket_url": "ws://localhost:8000",
+                "studies_dir": str(Path(__file__).parent.parent.parent.parent.parent / "studies"),
+                "learning_enabled": True,
+            }
+        )
+
+        # Subscribe to state updates
+        _orchestrator.subscribe(_broadcast_state_update)
+
+    return _orchestrator
+
+
+def _broadcast_state_update(state):
+    """Broadcast state updates to all WebSocket clients."""
+    asyncio.create_task(
+        _send_to_all_clients(
+            {
+                "type": "state_update",
+                "state": {
+                    "phase": state.phase.value,
+                    "iteration": state.iteration,
+                    "current_task": state.current_task,
+                    "last_update": state.last_update,
+                },
+            }
+        )
+    )
+
+
+async def _send_to_all_clients(message: Dict):
+    """Send message to all connected WebSocket clients."""
+    disconnected = []
+    for client in _websocket_clients:
+        try:
+            await client.send_json(message)
+        except Exception:
+            disconnected.append(client)
+
+    # Clean up disconnected clients
+    for client in disconnected:
+        if client in _websocket_clients:
+            _websocket_clients.remove(client)
+
+
+# ============================================================================
+# Request/Response Models
+# ============================================================================
+
+
+class StartCycleRequest(BaseModel):
+    """Request to start a development cycle."""
+
+    objective: str = Field(..., description="What to achieve")
+    context: Optional[Dict[str, Any]] = Field(default=None, description="Additional context")
+    max_iterations: Optional[int] = Field(default=10, description="Maximum iterations")
+
+
+class StepRequest(BaseModel):
+    """Request to execute a single step."""
+
+    phase: str = Field(..., description="Phase to execute: plan, implement, test, analyze")
+    data: Optional[Dict[str, Any]] = Field(default=None, description="Phase-specific data")
+
+
+class CycleStatusResponse(BaseModel):
+    """Response with cycle status."""
+
+    active: bool
+    phase: str
+    iteration: int
+    current_task: Optional[str]
+    last_update: str
+
+
+# ============================================================================
+# REST Endpoints
+# ============================================================================
+
+
+@router.get("/status")
+async def get_status() -> CycleStatusResponse:
+    """Get current DevLoop status."""
+    orchestrator = get_orchestrator()
+    state = orchestrator.get_state()
+
+    return CycleStatusResponse(
+        active=state["phase"] != "idle",
+        phase=state["phase"],
+        iteration=state["iteration"],
+        current_task=state.get("current_task"),
+        last_update=state["last_update"],
+    )
+
+
+@router.post("/start")
+async def start_cycle(request: StartCycleRequest, background_tasks: BackgroundTasks):
+    """
+    Start a new development cycle.
+
+    The cycle runs in the background and broadcasts progress via WebSocket.
+    """
+    global _active_cycle
+
+    orchestrator = get_orchestrator()
+
+    # Check if already running
+    if orchestrator.state.phase.value != "idle":
+        raise HTTPException(status_code=409, detail="A development cycle is already running")
+
+    # Start cycle in background
+    async def run_cycle():
+        global _active_cycle
+        try:
+            result = await orchestrator.run_development_cycle(
+                objective=request.objective,
+                context=request.context,
+                max_iterations=request.max_iterations,
+            )
+            _active_cycle = result
+
+            # Broadcast completion
+            await _send_to_all_clients(
+                {
+                    "type": "cycle_complete",
+                    "result": {
+                        "objective": result.objective,
+                        "status": result.status,
+                        "iterations": len(result.iterations),
+                        "duration_seconds": result.total_duration_seconds,
+                    },
+                }
+            )
+        except Exception as e:
+            await _send_to_all_clients({"type": "cycle_error", "error": str(e)})
+
+    background_tasks.add_task(run_cycle)
+
+    return {
+        "message": "Development cycle started",
+        "objective": request.objective,
+    }
+
+
+@router.post("/stop")
+async def stop_cycle():
+    """Stop the current development cycle."""
+    orchestrator = get_orchestrator()
+
+    if orchestrator.state.phase.value == "idle":
+        raise HTTPException(status_code=400, detail="No active cycle to stop")
+
+    # Set state to idle (will stop at next phase boundary)
+    orchestrator._update_state(phase=orchestrator.state.phase.__class__.IDLE, task="Stopping...")
+
+    return {"message": "Cycle stop requested"}
+
+
+@router.post("/step")
+async def execute_step(request: StepRequest):
+    """
+    Execute a single phase step.
+
+    Useful for manual control or debugging.
+    """
+    orchestrator = get_orchestrator()
+
+    if request.phase == "plan":
+        objective = request.data.get("objective", "") if request.data else ""
+        context = request.data.get("context") if request.data else None
+        result = await orchestrator.step_plan(objective, context)
+
+    elif request.phase == "implement":
+        plan = request.data if request.data else {}
+        result = await orchestrator.step_implement(plan)
+
+    elif request.phase == "test":
+        scenarios = request.data.get("scenarios", []) if request.data else []
+        result = await orchestrator.step_test(scenarios)
+
+    elif request.phase == "analyze":
+        test_results = request.data if request.data else {}
+        result = await orchestrator.step_analyze(test_results)
+
+    else:
+        raise HTTPException(
+            status_code=400,
+            detail=f"Unknown phase: {request.phase}. Valid: plan, implement, test, analyze",
+        )
+
+    return {"phase": request.phase, "result": result}
+
+
+@router.get("/history")
+async def get_history():
+    """Get history of past development cycles."""
+    orchestrator = get_orchestrator()
+    return orchestrator.export_history()
+
+
+@router.get("/last-cycle")
+async def get_last_cycle():
+    """Get details of the most recent cycle."""
+    global _active_cycle
+
+    if _active_cycle is None:
+        raise HTTPException(status_code=404, detail="No cycle has been run yet")
+
+    return {
+        "objective": _active_cycle.objective,
+        "status": _active_cycle.status,
+        "start_time": _active_cycle.start_time,
+        "end_time": _active_cycle.end_time,
+        "iterations": [
+            {
+                "iteration": it.iteration,
+                "success": it.success,
+                "duration_seconds": it.duration_seconds,
+                "has_plan": it.plan is not None,
+                "has_tests": it.test_results is not None,
+                "has_fixes": it.fixes is not None,
+            }
+            for it in _active_cycle.iterations
+        ],
+        "total_duration_seconds": _active_cycle.total_duration_seconds,
+    }
+
+
+@router.get("/health")
+async def health_check():
+    """Check DevLoop system health."""
+    orchestrator = get_orchestrator()
+
+    # Check dashboard connection
+    from optimization_engine.devloop import DashboardTestRunner
+
+    runner = DashboardTestRunner()
+    dashboard_health = await runner.run_health_check()
+
+    return {
+        "devloop": "healthy",
+        "orchestrator_state": orchestrator.get_state()["phase"],
+        "dashboard": dashboard_health,
+    }
+
+
+# ============================================================================
+# WebSocket Endpoint
+# ============================================================================
+
+
+@router.websocket("/ws")
+async def websocket_endpoint(websocket: WebSocket):
+    """
+    WebSocket endpoint for real-time DevLoop updates.
+
+    Messages sent:
+    - state_update: Phase/iteration changes
+    - cycle_complete: Cycle finished
+    - cycle_error: Cycle failed
+    - test_progress: Individual test results
+    """
+    await websocket.accept()
+    _websocket_clients.append(websocket)
+
+    orchestrator = get_orchestrator()
+
+    try:
+        # Send initial state
+        await websocket.send_json(
+            {
+                "type": "connection_ack",
+                "state": orchestrator.get_state(),
+            }
+        )
+
+        # Handle incoming messages
+        while True:
+            try:
+                data = await asyncio.wait_for(websocket.receive_json(), timeout=30.0)
+
+                msg_type = data.get("type")
+
+                if msg_type == "ping":
+                    await websocket.send_json({"type": "pong"})
+
+                elif msg_type == "get_state":
+                    await websocket.send_json(
+                        {
+                            "type": "state",
+                            "state": orchestrator.get_state(),
+                        }
+                    )
+
+                elif msg_type == "start_cycle":
+                    # Allow starting cycle via WebSocket
+                    objective = data.get("objective", "")
+                    context = data.get("context")
+
+                    asyncio.create_task(orchestrator.run_development_cycle(objective, context))
+
+                    await websocket.send_json(
+                        {
+                            "type": "cycle_started",
+                            "objective": objective,
+                        }
+                    )
+
+            except asyncio.TimeoutError:
+                # Send heartbeat
+                await websocket.send_json({"type": "heartbeat"})
+
+    except WebSocketDisconnect:
+        pass
+    finally:
+        if websocket in _websocket_clients:
+            _websocket_clients.remove(websocket)
+
+
+# ============================================================================
+# Convenience Endpoints for Common Tasks
+# ============================================================================
+
+
+@router.post("/create-study")
+async def create_study_cycle(
+    study_name: str,
+    problem_statement: Optional[str] = None,
+    background_tasks: BackgroundTasks = None,
+):
+    """
+    Convenience endpoint to start a study creation cycle.
+
+    This is a common workflow that combines planning, implementation, and testing.
+    """
+    orchestrator = get_orchestrator()
+
+    context = {
+        "study_name": study_name,
+        "task_type": "create_study",
+    }
+
+    if problem_statement:
+        context["problem_statement"] = problem_statement
+
+    # Start the cycle
+    async def run_cycle():
+        result = await orchestrator.run_development_cycle(
+            objective=f"Create optimization study: {study_name}",
+            context=context,
+        )
+        return result
+
+    if background_tasks:
+        background_tasks.add_task(run_cycle)
+        return {"message": f"Study creation cycle started for '{study_name}'"}
+    else:
+        result = await run_cycle()
+        return {
+            "message": f"Study '{study_name}' creation completed",
+            "status": result.status,
+            "iterations": len(result.iterations),
+        }
+
+
+@router.post("/run-tests")
+async def run_tests(scenarios: List[Dict[str, Any]]):
+    """
+    Run a set of test scenarios directly.
+
+    Useful for testing specific features without a full cycle.
+    """
+    from optimization_engine.devloop import DashboardTestRunner
+
+    runner = DashboardTestRunner()
+    results = await runner.run_test_suite(scenarios)
+
+    return results

atomizer-dashboard/backend/api/routes/optimization.py

@@ -245,17 +245,45 @@ def _get_study_error_info(study_dir: Path, results_dir: Path) -> dict:
 
 def _load_study_info(study_dir: Path, topic: Optional[str] = None) -> Optional[dict]:
     """Load study info from a study directory. Returns None if not a valid study."""
-    # Look for optimization config (check multiple locations)
-    config_file = study_dir / "optimization_config.json"
-    if not config_file.exists():
-        config_file = study_dir / "1_setup" / "optimization_config.json"
-    if not config_file.exists():
+    # Look for config file - prefer atomizer_spec.json (v2.0), fall back to legacy optimization_config.json
+    config_file = None
+    is_atomizer_spec = False
+
+    # Check for AtomizerSpec v2.0 first
+    for spec_path in [
+        study_dir / "atomizer_spec.json",
+        study_dir / "1_setup" / "atomizer_spec.json",
+    ]:
+        if spec_path.exists():
+            config_file = spec_path
+            is_atomizer_spec = True
+            break
+
+    # Fall back to legacy optimization_config.json
+    if config_file is None:
+        for legacy_path in [
+            study_dir / "optimization_config.json",
+            study_dir / "1_setup" / "optimization_config.json",
+        ]:
+            if legacy_path.exists():
+                config_file = legacy_path
+                break
+
+    if config_file is None:
         return None
 
     # Load config
     with open(config_file) as f:
         config = json.load(f)
 
+    # Normalize AtomizerSpec v2.0 to legacy format for compatibility
+    if is_atomizer_spec and "meta" in config:
+        # Extract study_name and description from meta
+        meta = config.get("meta", {})
+        config["study_name"] = meta.get("study_name", study_dir.name)
+        config["description"] = meta.get("description", "")
+        config["version"] = meta.get("version", "2.0")
+
     # Check if results directory exists (support both 2_results and 3_results)
     results_dir = study_dir / "2_results"
     if not results_dir.exists():
@@ -311,12 +339,21 @@ def _load_study_info(study_dir: Path, topic: Optional[str] = None) -> Optional[d
                 best_trial = min(history, key=lambda x: x["objective"])
                 best_value = best_trial["objective"]
 
-    # Get total trials from config (supports both formats)
-    total_trials = (
-        config.get("optimization_settings", {}).get("n_trials")
-        or config.get("optimization", {}).get("n_trials")
-        or config.get("trials", {}).get("n_trials", 50)
-    )
+    # Get total trials from config (supports AtomizerSpec v2.0 and legacy formats)
+    total_trials = None
+
+    # AtomizerSpec v2.0: optimization.budget.max_trials
+    if is_atomizer_spec:
+        total_trials = config.get("optimization", {}).get("budget", {}).get("max_trials")
+
+    # Legacy formats
+    if total_trials is None:
+        total_trials = (
+            config.get("optimization_settings", {}).get("n_trials")
+            or config.get("optimization", {}).get("n_trials")
+            or config.get("optimization", {}).get("max_trials")
+            or config.get("trials", {}).get("n_trials", 100)
+        )
 
     # Get accurate status using process detection
     status = get_accurate_study_status(study_dir.name, trial_count, total_trials, has_db)
@@ -380,7 +417,12 @@ async def list_studies():
                 continue
 
             # Check if this is a study (flat structure) or a topic folder (nested structure)
-            is_study = (item / "1_setup").exists() or (item / "optimization_config.json").exists()
+            # Support both AtomizerSpec v2.0 (atomizer_spec.json) and legacy (optimization_config.json)
+            is_study = (
+                (item / "1_setup").exists()
+                or (item / "atomizer_spec.json").exists()
+                or (item / "optimization_config.json").exists()
+            )
 
             if is_study:
                 # Flat structure: study directly in studies/
@@ -396,10 +438,12 @@ async def list_studies():
                     if sub_item.name.startswith("."):
                         continue
 
-                    # Check if this subdirectory is a study
-                    sub_is_study = (sub_item / "1_setup").exists() or (
-                        sub_item / "optimization_config.json"
-                    ).exists()
+                    # Check if this subdirectory is a study (AtomizerSpec v2.0 or legacy)
+                    sub_is_study = (
+                        (sub_item / "1_setup").exists()
+                        or (sub_item / "atomizer_spec.json").exists()
+                        or (sub_item / "optimization_config.json").exists()
+                    )
                     if sub_is_study:
                         study_info = _load_study_info(sub_item, topic=item.name)
                         if study_info:

atomizer-dashboard/backend/api/services/claude_readme.py

@@ -0,0 +1,396 @@
+"""
+Claude README Generator Service
+
+Generates intelligent README.md files for optimization studies
+using Claude Code CLI (not API) with study context from AtomizerSpec.
+"""
+
+import asyncio
+import json
+import subprocess
+from datetime import datetime
+from pathlib import Path
+from typing import Any, Dict, Optional
+
+# Base directory
+ATOMIZER_ROOT = Path(__file__).parent.parent.parent.parent.parent
+
+# Load skill prompt
+SKILL_PATH = ATOMIZER_ROOT / ".claude" / "skills" / "modules" / "study-readme-generator.md"
+
+
+def load_skill_prompt() -> str:
+    """Load the README generator skill prompt."""
+    if SKILL_PATH.exists():
+        return SKILL_PATH.read_text(encoding="utf-8")
+    return ""
+
+
+class ClaudeReadmeGenerator:
+    """Generate README.md files using Claude Code CLI."""
+
+    def __init__(self):
+        self.skill_prompt = load_skill_prompt()
+
+    def generate_readme(
+        self,
+        study_name: str,
+        spec: Dict[str, Any],
+        context_files: Optional[Dict[str, str]] = None,
+        topic: Optional[str] = None,
+    ) -> str:
+        """
+        Generate a README.md for a study using Claude Code CLI.
+
+        Args:
+            study_name: Name of the study
+            spec: Full AtomizerSpec v2.0 dict
+            context_files: Optional dict of {filename: content} for context
+            topic: Optional topic folder name
+
+        Returns:
+            Generated README.md content
+        """
+        # Build context for Claude
+        context = self._build_context(study_name, spec, context_files, topic)
+
+        # Build the prompt
+        prompt = self._build_prompt(context)
+
+        try:
+            # Run Claude Code CLI synchronously
+            result = self._run_claude_cli(prompt)
+
+            # Extract markdown content from response
+            readme_content = self._extract_markdown(result)
+
+            if readme_content:
+                return readme_content
+
+            # If no markdown found, return the whole response
+            return result if result else self._generate_fallback_readme(study_name, spec)
+
+        except Exception as e:
+            print(f"Claude CLI error: {e}")
+            return self._generate_fallback_readme(study_name, spec)
+
+    async def generate_readme_async(
+        self,
+        study_name: str,
+        spec: Dict[str, Any],
+        context_files: Optional[Dict[str, str]] = None,
+        topic: Optional[str] = None,
+    ) -> str:
+        """Async version of generate_readme."""
+        # Run in thread pool to not block
+        loop = asyncio.get_event_loop()
+        return await loop.run_in_executor(
+            None, lambda: self.generate_readme(study_name, spec, context_files, topic)
+        )
+
+    def _run_claude_cli(self, prompt: str) -> str:
+        """Run Claude Code CLI and get response."""
+        try:
+            # Use claude CLI with --print flag for non-interactive output
+            result = subprocess.run(
+                ["claude", "--print", prompt],
+                capture_output=True,
+                text=True,
+                timeout=120,  # 2 minute timeout
+                cwd=str(ATOMIZER_ROOT),
+            )
+
+            if result.returncode != 0:
+                error_msg = result.stderr or "Unknown error"
+                raise Exception(f"Claude CLI error: {error_msg}")
+
+            return result.stdout.strip()
+
+        except subprocess.TimeoutExpired:
+            raise Exception("Request timed out")
+        except FileNotFoundError:
+            raise Exception("Claude CLI not found. Make sure 'claude' is in PATH.")
+
+    def _build_context(
+        self,
+        study_name: str,
+        spec: Dict[str, Any],
+        context_files: Optional[Dict[str, str]],
+        topic: Optional[str],
+    ) -> Dict[str, Any]:
+        """Build the context object for Claude."""
+        meta = spec.get("meta", {})
+        model = spec.get("model", {})
+        introspection = model.get("introspection", {}) or {}
+
+        context = {
+            "study_name": study_name,
+            "topic": topic or meta.get("topic", "Other"),
+            "description": meta.get("description", ""),
+            "created": meta.get("created", datetime.now().isoformat()),
+            "status": meta.get("status", "draft"),
+            "design_variables": spec.get("design_variables", []),
+            "extractors": spec.get("extractors", []),
+            "objectives": spec.get("objectives", []),
+            "constraints": spec.get("constraints", []),
+            "optimization": spec.get("optimization", {}),
+            "introspection": {
+                "mass_kg": introspection.get("mass_kg"),
+                "volume_mm3": introspection.get("volume_mm3"),
+                "solver_type": introspection.get("solver_type"),
+                "expressions": introspection.get("expressions", []),
+                "expressions_count": len(introspection.get("expressions", [])),
+            },
+            "model_files": {
+                "sim": model.get("sim", {}).get("path") if model.get("sim") else None,
+                "prt": model.get("prt", {}).get("path") if model.get("prt") else None,
+                "fem": model.get("fem", {}).get("path") if model.get("fem") else None,
+            },
+        }
+
+        # Add context files if provided
+        if context_files:
+            context["context_files"] = context_files
+
+        return context
+
+    def _build_prompt(self, context: Dict[str, Any]) -> str:
+        """Build the prompt for Claude CLI."""
+
+        # Build context files section if available
+        context_files_section = ""
+        if context.get("context_files"):
+            context_files_section = "\n\n## User-Provided Context Files\n\nIMPORTANT: Use this information to understand the optimization goals, design variables, objectives, and constraints:\n\n"
+            for filename, content in context.get("context_files", {}).items():
+                context_files_section += f"### {filename}\n```\n{content}\n```\n\n"
+
+        # Remove context_files from JSON dump to avoid duplication
+        context_for_json = {k: v for k, v in context.items() if k != "context_files"}
+
+        prompt = f"""Generate a README.md for this FEA optimization study.
+
+## Study Technical Data
+
+```json
+{json.dumps(context_for_json, indent=2, default=str)}
+```
+{context_files_section}
+## Requirements
+
+1. Use the EXACT values from the technical data - no placeholders
+2. If context files are provided, extract:
+   - Design variable bounds (min/max)
+   - Optimization objectives (minimize/maximize what)
+   - Constraints (stress limits, etc.)
+   - Any specific requirements mentioned
+
+3. Format the README with these sections:
+   - Title (# Study Name)
+   - Overview (topic, date, status, description from context)
+   - Engineering Problem (what we're optimizing and why - from context files)
+   - Model Information (mass, solver, files)
+   - Design Variables (if context specifies bounds, include them in a table)
+   - Optimization Objectives (from context files)
+   - Constraints (from context files)
+   - Expressions Found (table of discovered expressions, highlight candidates)
+   - Next Steps (what needs to be configured)
+
+4. Keep it professional and concise
+5. Use proper markdown table formatting
+6. Include units where applicable
+7. For expressions table, show: name, value, units, is_candidate
+
+Generate ONLY the README.md content in markdown format, no explanations:"""
+
+        return prompt
+
+    def _extract_markdown(self, response: str) -> Optional[str]:
+        """Extract markdown content from Claude response."""
+        if not response:
+            return None
+
+        # If response starts with #, it's already markdown
+        if response.strip().startswith("#"):
+            return response.strip()
+
+        # Try to find markdown block
+        if "```markdown" in response:
+            start = response.find("```markdown") + len("```markdown")
+            end = response.find("```", start)
+            if end > start:
+                return response[start:end].strip()
+
+        if "```md" in response:
+            start = response.find("```md") + len("```md")
+            end = response.find("```", start)
+            if end > start:
+                return response[start:end].strip()
+
+        # Look for first # heading
+        lines = response.split("\n")
+        for i, line in enumerate(lines):
+            if line.strip().startswith("# "):
+                return "\n".join(lines[i:]).strip()
+
+        return None
+
+    def _generate_fallback_readme(self, study_name: str, spec: Dict[str, Any]) -> str:
+        """Generate a basic README if Claude fails."""
+        meta = spec.get("meta", {})
+        model = spec.get("model", {})
+        introspection = model.get("introspection", {}) or {}
+        dvs = spec.get("design_variables", [])
+        objs = spec.get("objectives", [])
+        cons = spec.get("constraints", [])
+        opt = spec.get("optimization", {})
+        expressions = introspection.get("expressions", [])
+
+        lines = [
+            f"# {study_name.replace('_', ' ').title()}",
+            "",
+            f"**Topic**: {meta.get('topic', 'Other')}",
+            f"**Created**: {meta.get('created', 'Unknown')[:10] if meta.get('created') else 'Unknown'}",
+            f"**Status**: {meta.get('status', 'draft')}",
+            "",
+        ]
+
+        if meta.get("description"):
+            lines.extend([meta["description"], ""])
+
+        # Model Information
+        lines.extend(
+            [
+                "## Model Information",
+                "",
+            ]
+        )
+
+        if introspection.get("mass_kg"):
+            lines.append(f"- **Mass**: {introspection['mass_kg']:.2f} kg")
+
+        sim_path = model.get("sim", {}).get("path") if model.get("sim") else None
+        if sim_path:
+            lines.append(f"- **Simulation**: {sim_path}")
+
+        lines.append("")
+
+        # Expressions Found
+        if expressions:
+            lines.extend(
+                [
+                    "## Expressions Found",
+                    "",
+                    "| Name | Value | Units | Candidate |",
+                    "|------|-------|-------|-----------|",
+                ]
+            )
+            for expr in expressions:
+                is_candidate = "✓" if expr.get("is_candidate") else ""
+                value = f"{expr.get('value', '-')}"
+                units = expr.get("units", "-")
+                lines.append(f"| {expr.get('name', '-')} | {value} | {units} | {is_candidate} |")
+            lines.append("")
+
+        # Design Variables (if configured)
+        if dvs:
+            lines.extend(
+                [
+                    "## Design Variables",
+                    "",
+                    "| Variable | Expression | Range | Units |",
+                    "|----------|------------|-------|-------|",
+                ]
+            )
+            for dv in dvs:
+                bounds = dv.get("bounds", {})
+                units = dv.get("units", "-")
+                lines.append(
+                    f"| {dv.get('name', 'Unknown')} | "
+                    f"{dv.get('expression_name', '-')} | "
+                    f"[{bounds.get('min', '-')}, {bounds.get('max', '-')}] | "
+                    f"{units} |"
+                )
+            lines.append("")
+
+        # Objectives
+        if objs:
+            lines.extend(
+                [
+                    "## Objectives",
+                    "",
+                    "| Objective | Direction | Weight |",
+                    "|-----------|-----------|--------|",
+                ]
+            )
+            for obj in objs:
+                lines.append(
+                    f"| {obj.get('name', 'Unknown')} | "
+                    f"{obj.get('direction', 'minimize')} | "
+                    f"{obj.get('weight', 1.0)} |"
+                )
+            lines.append("")
+
+        # Constraints
+        if cons:
+            lines.extend(
+                [
+                    "## Constraints",
+                    "",
+                    "| Constraint | Condition | Threshold |",
+                    "|------------|-----------|-----------|",
+                ]
+            )
+            for con in cons:
+                lines.append(
+                    f"| {con.get('name', 'Unknown')} | "
+                    f"{con.get('operator', '<=')} | "
+                    f"{con.get('threshold', '-')} |"
+                )
+            lines.append("")
+
+        # Algorithm
+        algo = opt.get("algorithm", {})
+        budget = opt.get("budget", {})
+        lines.extend(
+            [
+                "## Methodology",
+                "",
+                f"- **Algorithm**: {algo.get('type', 'TPE')}",
+                f"- **Max Trials**: {budget.get('max_trials', 100)}",
+                "",
+            ]
+        )
+
+        # Next Steps
+        lines.extend(
+            [
+                "## Next Steps",
+                "",
+            ]
+        )
+
+        if not dvs:
+            lines.append("- [ ] Configure design variables from discovered expressions")
+        if not objs:
+            lines.append("- [ ] Define optimization objectives")
+        if not dvs and not objs:
+            lines.append("- [ ] Open in Canvas Builder to complete configuration")
+        else:
+            lines.append("- [ ] Run baseline solve to validate setup")
+            lines.append("- [ ] Finalize study to move to studies folder")
+
+        lines.append("")
+
+        return "\n".join(lines)
+
+
+# Singleton instance
+_generator: Optional[ClaudeReadmeGenerator] = None
+
+
+def get_readme_generator() -> ClaudeReadmeGenerator:
+    """Get the singleton README generator instance."""
+    global _generator
+    if _generator is None:
+        _generator = ClaudeReadmeGenerator()
+    return _generator

atomizer-dashboard/backend/api/services/context_builder.py

@@ -26,6 +26,7 @@ class ContextBuilder:
         study_id: Optional[str] = None,
         conversation_history: Optional[List[Dict[str, Any]]] = None,
         canvas_state: Optional[Dict[str, Any]] = None,
+        spec_path: Optional[str] = None,
     ) -> str:
         """
         Build full system prompt with context.
@@ -35,6 +36,7 @@ class ContextBuilder:
             study_id: Optional study name to provide context for
             conversation_history: Optional recent messages for continuity
             canvas_state: Optional canvas state (nodes, edges) from the UI
+            spec_path: Optional path to the atomizer_spec.json file
 
         Returns:
             Complete system prompt string
@@ -45,7 +47,7 @@ class ContextBuilder:
         if canvas_state:
             node_count = len(canvas_state.get("nodes", []))
             print(f"[ContextBuilder] Including canvas context with {node_count} nodes")
-            parts.append(self._canvas_context(canvas_state))
+            parts.append(self._canvas_context(canvas_state, spec_path))
         else:
             print("[ContextBuilder] No canvas state provided")
 
@@ -57,7 +59,7 @@ class ContextBuilder:
         if conversation_history:
             parts.append(self._conversation_context(conversation_history))
 
-        parts.append(self._mode_instructions(mode))
+        parts.append(self._mode_instructions(mode, spec_path))
 
         return "\n\n---\n\n".join(parts)
 
@@ -298,7 +300,7 @@ Important guidelines:
 
         return context
 
-    def _canvas_context(self, canvas_state: Dict[str, Any]) -> str:
+    def _canvas_context(self, canvas_state: Dict[str, Any], spec_path: Optional[str] = None) -> str:
         """
         Build context from canvas state (nodes and edges).
 
@@ -317,6 +319,8 @@ Important guidelines:
         context += f"**Study Name**: {study_name}\n"
         if study_path:
             context += f"**Study Path**: {study_path}\n"
+        if spec_path:
+            context += f"**Spec File**: `{spec_path}`\n"
         context += "\n"
 
         # Group nodes by type
@@ -438,61 +442,100 @@ Important guidelines:
         context += f"Total edges: {len(edges)}\n"
         context += "Flow: Design Variables → Model → Solver → Extractors → Objectives/Constraints → Algorithm\n\n"
 
-        # Canvas modification instructions
-        context += """## Canvas Modification Tools
-
-**For AtomizerSpec v2.0 studies (preferred):**
-Use spec tools when working with v2.0 studies (check if study uses `atomizer_spec.json`):
-- `spec_modify` - Modify spec values using JSONPath (e.g., "design_variables[0].bounds.min")
-- `spec_add_node` - Add design variables, extractors, objectives, or constraints
-- `spec_remove_node` - Remove nodes from the spec
-- `spec_add_custom_extractor` - Add a Python-based custom extractor function
-
-**For Legacy Canvas (optimization_config.json):**
-- `canvas_add_node` - Add a new node (designVar, extractor, objective, constraint)
-- `canvas_update_node` - Update node properties (bounds, weights, names)
-- `canvas_remove_node` - Remove a node from the canvas
-- `canvas_connect_nodes` - Create an edge between nodes
-
-**Example user requests you can handle:**
-- "Add a design variable called hole_diameter with range 5-15 mm" → Use spec_add_node or canvas_add_node
-- "Change the weight of wfe_40_20 to 8" → Use spec_modify or canvas_update_node
-- "Remove the constraint node" → Use spec_remove_node or canvas_remove_node
-- "Add a custom extractor that computes stress ratio" → Use spec_add_custom_extractor
-
-Always respond with confirmation of changes made to the canvas/spec.
-"""
-
+        # Instructions will be in _mode_instructions based on spec_path
         return context
 
-    def _mode_instructions(self, mode: str) -> str:
+    def _mode_instructions(self, mode: str, spec_path: Optional[str] = None) -> str:
         """Mode-specific instructions"""
         if mode == "power":
-            return """# Power Mode Instructions
+            instructions = """# Power Mode Instructions
 
 You have **FULL ACCESS** to modify Atomizer studies. **DO NOT ASK FOR PERMISSION** - just do it.
 
-## Direct Actions (no confirmation needed):
-- **Add design variables**: Use `canvas_add_node` or `spec_add_node` with node_type="designVar"
-- **Add extractors**: Use `canvas_add_node` with node_type="extractor"
-- **Add objectives**: Use `canvas_add_node` with node_type="objective"
-- **Add constraints**: Use `canvas_add_node` with node_type="constraint"
-- **Update node properties**: Use `canvas_update_node` or `spec_modify`
-- **Remove nodes**: Use `canvas_remove_node`
-- **Edit atomizer_spec.json directly**: Use the Edit tool
+## CRITICAL: How to Modify the Spec
 
-## For custom extractors with Python code:
-Use `spec_add_custom_extractor` to add a custom function.
-
-## IMPORTANT:
-- You have --dangerously-skip-permissions enabled
-- The user has explicitly granted you power mode access
-- **ACT IMMEDIATELY** when asked to add/modify/remove things
-- Explain what you did AFTER doing it, not before
-- Do NOT say "I need permission" - you already have it
-
-Example: If user says "add a volume extractor", immediately use canvas_add_node to add it.
 """
+            if spec_path:
+                instructions += f"""**The spec file is at**: `{spec_path}`
+
+When asked to add/modify/remove design variables, extractors, objectives, or constraints:
+1. **Read the spec file first** using the Read tool
+2. **Edit the spec file** using the Edit tool to make precise changes
+3. **Confirm what you changed** in your response
+
+### AtomizerSpec v2.0 Structure
+
+The spec has these main arrays you can modify:
+- `design_variables` - Parameters to optimize
+- `extractors` - Physics extraction functions  
+- `objectives` - What to minimize/maximize
+- `constraints` - Limits that must be satisfied
+
+### Example: Add a Design Variable
+
+To add a design variable called "thickness" with bounds [1, 10]:
+
+1. Read the spec: `Read({spec_path})`
+2. Find the `"design_variables": [...]` array
+3. Add a new entry like:
+```json
+{{
+  "id": "dv_thickness",
+  "name": "thickness",
+  "expression_name": "thickness",
+  "type": "continuous",
+  "bounds": {{"min": 1, "max": 10}},
+  "baseline": 5,
+  "units": "mm",
+  "enabled": true
+}}
+```
+4. Use Edit tool to insert this into the array
+
+### Example: Add an Objective
+
+To add a "minimize mass" objective:
+```json
+{{
+  "id": "obj_mass",
+  "name": "mass",
+  "direction": "minimize",
+  "weight": 1.0,
+  "source": {{
+    "extractor_id": "ext_mass",
+    "output_name": "mass"
+  }}
+}}
+```
+
+### Example: Add an Extractor
+
+To add a mass extractor:
+```json
+{{
+  "id": "ext_mass",
+  "name": "mass",
+  "type": "mass",
+  "builtin": true,
+  "outputs": [{{"name": "mass", "units": "kg"}}]
+}}
+```
+
+"""
+            else:
+                instructions += """No spec file is currently set. Ask the user which study they want to work with.
+
+"""
+
+            instructions += """## IMPORTANT Rules:
+- You have --dangerously-skip-permissions enabled
+- **ACT IMMEDIATELY** when asked to add/modify/remove things
+- Use the **Edit** tool to modify the spec file directly
+- Generate unique IDs like `dv_<name>`, `ext_<name>`, `obj_<name>`, `con_<name>`
+- Explain what you changed AFTER doing it, not before
+- Do NOT say "I need permission" - you already have it
+"""
+            return instructions
         else:
             return """# User Mode Instructions
 
@@ -503,29 +546,11 @@ You can help with optimization workflows:
 - Generate reports
 - Explain FEA concepts
 
-**For code modifications**, suggest switching to Power Mode.
+**For modifying studies**, the user needs to switch to Power Mode.
 
-Available tools:
-- `list_studies`, `get_study_status`, `create_study`
-- `run_optimization`, `stop_optimization`, `get_optimization_status`
-- `get_trial_data`, `analyze_convergence`, `compare_trials`, `get_best_design`
-- `generate_report`, `export_data`
-- `explain_physics`, `recommend_method`, `query_extractors`
-
-**AtomizerSpec v2.0 Tools (preferred for new studies):**
-- `spec_get` - Get the full AtomizerSpec for a study
-- `spec_modify` - Modify spec values using JSONPath (e.g., "design_variables[0].bounds.min")
-- `spec_add_node` - Add design variables, extractors, objectives, or constraints
-- `spec_remove_node` - Remove nodes from the spec
-- `spec_validate` - Validate spec against JSON Schema
-- `spec_add_custom_extractor` - Add a Python-based custom extractor function
-- `spec_create_from_description` - Create a new study from natural language description
-
-**Canvas Tools (for visual workflow builder):**
-- `validate_canvas_intent` - Validate a canvas-generated optimization intent
-- `execute_canvas_intent` - Create a study from a canvas intent
-- `interpret_canvas_intent` - Analyze intent and provide recommendations
-
-When you receive a message containing "INTENT:" followed by JSON, this is from the Canvas UI.
-Parse the intent and use the appropriate canvas tool to process it.
+In user mode you can:
+- Read and explain study configurations
+- Analyze optimization results
+- Provide recommendations
+- Answer questions about FEA and optimization
 """

atomizer-dashboard/backend/api/services/session_manager.py

@@ -1,11 +1,15 @@
 """
 Session Manager
 
-Manages persistent Claude Code sessions with MCP integration.
+Manages persistent Claude Code sessions with direct file editing.
 Fixed for Windows compatibility - uses subprocess.Popen with ThreadPoolExecutor.
+
+Strategy: Claude edits atomizer_spec.json directly using Edit/Write tools
+(no MCP dependency for reliability).
 """
 
 import asyncio
+import hashlib
 import json
 import os
 import subprocess
@@ -26,6 +30,10 @@ MCP_SERVER_PATH = ATOMIZER_ROOT / "mcp-server" / "atomizer-tools"
 # Thread pool for subprocess operations (Windows compatible)
 _executor = ThreadPoolExecutor(max_workers=4)
 
+import logging
+
+logger = logging.getLogger(__name__)
+
 
 @dataclass
 class ClaudeSession:
@@ -130,6 +138,7 @@ class SessionManager:
         Send a message to a session and stream the response.
 
         Uses synchronous subprocess.Popen via ThreadPoolExecutor for Windows compatibility.
+        Claude edits atomizer_spec.json directly using Edit/Write tools (no MCP).
 
         Args:
             session_id: The session ID
@@ -147,45 +156,48 @@ class SessionManager:
         # Store user message
         self.store.add_message(session_id, "user", message)
 
+        # Get spec path and hash BEFORE Claude runs (to detect changes)
+        spec_path = self._get_spec_path(session.study_id) if session.study_id else None
+        spec_hash_before = self._get_file_hash(spec_path) if spec_path else None
+
         # Build context with conversation history AND canvas state
         history = self.store.get_history(session_id, limit=10)
         full_prompt = self.context_builder.build(
             mode=session.mode,
             study_id=session.study_id,
             conversation_history=history[:-1],
-            canvas_state=canvas_state,  # Pass canvas state for context
+            canvas_state=canvas_state,
+            spec_path=str(spec_path) if spec_path else None,  # Tell Claude where the spec is
         )
         full_prompt += f"\n\nUser: {message}\n\nRespond helpfully and concisely:"
 
-        # Build CLI arguments
+        # Build CLI arguments - NO MCP for reliability
         cli_args = ["claude", "--print"]
 
-        # Ensure MCP config exists
-        mcp_config_path = ATOMIZER_ROOT / f".claude-mcp-{session_id}.json"
-        if not mcp_config_path.exists():
-            mcp_config = self._build_mcp_config(session.mode)
-            with open(mcp_config_path, "w") as f:
-                json.dump(mcp_config, f)
-        cli_args.extend(["--mcp-config", str(mcp_config_path)])
-
         if session.mode == "user":
-            cli_args.extend([
-                "--allowedTools",
-                "Read Write(**/STUDY_REPORT.md) Write(**/3_results/*.md) Bash(python:*) mcp__atomizer-tools__*"
-            ])
+            # User mode: limited tools
+            cli_args.extend(
+                [
+                    "--allowedTools",
+                    "Read Bash(python:*)",
+                ]
+            )
         else:
+            # Power mode: full access to edit files
             cli_args.append("--dangerously-skip-permissions")
 
         cli_args.append("-")  # Read from stdin
 
         full_response = ""
         tool_calls: List[Dict] = []
+        process: Optional[subprocess.Popen] = None
 
         try:
             loop = asyncio.get_event_loop()
 
             # Run subprocess in thread pool (Windows compatible)
             def run_claude():
+                nonlocal process
                 try:
                     process = subprocess.Popen(
                         cli_args,
@@ -194,8 +206,8 @@ class SessionManager:
                         stderr=subprocess.PIPE,
                         cwd=str(ATOMIZER_ROOT),
                         text=True,
-                        encoding='utf-8',
-                        errors='replace',
+                        encoding="utf-8",
+                        errors="replace",
                     )
                     stdout, stderr = process.communicate(input=full_prompt, timeout=300)
                     return {
@@ -204,10 +216,13 @@ class SessionManager:
                         "returncode": process.returncode,
                     }
                 except subprocess.TimeoutExpired:
-                    process.kill()
+                    if process:
+                        process.kill()
                     return {"error": "Response timeout (5 minutes)"}
                 except FileNotFoundError:
-                    return {"error": "Claude CLI not found in PATH. Install with: npm install -g @anthropic-ai/claude-code"}
+                    return {
+                        "error": "Claude CLI not found in PATH. Install with: npm install -g @anthropic-ai/claude-code"
+                    }
                 except Exception as e:
                     return {"error": str(e)}
 
@@ -219,24 +234,14 @@ class SessionManager:
                 full_response = result["stdout"] or ""
 
                 if full_response:
-                    # Check if response contains canvas modifications (from MCP tools)
-                    import logging
-                    logger = logging.getLogger(__name__)
-
-                    modifications = self._extract_canvas_modifications(full_response)
-                    logger.info(f"[SEND_MSG] Found {len(modifications)} canvas modifications to send")
-
-                    for mod in modifications:
-                        logger.info(f"[SEND_MSG] Sending canvas_modification: {mod.get('action')} {mod.get('nodeType')}")
-                        yield {"type": "canvas_modification", "modification": mod}
-
-                    # Always send the text response
+                    # Always send the text response first
                     yield {"type": "text", "content": full_response}
 
                 if result["returncode"] != 0 and result["stderr"]:
-                    yield {"type": "error", "message": f"CLI error: {result['stderr']}"}
+                    logger.warning(f"[SEND_MSG] CLI stderr: {result['stderr']}")
 
         except Exception as e:
+            logger.error(f"[SEND_MSG] Exception: {e}")
             yield {"type": "error", "message": str(e)}
 
         # Store assistant response
@@ -248,8 +253,46 @@ class SessionManager:
                 tool_calls=tool_calls if tool_calls else None,
             )
 
+        # Check if spec was modified by comparing hashes
+        if spec_path and session.mode == "power" and session.study_id:
+            spec_hash_after = self._get_file_hash(spec_path)
+            if spec_hash_before != spec_hash_after:
+                logger.info(f"[SEND_MSG] Spec file was modified! Sending update.")
+                spec_update = await self._check_spec_updated(session.study_id)
+                if spec_update:
+                    yield {
+                        "type": "spec_updated",
+                        "spec": spec_update,
+                        "tool": "direct_edit",
+                        "reason": "Claude modified spec file directly",
+                    }
+
         yield {"type": "done", "tool_calls": tool_calls}
 
+    def _get_spec_path(self, study_id: str) -> Optional[Path]:
+        """Get the atomizer_spec.json path for a study."""
+        if not study_id:
+            return None
+
+        if study_id.startswith("draft_"):
+            spec_path = ATOMIZER_ROOT / "studies" / "_inbox" / study_id / "atomizer_spec.json"
+        else:
+            spec_path = ATOMIZER_ROOT / "studies" / study_id / "atomizer_spec.json"
+            if not spec_path.exists():
+                spec_path = ATOMIZER_ROOT / "studies" / study_id / "1_setup" / "atomizer_spec.json"
+
+        return spec_path if spec_path.exists() else None
+
+    def _get_file_hash(self, path: Optional[Path]) -> Optional[str]:
+        """Get MD5 hash of a file for change detection."""
+        if not path or not path.exists():
+            return None
+        try:
+            with open(path, "rb") as f:
+                return hashlib.md5(f.read()).hexdigest()
+        except Exception:
+            return None
+
     async def switch_mode(
         self,
         session_id: str,
@@ -313,6 +356,7 @@ class SessionManager:
         """
         import re
         import logging
+
         logger = logging.getLogger(__name__)
 
         modifications = []
@@ -327,14 +371,16 @@ class SessionManager:
 
         try:
             # Method 1: Look for JSON in code fences
-            code_block_pattern = r'```(?:json)?\s*([\s\S]*?)```'
+            code_block_pattern = r"```(?:json)?\s*([\s\S]*?)```"
             for match in re.finditer(code_block_pattern, response):
                 block_content = match.group(1).strip()
                 try:
                     obj = json.loads(block_content)
-                    if isinstance(obj, dict) and 'modification' in obj:
-                        logger.info(f"[CANVAS_MOD] Found modification in code fence: {obj['modification']}")
-                        modifications.append(obj['modification'])
+                    if isinstance(obj, dict) and "modification" in obj:
+                        logger.info(
+                            f"[CANVAS_MOD] Found modification in code fence: {obj['modification']}"
+                        )
+                        modifications.append(obj["modification"])
                 except json.JSONDecodeError:
                     continue
 
@@ -342,7 +388,7 @@ class SessionManager:
             # This handles nested objects correctly
             i = 0
             while i < len(response):
-                if response[i] == '{':
+                if response[i] == "{":
                     # Found a potential JSON start, find matching close
                     brace_count = 1
                     j = i + 1
@@ -354,14 +400,14 @@ class SessionManager:
 
                         if escape_next:
                             escape_next = False
-                        elif char == '\\':
+                        elif char == "\\":
                             escape_next = True
                         elif char == '"' and not escape_next:
                             in_string = not in_string
                         elif not in_string:
-                            if char == '{':
+                            if char == "{":
                                 brace_count += 1
-                            elif char == '}':
+                            elif char == "}":
                                 brace_count -= 1
                         j += 1
 
@@ -369,11 +415,13 @@ class SessionManager:
                         potential_json = response[i:j]
                         try:
                             obj = json.loads(potential_json)
-                            if isinstance(obj, dict) and 'modification' in obj:
-                                mod = obj['modification']
+                            if isinstance(obj, dict) and "modification" in obj:
+                                mod = obj["modification"]
                                 # Avoid duplicates
                                 if mod not in modifications:
-                                    logger.info(f"[CANVAS_MOD] Found inline modification: action={mod.get('action')}, nodeType={mod.get('nodeType')}")
+                                    logger.info(
+                                        f"[CANVAS_MOD] Found inline modification: action={mod.get('action')}, nodeType={mod.get('nodeType')}"
+                                    )
                                     modifications.append(mod)
                         except json.JSONDecodeError as e:
                             # Not valid JSON, skip
@@ -388,6 +436,43 @@ class SessionManager:
         logger.info(f"[CANVAS_MOD] Extracted {len(modifications)} modification(s)")
         return modifications
 
+    async def _check_spec_updated(self, study_id: str) -> Optional[Dict]:
+        """
+        Check if the atomizer_spec.json was modified and return the updated spec.
+
+        For drafts in _inbox/, we check the spec file directly.
+        """
+        import logging
+
+        logger = logging.getLogger(__name__)
+
+        try:
+            # Determine spec path based on study_id
+            if study_id.startswith("draft_"):
+                spec_path = ATOMIZER_ROOT / "studies" / "_inbox" / study_id / "atomizer_spec.json"
+            else:
+                # Regular study path
+                spec_path = ATOMIZER_ROOT / "studies" / study_id / "atomizer_spec.json"
+                if not spec_path.exists():
+                    spec_path = (
+                        ATOMIZER_ROOT / "studies" / study_id / "1_setup" / "atomizer_spec.json"
+                    )
+
+            if not spec_path.exists():
+                logger.debug(f"[SPEC_CHECK] Spec not found at {spec_path}")
+                return None
+
+            # Read and return the spec
+            with open(spec_path, "r", encoding="utf-8") as f:
+                spec = json.load(f)
+
+            logger.info(f"[SPEC_CHECK] Loaded spec from {spec_path}")
+            return spec
+
+        except Exception as e:
+            logger.error(f"[SPEC_CHECK] Error checking spec: {e}")
+            return None
+
     def _build_mcp_config(self, mode: Literal["user", "power"]) -> dict:
         """Build MCP configuration for Claude"""
         return {

atomizer-dashboard/backend/api/services/spec_manager.py

@@ -47,11 +47,13 @@ from optimization_engine.config.spec_validator import (
 
 class SpecManagerError(Exception):
     """Base error for SpecManager operations."""
+
     pass
 
 
 class SpecNotFoundError(SpecManagerError):
     """Raised when spec file doesn't exist."""
+
     pass
 
 
@@ -118,7 +120,7 @@ class SpecManager:
         if not self.spec_path.exists():
             raise SpecNotFoundError(f"Spec not found: {self.spec_path}")
 
-        with open(self.spec_path, 'r', encoding='utf-8') as f:
+        with open(self.spec_path, "r", encoding="utf-8") as f:
             data = json.load(f)
 
         if validate:
@@ -141,14 +143,15 @@ class SpecManager:
         if not self.spec_path.exists():
             raise SpecNotFoundError(f"Spec not found: {self.spec_path}")
 
-        with open(self.spec_path, 'r', encoding='utf-8') as f:
+        with open(self.spec_path, "r", encoding="utf-8") as f:
             return json.load(f)
 
     def save(
         self,
         spec: Union[AtomizerSpec, Dict[str, Any]],
         modified_by: str = "api",
-        expected_hash: Optional[str] = None
+        expected_hash: Optional[str] = None,
+        skip_validation: bool = False,
     ) -> str:
         """
         Save spec with validation and broadcast.
@@ -157,6 +160,7 @@ class SpecManager:
             spec: Spec to save (AtomizerSpec or dict)
             modified_by: Who/what is making the change
             expected_hash: If provided, verify current file hash matches
+            skip_validation: If True, skip strict validation (for draft specs)
 
         Returns:
             New spec hash
@@ -167,7 +171,7 @@ class SpecManager:
         """
         # Convert to dict if needed
         if isinstance(spec, AtomizerSpec):
-            data = spec.model_dump(mode='json')
+            data = spec.model_dump(mode="json")
         else:
             data = spec
 
@@ -176,24 +180,30 @@ class SpecManager:
             current_hash = self.get_hash()
             if current_hash != expected_hash:
                 raise SpecConflictError(
-                    "Spec was modified by another client",
-                    current_hash=current_hash
+                    "Spec was modified by another client", current_hash=current_hash
                 )
 
         # Update metadata
-        now = datetime.now(timezone.utc).isoformat().replace('+00:00', 'Z')
+        now = datetime.now(timezone.utc).isoformat().replace("+00:00", "Z")
         data["meta"]["modified"] = now
         data["meta"]["modified_by"] = modified_by
 
-        # Validate
-        self.validator.validate(data, strict=True)
+        # Validate (skip for draft specs or when explicitly requested)
+        status = data.get("meta", {}).get("status", "draft")
+        is_draft = status in ("draft", "introspected", "configured")
+
+        if not skip_validation and not is_draft:
+            self.validator.validate(data, strict=True)
+        elif not skip_validation:
+            # For draft specs, just validate non-strictly (collect warnings only)
+            self.validator.validate(data, strict=False)
 
         # Compute new hash
         new_hash = self._compute_hash(data)
 
         # Atomic write (write to temp, then rename)
-        temp_path = self.spec_path.with_suffix('.tmp')
-        with open(temp_path, 'w', encoding='utf-8') as f:
+        temp_path = self.spec_path.with_suffix(".tmp")
+        with open(temp_path, "w", encoding="utf-8") as f:
             json.dump(data, f, indent=2, ensure_ascii=False)
 
         temp_path.replace(self.spec_path)
@@ -202,12 +212,9 @@ class SpecManager:
         self._last_hash = new_hash
 
         # Broadcast to subscribers
-        self._broadcast({
-            "type": "spec_updated",
-            "hash": new_hash,
-            "modified_by": modified_by,
-            "timestamp": now
-        })
+        self._broadcast(
+            {"type": "spec_updated", "hash": new_hash, "modified_by": modified_by, "timestamp": now}
+        )
 
         return new_hash
 
@@ -219,7 +226,7 @@ class SpecManager:
         """Get current spec hash."""
         if not self.spec_path.exists():
             return ""
-        with open(self.spec_path, 'r', encoding='utf-8') as f:
+        with open(self.spec_path, "r", encoding="utf-8") as f:
             data = json.load(f)
         return self._compute_hash(data)
 
@@ -240,12 +247,7 @@ class SpecManager:
     # Patch Operations
     # =========================================================================
 
-    def patch(
-        self,
-        path: str,
-        value: Any,
-        modified_by: str = "api"
-    ) -> AtomizerSpec:
+    def patch(self, path: str, value: Any, modified_by: str = "api") -> AtomizerSpec:
         """
         Apply a JSONPath-style modification.
 
@@ -306,7 +308,7 @@ class SpecManager:
         """Parse JSONPath into parts."""
         # Handle both dot notation and bracket notation
         parts = []
-        for part in re.split(r'\.|\[|\]', path):
+        for part in re.split(r"\.|\[|\]", path):
             if part:
                 parts.append(part)
         return parts
@@ -316,10 +318,7 @@ class SpecManager:
     # =========================================================================
 
     def add_node(
-        self,
-        node_type: str,
-        node_data: Dict[str, Any],
-        modified_by: str = "canvas"
+        self, node_type: str, node_data: Dict[str, Any], modified_by: str = "canvas"
     ) -> str:
         """
         Add a new node (design var, extractor, objective, constraint).
@@ -353,20 +352,19 @@ class SpecManager:
         self.save(data, modified_by)
 
         # Broadcast node addition
-        self._broadcast({
-            "type": "node_added",
-            "node_type": node_type,
-            "node_id": node_id,
-            "modified_by": modified_by
-        })
+        self._broadcast(
+            {
+                "type": "node_added",
+                "node_type": node_type,
+                "node_id": node_id,
+                "modified_by": modified_by,
+            }
+        )
 
         return node_id
 
     def update_node(
-        self,
-        node_id: str,
-        updates: Dict[str, Any],
-        modified_by: str = "canvas"
+        self, node_id: str, updates: Dict[str, Any], modified_by: str = "canvas"
     ) -> None:
         """
         Update an existing node.
@@ -396,11 +394,7 @@ class SpecManager:
 
         self.save(data, modified_by)
 
-    def remove_node(
-        self,
-        node_id: str,
-        modified_by: str = "canvas"
-    ) -> None:
+    def remove_node(self, node_id: str, modified_by: str = "canvas") -> None:
         """
         Remove a node and all edges referencing it.
 
@@ -427,24 +421,18 @@ class SpecManager:
         # Remove edges referencing this node
         if "canvas" in data and data["canvas"] and "edges" in data["canvas"]:
             data["canvas"]["edges"] = [
-                e for e in data["canvas"]["edges"]
+                e
+                for e in data["canvas"]["edges"]
                 if e.get("source") != node_id and e.get("target") != node_id
             ]
 
         self.save(data, modified_by)
 
         # Broadcast node removal
-        self._broadcast({
-            "type": "node_removed",
-            "node_id": node_id,
-            "modified_by": modified_by
-        })
+        self._broadcast({"type": "node_removed", "node_id": node_id, "modified_by": modified_by})
 
     def update_node_position(
-        self,
-        node_id: str,
-        position: Dict[str, float],
-        modified_by: str = "canvas"
+        self, node_id: str, position: Dict[str, float], modified_by: str = "canvas"
     ) -> None:
         """
         Update a node's canvas position.
@@ -456,12 +444,7 @@ class SpecManager:
         """
         self.update_node(node_id, {"canvas_position": position}, modified_by)
 
-    def add_edge(
-        self,
-        source: str,
-        target: str,
-        modified_by: str = "canvas"
-    ) -> None:
+    def add_edge(self, source: str, target: str, modified_by: str = "canvas") -> None:
         """
         Add a canvas edge between nodes.
 
@@ -483,19 +466,11 @@ class SpecManager:
             if edge.get("source") == source and edge.get("target") == target:
                 return  # Already exists
 
-        data["canvas"]["edges"].append({
-            "source": source,
-            "target": target
-        })
+        data["canvas"]["edges"].append({"source": source, "target": target})
 
         self.save(data, modified_by)
 
-    def remove_edge(
-        self,
-        source: str,
-        target: str,
-        modified_by: str = "canvas"
-    ) -> None:
+    def remove_edge(self, source: str, target: str, modified_by: str = "canvas") -> None:
         """
         Remove a canvas edge.
 
@@ -508,7 +483,8 @@ class SpecManager:
 
         if "canvas" in data and data["canvas"] and "edges" in data["canvas"]:
             data["canvas"]["edges"] = [
-                e for e in data["canvas"]["edges"]
+                e
+                for e in data["canvas"]["edges"]
                 if not (e.get("source") == source and e.get("target") == target)
             ]
 
@@ -524,7 +500,7 @@ class SpecManager:
         code: str,
         outputs: List[str],
         description: Optional[str] = None,
-        modified_by: str = "claude"
+        modified_by: str = "claude",
     ) -> str:
         """
         Add a custom extractor function.
@@ -546,9 +522,7 @@ class SpecManager:
         try:
             compile(code, f"<custom:{name}>", "exec")
         except SyntaxError as e:
-            raise SpecValidationError(
-                f"Invalid Python syntax: {e.msg} at line {e.lineno}"
-            )
+            raise SpecValidationError(f"Invalid Python syntax: {e.msg} at line {e.lineno}")
 
         data = self.load_raw()
 
@@ -561,13 +535,9 @@ class SpecManager:
             "name": description or f"Custom: {name}",
             "type": "custom_function",
             "builtin": False,
-            "function": {
-                "name": name,
-                "module": "custom_extractors.dynamic",
-                "source_code": code
-            },
+            "function": {"name": name, "module": "custom_extractors.dynamic", "source_code": code},
             "outputs": [{"name": o, "metric": "custom"} for o in outputs],
-            "canvas_position": self._auto_position("extractor", data)
+            "canvas_position": self._auto_position("extractor", data),
         }
 
         data["extractors"].append(extractor)
@@ -580,7 +550,7 @@ class SpecManager:
         extractor_id: str,
         code: Optional[str] = None,
         outputs: Optional[List[str]] = None,
-        modified_by: str = "claude"
+        modified_by: str = "claude",
     ) -> None:
         """
         Update an existing custom function.
@@ -611,9 +581,7 @@ class SpecManager:
             try:
                 compile(code, f"<custom:{extractor_id}>", "exec")
             except SyntaxError as e:
-                raise SpecValidationError(
-                    f"Invalid Python syntax: {e.msg} at line {e.lineno}"
-                )
+                raise SpecValidationError(f"Invalid Python syntax: {e.msg} at line {e.lineno}")
             if "function" not in extractor:
                 extractor["function"] = {}
             extractor["function"]["source_code"] = code
@@ -672,7 +640,7 @@ class SpecManager:
             "design_variable": "dv",
             "extractor": "ext",
             "objective": "obj",
-            "constraint": "con"
+            "constraint": "con",
         }
         prefix = prefix_map.get(node_type, node_type[:3])
 
@@ -697,7 +665,7 @@ class SpecManager:
             "design_variable": "design_variables",
             "extractor": "extractors",
             "objective": "objectives",
-            "constraint": "constraints"
+            "constraint": "constraints",
         }
         return section_map.get(node_type, node_type + "s")
 
@@ -709,7 +677,7 @@ class SpecManager:
             "design_variable": 50,
             "extractor": 740,
             "objective": 1020,
-            "constraint": 1020
+            "constraint": 1020,
         }
 
         x = x_positions.get(node_type, 400)
@@ -729,11 +697,123 @@ class SpecManager:
 
         return {"x": x, "y": y}
 
+    # =========================================================================
+    # Intake Workflow Methods
+    # =========================================================================
+
+    def update_status(self, status: str, modified_by: str = "api") -> None:
+        """
+        Update the spec status field.
+
+        Args:
+            status: New status (draft, introspected, configured, validated, ready, running, completed, failed)
+            modified_by: Who/what is making the change
+        """
+        data = self.load_raw()
+        data["meta"]["status"] = status
+        self.save(data, modified_by)
+
+    def get_status(self) -> str:
+        """
+        Get the current spec status.
+
+        Returns:
+            Current status string
+        """
+        if not self.exists():
+            return "unknown"
+        data = self.load_raw()
+        return data.get("meta", {}).get("status", "draft")
+
+    def add_introspection(
+        self, introspection_data: Dict[str, Any], modified_by: str = "introspection"
+    ) -> None:
+        """
+        Add introspection data to the spec's model section.
+
+        Args:
+            introspection_data: Dict with timestamp, expressions, mass_kg, etc.
+            modified_by: Who/what is making the change
+        """
+        data = self.load_raw()
+
+        if "model" not in data:
+            data["model"] = {}
+
+        data["model"]["introspection"] = introspection_data
+        data["meta"]["status"] = "introspected"
+
+        self.save(data, modified_by)
+
+    def add_baseline(
+        self, baseline_data: Dict[str, Any], modified_by: str = "baseline_solve"
+    ) -> None:
+        """
+        Add baseline solve results to introspection data.
+
+        Args:
+            baseline_data: Dict with timestamp, solve_time_seconds, mass_kg, etc.
+            modified_by: Who/what is making the change
+        """
+        data = self.load_raw()
+
+        if "model" not in data:
+            data["model"] = {}
+        if "introspection" not in data["model"] or data["model"]["introspection"] is None:
+            data["model"]["introspection"] = {}
+
+        data["model"]["introspection"]["baseline"] = baseline_data
+
+        # Update status based on baseline success
+        if baseline_data.get("success", False):
+            data["meta"]["status"] = "validated"
+
+        self.save(data, modified_by)
+
+    def set_topic(self, topic: str, modified_by: str = "api") -> None:
+        """
+        Set the spec's topic field.
+
+        Args:
+            topic: Topic folder name
+            modified_by: Who/what is making the change
+        """
+        data = self.load_raw()
+        data["meta"]["topic"] = topic
+        self.save(data, modified_by)
+
+    def get_introspection(self) -> Optional[Dict[str, Any]]:
+        """
+        Get introspection data from spec.
+
+        Returns:
+            Introspection dict or None if not present
+        """
+        if not self.exists():
+            return None
+        data = self.load_raw()
+        return data.get("model", {}).get("introspection")
+
+    def get_design_candidates(self) -> List[Dict[str, Any]]:
+        """
+        Get expressions marked as design variable candidates.
+
+        Returns:
+            List of expression dicts where is_candidate=True
+        """
+        introspection = self.get_introspection()
+        if not introspection:
+            return []
+
+        expressions = introspection.get("expressions", [])
+        return [e for e in expressions if e.get("is_candidate", False)]
+
 
 # =========================================================================
 # Factory Function
 # =========================================================================
 
+
 def get_spec_manager(study_path: Union[str, Path]) -> SpecManager:
     """
     Get a SpecManager instance for a study.

atomizer-dashboard/frontend/src/App.tsx

@@ -9,6 +9,7 @@ import Analysis from './pages/Analysis';
 import Insights from './pages/Insights';
 import Results from './pages/Results';
 import CanvasView from './pages/CanvasView';
+import Studio from './pages/Studio';
 
 const queryClient = new QueryClient({
   defaultOptions: {
@@ -32,6 +33,10 @@ function App() {
             <Route path="canvas" element={<CanvasView />} />
             <Route path="canvas/*" element={<CanvasView />} />
 
+            {/* Studio - unified study creation environment */}
+            <Route path="studio" element={<Studio />} />
+            <Route path="studio/:draftId" element={<Studio />} />
+
             {/* Study pages - with sidebar layout */}
             <Route element={<MainLayout />}>
               <Route path="setup" element={<Setup />} />

atomizer-dashboard/frontend/src/api/intake.ts

@@ -0,0 +1,411 @@
+/**
+ * Intake API Client
+ *
+ * API client methods for the study intake workflow.
+ */
+
+import {
+  CreateInboxRequest,
+  CreateInboxResponse,
+  IntrospectRequest,
+  IntrospectResponse,
+  ListInboxResponse,
+  ListTopicsResponse,
+  InboxStudyDetail,
+  GenerateReadmeResponse,
+  FinalizeRequest,
+  FinalizeResponse,
+  UploadFilesResponse,
+} from '../types/intake';
+
+const API_BASE = '/api';
+
+/**
+ * Intake API client for study creation workflow.
+ */
+export const intakeApi = {
+  /**
+   * Create a new inbox study folder with initial spec.
+   */
+  async createInbox(request: CreateInboxRequest): Promise<CreateInboxResponse> {
+    const response = await fetch(`${API_BASE}/intake/create`, {
+      method: 'POST',
+      headers: { 'Content-Type': 'application/json' },
+      body: JSON.stringify(request),
+    });
+
+    if (!response.ok) {
+      const error = await response.json();
+      throw new Error(error.detail || 'Failed to create inbox study');
+    }
+
+    return response.json();
+  },
+
+  /**
+   * Run NX introspection on an inbox study.
+   */
+  async introspect(request: IntrospectRequest): Promise<IntrospectResponse> {
+    const response = await fetch(`${API_BASE}/intake/introspect`, {
+      method: 'POST',
+      headers: { 'Content-Type': 'application/json' },
+      body: JSON.stringify(request),
+    });
+
+    if (!response.ok) {
+      const error = await response.json();
+      throw new Error(error.detail || 'Introspection failed');
+    }
+
+    return response.json();
+  },
+
+  /**
+   * List all studies in the inbox.
+   */
+  async listInbox(): Promise<ListInboxResponse> {
+    const response = await fetch(`${API_BASE}/intake/list`);
+
+    if (!response.ok) {
+      throw new Error('Failed to fetch inbox studies');
+    }
+
+    return response.json();
+  },
+
+  /**
+   * List existing topic folders.
+   */
+  async listTopics(): Promise<ListTopicsResponse> {
+    const response = await fetch(`${API_BASE}/intake/topics`);
+
+    if (!response.ok) {
+      throw new Error('Failed to fetch topics');
+    }
+
+    return response.json();
+  },
+
+  /**
+   * Get detailed information about an inbox study.
+   */
+  async getInboxStudy(studyName: string): Promise<InboxStudyDetail> {
+    const response = await fetch(`${API_BASE}/intake/${encodeURIComponent(studyName)}`);
+
+    if (!response.ok) {
+      const error = await response.json();
+      throw new Error(error.detail || 'Failed to fetch inbox study');
+    }
+
+    return response.json();
+  },
+
+  /**
+   * Delete an inbox study.
+   */
+  async deleteInboxStudy(studyName: string): Promise<{ success: boolean; deleted: string }> {
+    const response = await fetch(`${API_BASE}/intake/${encodeURIComponent(studyName)}`, {
+      method: 'DELETE',
+    });
+
+    if (!response.ok) {
+      const error = await response.json();
+      throw new Error(error.detail || 'Failed to delete inbox study');
+    }
+
+    return response.json();
+  },
+
+  /**
+   * Generate README for an inbox study using Claude AI.
+   */
+  async generateReadme(studyName: string): Promise<GenerateReadmeResponse> {
+    const response = await fetch(
+      `${API_BASE}/intake/${encodeURIComponent(studyName)}/readme`,
+      { method: 'POST' }
+    );
+
+    if (!response.ok) {
+      const error = await response.json();
+      throw new Error(error.detail || 'README generation failed');
+    }
+
+    return response.json();
+  },
+
+  /**
+   * Finalize an inbox study and move to studies directory.
+   */
+  async finalize(studyName: string, request: FinalizeRequest): Promise<FinalizeResponse> {
+    const response = await fetch(
+      `${API_BASE}/intake/${encodeURIComponent(studyName)}/finalize`,
+      {
+        method: 'POST',
+        headers: { 'Content-Type': 'application/json' },
+        body: JSON.stringify(request),
+      }
+    );
+
+    if (!response.ok) {
+      const error = await response.json();
+      throw new Error(error.detail || 'Finalization failed');
+    }
+
+    return response.json();
+  },
+
+  /**
+   * Upload model files to an inbox study.
+   */
+  async uploadFiles(studyName: string, files: File[]): Promise<UploadFilesResponse> {
+    const formData = new FormData();
+    files.forEach((file) => {
+      formData.append('files', file);
+    });
+
+    const response = await fetch(
+      `${API_BASE}/intake/${encodeURIComponent(studyName)}/upload`,
+      {
+        method: 'POST',
+        body: formData,
+      }
+    );
+
+    if (!response.ok) {
+      const error = await response.json();
+      throw new Error(error.detail || 'File upload failed');
+    }
+
+    return response.json();
+  },
+
+  /**
+   * Upload context files to an inbox study.
+   * Context files help Claude understand optimization goals.
+   */
+  async uploadContextFiles(studyName: string, files: File[]): Promise<UploadFilesResponse> {
+    const formData = new FormData();
+    files.forEach((file) => {
+      formData.append('files', file);
+    });
+
+    const response = await fetch(
+      `${API_BASE}/intake/${encodeURIComponent(studyName)}/context`,
+      {
+        method: 'POST',
+        body: formData,
+      }
+    );
+
+    if (!response.ok) {
+      const error = await response.json();
+      throw new Error(error.detail || 'Context file upload failed');
+    }
+
+    return response.json();
+  },
+
+  /**
+   * List context files for an inbox study.
+   */
+  async listContextFiles(studyName: string): Promise<{
+    study_name: string;
+    context_files: Array<{ name: string; path: string; size: number; extension: string }>;
+    total: number;
+  }> {
+    const response = await fetch(
+      `${API_BASE}/intake/${encodeURIComponent(studyName)}/context`
+    );
+
+    if (!response.ok) {
+      throw new Error('Failed to list context files');
+    }
+
+    return response.json();
+  },
+
+  /**
+   * Delete a context file from an inbox study.
+   */
+  async deleteContextFile(studyName: string, filename: string): Promise<{ success: boolean; deleted: string }> {
+    const response = await fetch(
+      `${API_BASE}/intake/${encodeURIComponent(studyName)}/context/${encodeURIComponent(filename)}`,
+      { method: 'DELETE' }
+    );
+
+    if (!response.ok) {
+      const error = await response.json();
+      throw new Error(error.detail || 'Failed to delete context file');
+    }
+
+    return response.json();
+  },
+
+  /**
+   * Create design variables from selected expressions.
+   */
+  async createDesignVariables(
+    studyName: string, 
+    expressionNames: string[],
+    options?: { autoBounds?: boolean; boundFactor?: number }
+  ): Promise<{
+    success: boolean;
+    study_name: string;
+    created: Array<{
+      id: string;
+      name: string;
+      expression_name: string;
+      bounds_min: number;
+      bounds_max: number;
+      baseline: number;
+      units: string | null;
+    }>;
+    total_created: number;
+  }> {
+    const response = await fetch(
+      `${API_BASE}/intake/${encodeURIComponent(studyName)}/design-variables`,
+      {
+        method: 'POST',
+        headers: { 'Content-Type': 'application/json' },
+        body: JSON.stringify({
+          expression_names: expressionNames,
+          auto_bounds: options?.autoBounds ?? true,
+          bound_factor: options?.boundFactor ?? 0.5,
+        }),
+      }
+    );
+
+    if (!response.ok) {
+      const error = await response.json();
+      throw new Error(error.detail || 'Failed to create design variables');
+    }
+
+    return response.json();
+  },
+
+  // ===========================================================================
+  // Studio Endpoints (Atomizer Studio - Unified Creation Environment)
+  // ===========================================================================
+
+  /**
+   * Create an anonymous draft study for Studio workflow.
+   * Returns a temporary draft_id that can be renamed during finalization.
+   */
+  async createDraft(): Promise<{
+    success: boolean;
+    draft_id: string;
+    inbox_path: string;
+    spec_path: string;
+    status: string;
+  }> {
+    const response = await fetch(`${API_BASE}/intake/draft`, {
+      method: 'POST',
+    });
+
+    if (!response.ok) {
+      const error = await response.json();
+      throw new Error(error.detail || 'Failed to create draft');
+    }
+
+    return response.json();
+  },
+
+  /**
+   * Get extracted text content from context files.
+   * Used for AI context injection.
+   */
+  async getContextContent(studyName: string): Promise<{
+    success: boolean;
+    study_name: string;
+    content: string;
+    files_read: Array<{
+      name: string;
+      extension: string;
+      size: number;
+      status: string;
+      characters?: number;
+      error?: string;
+    }>;
+    total_characters: number;
+  }> {
+    const response = await fetch(
+      `${API_BASE}/intake/${encodeURIComponent(studyName)}/context/content`
+    );
+
+    if (!response.ok) {
+      const error = await response.json();
+      throw new Error(error.detail || 'Failed to get context content');
+    }
+
+    return response.json();
+  },
+
+  /**
+   * Finalize a Studio draft with rename support.
+   * Enhanced version that supports renaming draft_xxx to proper names.
+   */
+  async finalizeStudio(
+    studyName: string,
+    request: {
+      topic: string;
+      newName?: string;
+      runBaseline?: boolean;
+    }
+  ): Promise<{
+    success: boolean;
+    original_name: string;
+    final_name: string;
+    final_path: string;
+    status: string;
+    baseline_success: boolean | null;
+    readme_generated: boolean;
+  }> {
+    const response = await fetch(
+      `${API_BASE}/intake/${encodeURIComponent(studyName)}/finalize/studio`,
+      {
+        method: 'POST',
+        headers: { 'Content-Type': 'application/json' },
+        body: JSON.stringify({
+          topic: request.topic,
+          new_name: request.newName,
+          run_baseline: request.runBaseline ?? false,
+        }),
+      }
+    );
+
+    if (!response.ok) {
+      const error = await response.json();
+      throw new Error(error.detail || 'Studio finalization failed');
+    }
+
+    return response.json();
+  },
+
+  /**
+   * Get complete draft information for Studio UI.
+   * Convenience endpoint that returns everything the Studio needs.
+   */
+  async getStudioDraft(studyName: string): Promise<{
+    success: boolean;
+    draft_id: string;
+    spec: Record<string, unknown>;
+    model_files: string[];
+    context_files: string[];
+    introspection_available: boolean;
+    design_variable_count: number;
+    objective_count: number;
+  }> {
+    const response = await fetch(
+      `${API_BASE}/intake/${encodeURIComponent(studyName)}/studio`
+    );
+
+    if (!response.ok) {
+      const error = await response.json();
+      throw new Error(error.detail || 'Failed to get studio draft');
+    }
+
+    return response.json();
+  },
+};
+
+export default intakeApi;

atomizer-dashboard/frontend/src/components/canvas/SpecRenderer.tsx

@@ -235,6 +235,7 @@ function SpecRendererInner({
     clearSelection,
     updateNodePosition,
     addNode,
+    updateNode,
     addEdge,
     removeEdge,
     removeNode,
@@ -272,6 +273,15 @@ function SpecRendererInner({
   const [showResults, setShowResults] = useState(false);
   const [validationStatus, setValidationStatus] = useState<'valid' | 'invalid' | 'unchecked'>('unchecked');
 
+  // When connecting Extractor → Objective/Constraint and the extractor has multiple outputs,
+  // we prompt the user to choose which output_name to use.
+  const [pendingOutputSelect, setPendingOutputSelect] = useState<null | {
+    sourceId: string;
+    targetId: string;
+    outputNames: string[];
+    selected: string;
+  }>(null);
+
   // Build trial history for sparklines (extract objective values from recent trials)
   const trialHistory = useMemo(() => {
     const history: Record<string, number[]> = {};
@@ -412,6 +422,89 @@ function SpecRendererInner({
     }
   }, [studyId, loadSpec, onStudyChange]);
 
+  // -------------------------------------------------------------------------
+  // Option A: Edge projection sync (source fields are truth)
+  // Keep canvas edges in sync when user edits objective/constraint source in panels.
+  // We only enforce Extractor -> Objective/Constraint wiring edges here.
+  // -------------------------------------------------------------------------
+
+  const isEdgeSyncingRef = useRef(false);
+
+  useEffect(() => {
+    if (!spec || !studyId) return;
+    if (isEdgeSyncingRef.current) return;
+
+    const current = spec.canvas?.edges || [];
+
+    // Compute desired extractor->objective/constraint edges from source fields
+    const desiredPairs = new Set<string>();
+
+    for (const obj of spec.objectives || []) {
+      const extractorId = obj.source?.extractor_id;
+      const outputName = obj.source?.output_name;
+      if (extractorId && outputName && extractorId !== '__UNSET__' && outputName !== '__UNSET__') {
+        desiredPairs.add(`${extractorId}__${obj.id}`);
+      }
+    }
+
+    for (const con of spec.constraints || []) {
+      const extractorId = con.source?.extractor_id;
+      const outputName = con.source?.output_name;
+      if (extractorId && outputName && extractorId !== '__UNSET__' && outputName !== '__UNSET__') {
+        desiredPairs.add(`${extractorId}__${con.id}`);
+      }
+    }
+
+    // Identify current wiring edges (ext_* -> obj_*/con_*)
+    const currentWiringPairs = new Set<string>();
+    for (const e of current) {
+      if (e.source?.startsWith('ext_') && (e.target?.startsWith('obj_') || e.target?.startsWith('con_'))) {
+        currentWiringPairs.add(`${e.source}__${e.target}`);
+      }
+    }
+
+    // Determine adds/removes
+    const toAdd: Array<{ source: string; target: string }> = [];
+    for (const key of desiredPairs) {
+      if (!currentWiringPairs.has(key)) {
+        const [source, target] = key.split('__');
+        toAdd.push({ source, target });
+      }
+    }
+
+    const toRemove: Array<{ source: string; target: string }> = [];
+    for (const key of currentWiringPairs) {
+      if (!desiredPairs.has(key)) {
+        const [source, target] = key.split('__');
+        toRemove.push({ source, target });
+      }
+    }
+
+    if (toAdd.length === 0 && toRemove.length === 0) return;
+
+    isEdgeSyncingRef.current = true;
+
+    (async () => {
+      try {
+        // Remove stale edges first
+        for (const e of toRemove) {
+          await removeEdge(e.source, e.target);
+        }
+        // Add missing edges
+        for (const e of toAdd) {
+          await addEdge(e.source, e.target);
+        }
+      } catch (err) {
+        console.error('[SpecRenderer] Edge projection sync failed:', err);
+      } finally {
+        // Small delay avoids re-entrancy storms when backend broadcasts updates
+        setTimeout(() => {
+          isEdgeSyncingRef.current = false;
+        }, 250);
+      }
+    })();
+  }, [spec, studyId, addEdge, removeEdge]);
+
   // Convert spec to ReactFlow nodes
   const nodes = useMemo(() => {
     const baseNodes = specToNodes(spec);
@@ -521,34 +614,111 @@ function SpecRendererInner({
     (changes: EdgeChange[]) => {
       if (!editable) return;
 
+      const classify = (id: string): string => {
+        if (id === 'model' || id === 'solver' || id === 'algorithm' || id === 'surrogate') return id;
+        const prefix = id.split('_')[0];
+        if (prefix === 'dv') return 'designVar';
+        if (prefix === 'ext') return 'extractor';
+        if (prefix === 'obj') return 'objective';
+        if (prefix === 'con') return 'constraint';
+        return 'unknown';
+      };
+
       for (const change of changes) {
         if (change.type === 'remove') {
           // Find the edge being removed
           const edge = edges.find((e) => e.id === change.id);
-          if (edge) {
-            removeEdge(edge.source, edge.target).catch((err) => {
-              console.error('Failed to remove edge:', err);
+          if (!edge) continue;
+
+          const sourceType = classify(edge.source);
+          const targetType = classify(edge.target);
+
+          // First remove the visual edge
+          removeEdge(edge.source, edge.target).catch((err) => {
+            console.error('Failed to remove edge:', err);
+            setError(err.message);
+          });
+
+          // Option A truth model: if we removed Extractor -> Objective/Constraint,
+          // clear the target's source to avoid stale runnable config.
+          if (sourceType === 'extractor' && (targetType === 'objective' || targetType === 'constraint')) {
+            updateNode(edge.target, {
+              // Objective/constraint.source is required by schema.
+              // Use explicit UNSET placeholders so validation can catch it
+              // without risking accidental execution.
+              source: { extractor_id: '__UNSET__', output_name: '__UNSET__' },
+            }).catch((err) => {
+              console.error('Failed to clear source on node:', err);
               setError(err.message);
             });
           }
         }
       }
     },
-    [editable, edges, removeEdge, setError]
+    [editable, edges, removeEdge, setError, updateNode]
   );
 
   // Handle new connections
   const onConnect = useCallback(
-    (connection: Connection) => {
+    async (connection: Connection) => {
       if (!editable) return;
       if (!connection.source || !connection.target) return;
 
-      addEdge(connection.source, connection.target).catch((err) => {
-        console.error('Failed to add edge:', err);
-        setError(err.message);
-      });
+      const sourceId = connection.source;
+      const targetId = connection.target;
+
+      // Helper: classify nodes by ID (synthetic vs spec-backed)
+      const classify = (id: string): string => {
+        if (id === 'model' || id === 'solver' || id === 'algorithm' || id === 'surrogate') return id;
+        const prefix = id.split('_')[0];
+        if (prefix === 'dv') return 'designVar';
+        if (prefix === 'ext') return 'extractor';
+        if (prefix === 'obj') return 'objective';
+        if (prefix === 'con') return 'constraint';
+        return 'unknown';
+      };
+
+      const sourceType = classify(sourceId);
+      const targetType = classify(targetId);
+
+      try {
+        // Option A truth model: objective/constraint source is the real linkage.
+        // When user connects Extractor -> Objective/Constraint, we must choose an output_name.
+        if (spec && sourceType === 'extractor' && (targetType === 'objective' || targetType === 'constraint')) {
+          const ext = spec.extractors.find((e) => e.id === sourceId);
+          const outputNames = (ext?.outputs || []).map((o) => o.name).filter(Boolean);
+
+          // If extractor has multiple outputs, prompt the user.
+          if (outputNames.length > 1) {
+            const preferred = outputNames.includes('value') ? 'value' : outputNames[0];
+            setPendingOutputSelect({
+              sourceId,
+              targetId,
+              outputNames,
+              selected: preferred,
+            });
+            return;
+          }
+
+          // Single (or zero) output: choose deterministically.
+          const outputName = outputNames[0] || 'value';
+
+          // Persist edge + runnable source.
+          await addEdge(sourceId, targetId);
+          await updateNode(targetId, {
+            source: { extractor_id: sourceId, output_name: outputName },
+          });
+          return;
+        }
+
+        // Default: just persist the visual edge.
+        await addEdge(sourceId, targetId);
+      } catch (err) {
+        console.error('Failed to add connection:', err);
+        setError(err instanceof Error ? err.message : 'Failed to add connection');
+      }
     },
-    [editable, addEdge, setError]
+    [editable, addEdge, setError, spec, updateNode, setPendingOutputSelect]
   );
 
   // Handle node clicks for selection
@@ -687,6 +857,34 @@ function SpecRendererInner({
     [editable, addNode, selectNode, setError, localNodes]
   );
 
+  // -------------------------------------------------------------------------
+  // Output selection modal handlers (Extractor → Objective/Constraint)
+  // -------------------------------------------------------------------------
+
+  const confirmOutputSelection = useCallback(async () => {
+    if (!pendingOutputSelect) return;
+
+    const { sourceId, targetId, selected } = pendingOutputSelect;
+
+    try {
+      // Persist edge + runnable source wiring
+      await addEdge(sourceId, targetId);
+      await updateNode(targetId, {
+        source: { extractor_id: sourceId, output_name: selected },
+      });
+    } catch (err) {
+      console.error('Failed to apply output selection:', err);
+      setError(err instanceof Error ? err.message : 'Failed to apply output selection');
+    } finally {
+      setPendingOutputSelect(null);
+    }
+  }, [pendingOutputSelect, addEdge, updateNode, setError]);
+
+  const cancelOutputSelection = useCallback(() => {
+    // User canceled: do not create the edge, do not update source
+    setPendingOutputSelect(null);
+  }, []);
+
   // Loading state
   if (showLoadingOverlay && isLoading && !spec) {
     return (
@@ -769,6 +967,55 @@ function SpecRendererInner({
         </div>
       )}
 
+      {/* Output selection modal (Extractor → Objective/Constraint) */}
+      {pendingOutputSelect && (
+        <div className="absolute inset-0 z-30 flex items-center justify-center bg-black/60 backdrop-blur-sm">
+          <div className="w-[520px] max-w-[90vw] bg-dark-850 border border-dark-600 rounded-xl shadow-2xl p-5">
+            <h3 className="text-white font-semibold text-lg">Select extractor output</h3>
+            <p className="text-sm text-dark-300 mt-1">
+              This extractor provides multiple outputs. Choose which output the target should use.
+            </p>
+
+            <div className="mt-4">
+              <label className="block text-sm font-medium text-dark-300 mb-1">Output</label>
+              <select
+                value={pendingOutputSelect.selected}
+                onChange={(e) =>
+                  setPendingOutputSelect((prev) =>
+                    prev ? { ...prev, selected: e.target.value } : prev
+                  )
+                }
+                className="w-full px-3 py-2 bg-dark-800 border border-dark-600 text-white rounded-lg focus:border-primary-500 focus:outline-none transition-colors"
+              >
+                {pendingOutputSelect.outputNames.map((name) => (
+                  <option key={name} value={name}>
+                    {name}
+                  </option>
+                ))}
+              </select>
+              <p className="text-xs text-dark-500 mt-2">
+                Tip: we default to <span className="text-dark-300 font-medium">value</span> when available.
+              </p>
+            </div>
+
+            <div className="mt-5 flex justify-end gap-2">
+              <button
+                onClick={cancelOutputSelection}
+                className="px-4 py-2 bg-dark-700 text-dark-200 hover:bg-dark-600 rounded-lg border border-dark-600 transition-colors"
+              >
+                Cancel
+              </button>
+              <button
+                onClick={confirmOutputSelection}
+                className="px-4 py-2 bg-primary-600 text-white hover:bg-primary-500 rounded-lg border border-primary-500 transition-colors"
+              >
+                Connect
+              </button>
+            </div>
+          </div>
+        </div>
+      )}
+
       <ReactFlow
         nodes={localNodes}
         edges={edges}
@@ -777,6 +1024,8 @@ function SpecRendererInner({
         onConnect={onConnect}
         onInit={(instance) => {
           reactFlowInstance.current = instance;
+          // Auto-fit view on init with padding
+          setTimeout(() => instance.fitView({ padding: 0.2, duration: 300 }), 100);
         }}
         onDragOver={onDragOver}
         onDrop={onDrop}
@@ -785,6 +1034,7 @@ function SpecRendererInner({
         onPaneClick={onPaneClick}
         nodeTypes={nodeTypes}
         fitView
+        fitViewOptions={{ padding: 0.2, includeHiddenNodes: false }}
         deleteKeyCode={null} // We handle delete ourselves
         nodesDraggable={editable}
         nodesConnectable={editable}

atomizer-dashboard/frontend/src/components/canvas/panels/NodeConfigPanelV2.tsx

@@ -820,6 +820,34 @@ interface ObjectiveNodeConfigProps {
 }
 
 function ObjectiveNodeConfig({ node, onChange }: ObjectiveNodeConfigProps) {
+  const spec = useSpec();
+  const extractors = spec?.extractors || [];
+
+  const currentExtractorId = node.source?.extractor_id || '__UNSET__';
+  const currentOutputName = node.source?.output_name || '__UNSET__';
+
+  const selectedExtractor = extractors.find((e) => e.id === currentExtractorId);
+  const outputOptions = selectedExtractor?.outputs?.map((o) => o.name) || [];
+
+  const handleExtractorChange = (extractorId: string) => {
+    // Reset output_name to a sensible default when extractor changes
+    const ext = extractors.find((e) => e.id === extractorId);
+    const outs = ext?.outputs?.map((o) => o.name) || [];
+    const preferred = outs.includes('value') ? 'value' : outs[0] || '__UNSET__';
+
+    onChange('source', {
+      extractor_id: extractorId,
+      output_name: preferred,
+    });
+  };
+
+  const handleOutputChange = (outputName: string) => {
+    onChange('source', {
+      extractor_id: currentExtractorId,
+      output_name: outputName,
+    });
+  };
+
   return (
     <>
       <div>
@@ -831,6 +859,45 @@ function ObjectiveNodeConfig({ node, onChange }: ObjectiveNodeConfigProps) {
           className={inputClass}
         />
       </div>
+
+      <div>
+        <label className={labelClass}>Source Extractor</label>
+        <select
+          value={currentExtractorId}
+          onChange={(e) => handleExtractorChange(e.target.value)}
+          className={selectClass}
+        >
+          <option value="__UNSET__">(not connected)</option>
+          {extractors.map((ext) => (
+            <option key={ext.id} value={ext.id}>
+              {ext.id} — {ext.name}
+            </option>
+          ))}
+        </select>
+      </div>
+
+      <div>
+        <label className={labelClass}>Source Output</label>
+        <select
+          value={currentOutputName}
+          onChange={(e) => handleOutputChange(e.target.value)}
+          className={selectClass}
+          disabled={currentExtractorId === '__UNSET__'}
+        >
+          {currentExtractorId === '__UNSET__' ? (
+            <option value="__UNSET__">(select an extractor)</option>
+          ) : (
+            outputOptions.map((name) => (
+              <option key={name} value={name}>
+                {name}
+              </option>
+            ))
+          )}
+        </select>
+        <p className="text-xs text-dark-500 mt-1">
+          This drives execution. Canvas wires are just a visual check.
+        </p>
+      </div>
       
       <div>
         <label className={labelClass}>Direction</label>
@@ -877,6 +944,33 @@ interface ConstraintNodeConfigProps {
 }
 
 function ConstraintNodeConfig({ node, onChange }: ConstraintNodeConfigProps) {
+  const spec = useSpec();
+  const extractors = spec?.extractors || [];
+
+  const currentExtractorId = node.source?.extractor_id || '__UNSET__';
+  const currentOutputName = node.source?.output_name || '__UNSET__';
+
+  const selectedExtractor = extractors.find((e) => e.id === currentExtractorId);
+  const outputOptions = selectedExtractor?.outputs?.map((o) => o.name) || [];
+
+  const handleExtractorChange = (extractorId: string) => {
+    const ext = extractors.find((e) => e.id === extractorId);
+    const outs = ext?.outputs?.map((o) => o.name) || [];
+    const preferred = outs.includes('value') ? 'value' : outs[0] || '__UNSET__';
+
+    onChange('source', {
+      extractor_id: extractorId,
+      output_name: preferred,
+    });
+  };
+
+  const handleOutputChange = (outputName: string) => {
+    onChange('source', {
+      extractor_id: currentExtractorId,
+      output_name: outputName,
+    });
+  };
+
   return (
     <>
       <div>
@@ -888,6 +982,45 @@ function ConstraintNodeConfig({ node, onChange }: ConstraintNodeConfigProps) {
           className={inputClass}
         />
       </div>
+
+      <div>
+        <label className={labelClass}>Source Extractor</label>
+        <select
+          value={currentExtractorId}
+          onChange={(e) => handleExtractorChange(e.target.value)}
+          className={selectClass}
+        >
+          <option value="__UNSET__">(not connected)</option>
+          {extractors.map((ext) => (
+            <option key={ext.id} value={ext.id}>
+              {ext.id} — {ext.name}
+            </option>
+          ))}
+        </select>
+      </div>
+
+      <div>
+        <label className={labelClass}>Source Output</label>
+        <select
+          value={currentOutputName}
+          onChange={(e) => handleOutputChange(e.target.value)}
+          className={selectClass}
+          disabled={currentExtractorId === '__UNSET__'}
+        >
+          {currentExtractorId === '__UNSET__' ? (
+            <option value="__UNSET__">(select an extractor)</option>
+          ) : (
+            outputOptions.map((name) => (
+              <option key={name} value={name}>
+                {name}
+              </option>
+            ))
+          )}
+        </select>
+        <p className="text-xs text-dark-500 mt-1">
+          This drives execution. Canvas wires are just a visual check.
+        </p>
+      </div>
       
       <div className="grid grid-cols-2 gap-2">
         <div>
@@ -897,24 +1030,37 @@ function ConstraintNodeConfig({ node, onChange }: ConstraintNodeConfigProps) {
             onChange={(e) => onChange('type', e.target.value)}
             className={selectClass}
           >
-            <option value="less_than">&lt; Less than</option>
-            <option value="less_equal">&lt;= Less or equal</option>
-            <option value="greater_than">&gt; Greater than</option>
-            <option value="greater_equal">&gt;= Greater or equal</option>
-            <option value="equal">= Equal</option>
+            <option value="hard">Hard</option>
+            <option value="soft">Soft</option>
           </select>
+          <p className="text-xs text-dark-500 mt-1">Spec type (hard/soft). Operator is set below.</p>
         </div>
         <div>
-          <label className={labelClass}>Threshold</label>
-          <input
-            type="number"
-            value={node.threshold}
-            onChange={(e) => onChange('threshold', parseFloat(e.target.value))}
-            className={inputClass}
-          />
+          <label className={labelClass}>Operator</label>
+          <select
+            value={node.operator}
+            onChange={(e) => onChange('operator', e.target.value)}
+            className={selectClass}
+          >
+            <option value="<=">&lt;=</option>
+            <option value="<">&lt;</option>
+            <option value=">=">&gt;=</option>
+            <option value=">">&gt;</option>
+            <option value="==">==</option>
+          </select>
         </div>
       </div>
 
+      <div>
+        <label className={labelClass}>Threshold</label>
+        <input
+          type="number"
+          value={node.threshold}
+          onChange={(e) => onChange('threshold', parseFloat(e.target.value))}
+          className={inputClass}
+        />
+      </div>
+
     </>
   );
 }

atomizer-dashboard/frontend/src/components/devloop/DevLoopPanel.tsx

@@ -0,0 +1,342 @@
+/**
+ * DevLoopPanel - Control panel for closed-loop development
+ * 
+ * Features:
+ * - Start/stop development cycles
+ * - Real-time phase monitoring
+ * - Iteration history view
+ * - Test result visualization
+ */
+
+import { useState, useEffect, useCallback } from 'react';
+import {
+  PlayCircle,
+  StopCircle,
+  RefreshCw,
+  CheckCircle,
+  XCircle,
+  AlertCircle,
+  Clock,
+  ListChecks,
+  Zap,
+  ChevronDown,
+  ChevronRight,
+} from 'lucide-react';
+import useWebSocket from 'react-use-websocket';
+
+interface LoopState {
+  phase: string;
+  iteration: number;
+  current_task: string | null;
+  last_update: string;
+}
+
+interface CycleResult {
+  objective: string;
+  status: string;
+  iterations: number;
+  duration_seconds: number;
+}
+
+interface TestResult {
+  scenario_id: string;
+  scenario_name: string;
+  passed: boolean;
+  duration_ms: number;
+  error?: string;
+}
+
+const PHASE_COLORS: Record<string, string> = {
+  idle: 'bg-gray-500',
+  planning: 'bg-blue-500',
+  implementing: 'bg-purple-500',
+  testing: 'bg-yellow-500',
+  analyzing: 'bg-orange-500',
+  fixing: 'bg-red-500',
+  verifying: 'bg-green-500',
+};
+
+const PHASE_ICONS: Record<string, React.ReactNode> = {
+  idle: <Clock className="w-4 h-4" />,
+  planning: <ListChecks className="w-4 h-4" />,
+  implementing: <Zap className="w-4 h-4" />,
+  testing: <RefreshCw className="w-4 h-4 animate-spin" />,
+  analyzing: <AlertCircle className="w-4 h-4" />,
+  fixing: <Zap className="w-4 h-4" />,
+  verifying: <CheckCircle className="w-4 h-4" />,
+};
+
+export function DevLoopPanel() {
+  const [state, setState] = useState<LoopState>({
+    phase: 'idle',
+    iteration: 0,
+    current_task: null,
+    last_update: new Date().toISOString(),
+  });
+  const [objective, setObjective] = useState('');
+  const [history, setHistory] = useState<CycleResult[]>([]);
+  const [testResults, setTestResults] = useState<TestResult[]>([]);
+  const [expanded, setExpanded] = useState(true);
+  const [isStarting, setIsStarting] = useState(false);
+
+  // WebSocket connection for real-time updates
+  const { lastJsonMessage, readyState } = useWebSocket(
+    'ws://localhost:8000/api/devloop/ws',
+    {
+      shouldReconnect: () => true,
+      reconnectInterval: 3000,
+    }
+  );
+
+  // Handle WebSocket messages
+  useEffect(() => {
+    if (!lastJsonMessage) return;
+
+    const msg = lastJsonMessage as any;
+
+    switch (msg.type) {
+      case 'connection_ack':
+      case 'state_update':
+      case 'state':
+        if (msg.state) {
+          setState(msg.state);
+        }
+        break;
+      case 'cycle_complete':
+        setHistory(prev => [msg.result, ...prev].slice(0, 10));
+        setIsStarting(false);
+        break;
+      case 'cycle_error':
+        console.error('DevLoop error:', msg.error);
+        setIsStarting(false);
+        break;
+      case 'test_progress':
+        if (msg.result) {
+          setTestResults(prev => [...prev, msg.result]);
+        }
+        break;
+    }
+  }, [lastJsonMessage]);
+
+  // Start a development cycle
+  const startCycle = useCallback(async () => {
+    if (!objective.trim()) return;
+
+    setIsStarting(true);
+    setTestResults([]);
+
+    try {
+      const response = await fetch('http://localhost:8000/api/devloop/start', {
+        method: 'POST',
+        headers: { 'Content-Type': 'application/json' },
+        body: JSON.stringify({
+          objective: objective.trim(),
+          max_iterations: 10,
+        }),
+      });
+
+      if (!response.ok) {
+        const error = await response.json();
+        console.error('Failed to start cycle:', error);
+        setIsStarting(false);
+      }
+    } catch (error) {
+      console.error('Failed to start cycle:', error);
+      setIsStarting(false);
+    }
+  }, [objective]);
+
+  // Stop the current cycle
+  const stopCycle = useCallback(async () => {
+    try {
+      await fetch('http://localhost:8000/api/devloop/stop', {
+        method: 'POST',
+      });
+    } catch (error) {
+      console.error('Failed to stop cycle:', error);
+    }
+  }, []);
+
+  // Quick start: Create support_arm study
+  const quickStartSupportArm = useCallback(() => {
+    setObjective('Create support_arm optimization study with 5 design variables (center_space, arm_thk, arm_angle, end_thk, base_thk), objectives (minimize displacement, minimize mass), and stress constraint (< 30% yield)');
+    // Auto-start after a brief delay
+    setTimeout(() => {
+      startCycle();
+    }, 500);
+  }, [startCycle]);
+
+  const isActive = state.phase !== 'idle';
+  const wsConnected = readyState === WebSocket.OPEN;
+
+  return (
+    <div className="bg-gray-900 rounded-lg border border-gray-700 overflow-hidden">
+      {/* Header */}
+      <div
+        className="flex items-center justify-between px-4 py-3 bg-gray-800 cursor-pointer"
+        onClick={() => setExpanded(!expanded)}
+      >
+        <div className="flex items-center gap-2">
+          {expanded ? (
+            <ChevronDown className="w-4 h-4 text-gray-400" />
+          ) : (
+            <ChevronRight className="w-4 h-4 text-gray-400" />
+          )}
+          <RefreshCw className="w-5 h-5 text-blue-400" />
+          <h3 className="font-semibold text-white">DevLoop Control</h3>
+        </div>
+        
+        {/* Status indicator */}
+        <div className="flex items-center gap-2">
+          <div
+            className={`w-2 h-2 rounded-full ${
+              wsConnected ? 'bg-green-500' : 'bg-red-500'
+            }`}
+          />
+          <span className={`px-2 py-1 text-xs rounded ${PHASE_COLORS[state.phase]} text-white`}>
+            {state.phase.toUpperCase()}
+          </span>
+        </div>
+      </div>
+
+      {expanded && (
+        <div className="p-4 space-y-4">
+          {/* Objective Input */}
+          <div>
+            <label className="block text-sm text-gray-400 mb-1">
+              Development Objective
+            </label>
+            <textarea
+              value={objective}
+              onChange={(e) => setObjective(e.target.value)}
+              placeholder="e.g., Create support_arm optimization study..."
+              className="w-full px-3 py-2 bg-gray-800 border border-gray-600 rounded text-white text-sm resize-none h-20"
+              disabled={isActive}
+            />
+          </div>
+
+          {/* Quick Actions */}
+          <div className="flex gap-2">
+            <button
+              onClick={quickStartSupportArm}
+              disabled={isActive}
+              className="px-3 py-1.5 bg-purple-600 hover:bg-purple-700 disabled:bg-gray-600 text-white text-sm rounded flex items-center gap-1"
+            >
+              <Zap className="w-4 h-4" />
+              Quick: support_arm
+            </button>
+          </div>
+
+          {/* Control Buttons */}
+          <div className="flex gap-2">
+            {!isActive ? (
+              <button
+                onClick={startCycle}
+                disabled={!objective.trim() || isStarting}
+                className="flex-1 px-4 py-2 bg-green-600 hover:bg-green-700 disabled:bg-gray-600 text-white rounded flex items-center justify-center gap-2"
+              >
+                <PlayCircle className="w-5 h-5" />
+                {isStarting ? 'Starting...' : 'Start Cycle'}
+              </button>
+            ) : (
+              <button
+                onClick={stopCycle}
+                className="flex-1 px-4 py-2 bg-red-600 hover:bg-red-700 text-white rounded flex items-center justify-center gap-2"
+              >
+                <StopCircle className="w-5 h-5" />
+                Stop Cycle
+              </button>
+            )}
+          </div>
+
+          {/* Current Phase Progress */}
+          {isActive && (
+            <div className="bg-gray-800 rounded p-3 space-y-2">
+              <div className="flex items-center gap-2">
+                {PHASE_ICONS[state.phase]}
+                <span className="text-sm text-white font-medium">
+                  {state.phase.charAt(0).toUpperCase() + state.phase.slice(1)}
+                </span>
+                <span className="text-xs text-gray-400">
+                  Iteration {state.iteration + 1}
+                </span>
+              </div>
+              {state.current_task && (
+                <p className="text-xs text-gray-400 truncate">
+                  {state.current_task}
+                </p>
+              )}
+            </div>
+          )}
+
+          {/* Test Results */}
+          {testResults.length > 0 && (
+            <div className="bg-gray-800 rounded p-3">
+              <h4 className="text-sm font-medium text-white mb-2">Test Results</h4>
+              <div className="space-y-1 max-h-32 overflow-y-auto">
+                {testResults.map((test, i) => (
+                  <div
+                    key={`${test.scenario_id}-${i}`}
+                    className="flex items-center gap-2 text-xs"
+                  >
+                    {test.passed ? (
+                      <CheckCircle className="w-3 h-3 text-green-500" />
+                    ) : (
+                      <XCircle className="w-3 h-3 text-red-500" />
+                    )}
+                    <span className="text-gray-300 truncate flex-1">
+                      {test.scenario_name}
+                    </span>
+                    <span className="text-gray-500">
+                      {test.duration_ms.toFixed(0)}ms
+                    </span>
+                  </div>
+                ))}
+              </div>
+            </div>
+          )}
+
+          {/* History */}
+          {history.length > 0 && (
+            <div className="bg-gray-800 rounded p-3">
+              <h4 className="text-sm font-medium text-white mb-2">Recent Cycles</h4>
+              <div className="space-y-2">
+                {history.slice(0, 3).map((cycle, i) => (
+                  <div
+                    key={i}
+                    className="flex items-center justify-between text-xs"
+                  >
+                    <span className="text-gray-300 truncate flex-1">
+                      {cycle.objective.substring(0, 40)}...
+                    </span>
+                    <span
+                      className={`px-1.5 py-0.5 rounded ${
+                        cycle.status === 'completed'
+                          ? 'bg-green-900 text-green-300'
+                          : 'bg-yellow-900 text-yellow-300'
+                      }`}
+                    >
+                      {cycle.status}
+                    </span>
+                  </div>
+                ))}
+              </div>
+            </div>
+          )}
+
+          {/* Phase Legend */}
+          <div className="grid grid-cols-4 gap-2 text-xs">
+            {Object.entries(PHASE_COLORS).map(([phase, color]) => (
+              <div key={phase} className="flex items-center gap-1">
+                <div className={`w-2 h-2 rounded ${color}`} />
+                <span className="text-gray-400 capitalize">{phase}</span>
+              </div>
+            ))}
+          </div>
+        </div>
+      )}
+    </div>
+  );
+}
+
+export default DevLoopPanel;

atomizer-dashboard/frontend/src/components/intake/ContextFileUpload.tsx

@@ -0,0 +1,292 @@
+/**
+ * ContextFileUpload - Upload context files for study configuration
+ *
+ * Allows uploading markdown, text, PDF, and image files that help
+ * Claude understand optimization goals and generate better documentation.
+ */
+
+import React, { useState, useEffect, useRef, useCallback } from 'react';
+import { Upload, FileText, X, Loader2, AlertCircle, CheckCircle, Trash2, BookOpen } from 'lucide-react';
+import { intakeApi } from '../../api/intake';
+
+interface ContextFileUploadProps {
+  studyName: string;
+  onUploadComplete: () => void;
+}
+
+interface ContextFile {
+  name: string;
+  path: string;
+  size: number;
+  extension: string;
+}
+
+interface FileStatus {
+  file: File;
+  status: 'pending' | 'uploading' | 'success' | 'error';
+  message?: string;
+}
+
+const VALID_EXTENSIONS = ['.md', '.txt', '.pdf', '.png', '.jpg', '.jpeg', '.json', '.csv'];
+
+export const ContextFileUpload: React.FC<ContextFileUploadProps> = ({
+  studyName,
+  onUploadComplete,
+}) => {
+  const [contextFiles, setContextFiles] = useState<ContextFile[]>([]);
+  const [pendingFiles, setPendingFiles] = useState<FileStatus[]>([]);
+  const [isUploading, setIsUploading] = useState(false);
+  const [error, setError] = useState<string | null>(null);
+  const fileInputRef = useRef<HTMLInputElement>(null);
+
+  // Load existing context files
+  const loadContextFiles = useCallback(async () => {
+    try {
+      const response = await intakeApi.listContextFiles(studyName);
+      setContextFiles(response.context_files);
+    } catch (err) {
+      console.error('Failed to load context files:', err);
+    }
+  }, [studyName]);
+
+  useEffect(() => {
+    loadContextFiles();
+  }, [loadContextFiles]);
+
+  const validateFile = (file: File): { valid: boolean; reason?: string } => {
+    const ext = '.' + file.name.split('.').pop()?.toLowerCase();
+    if (!VALID_EXTENSIONS.includes(ext)) {
+      return { valid: false, reason: `Invalid type: ${ext}` };
+    }
+    // Max 10MB per file
+    if (file.size > 10 * 1024 * 1024) {
+      return { valid: false, reason: 'File too large (max 10MB)' };
+    }
+    return { valid: true };
+  };
+
+  const addFiles = useCallback((newFiles: File[]) => {
+    const validFiles: FileStatus[] = [];
+    
+    for (const file of newFiles) {
+      // Skip duplicates
+      if (pendingFiles.some(f => f.file.name === file.name)) {
+        continue;
+      }
+      if (contextFiles.some(f => f.name === file.name)) {
+        continue;
+      }
+      
+      const validation = validateFile(file);
+      if (validation.valid) {
+        validFiles.push({ file, status: 'pending' });
+      } else {
+        validFiles.push({ file, status: 'error', message: validation.reason });
+      }
+    }
+    
+    setPendingFiles(prev => [...prev, ...validFiles]);
+  }, [pendingFiles, contextFiles]);
+
+  const handleFileSelect = useCallback((e: React.ChangeEvent<HTMLInputElement>) => {
+    const selectedFiles = Array.from(e.target.files || []);
+    addFiles(selectedFiles);
+    e.target.value = '';
+  }, [addFiles]);
+
+  const removeFile = (index: number) => {
+    setPendingFiles(prev => prev.filter((_, i) => i !== index));
+  };
+
+  const handleUpload = async () => {
+    const filesToUpload = pendingFiles.filter(f => f.status === 'pending');
+    if (filesToUpload.length === 0) return;
+
+    setIsUploading(true);
+    setError(null);
+
+    try {
+      const response = await intakeApi.uploadContextFiles(
+        studyName,
+        filesToUpload.map(f => f.file)
+      );
+
+      // Update pending file statuses
+      const uploadResults = new Map(
+        response.uploaded_files.map(f => [f.name, f.status === 'uploaded'])
+      );
+
+      setPendingFiles(prev => prev.map(f => {
+        if (f.status !== 'pending') return f;
+        const success = uploadResults.get(f.file.name);
+        return {
+          ...f,
+          status: success ? 'success' : 'error',
+          message: success ? undefined : 'Upload failed',
+        };
+      }));
+
+      // Refresh and clear after a moment
+      setTimeout(() => {
+        setPendingFiles(prev => prev.filter(f => f.status !== 'success'));
+        loadContextFiles();
+        onUploadComplete();
+      }, 1500);
+
+    } catch (err) {
+      setError(err instanceof Error ? err.message : 'Upload failed');
+    } finally {
+      setIsUploading(false);
+    }
+  };
+
+  const handleDeleteFile = async (filename: string) => {
+    try {
+      await intakeApi.deleteContextFile(studyName, filename);
+      loadContextFiles();
+    } catch (err) {
+      setError(err instanceof Error ? err.message : 'Delete failed');
+    }
+  };
+
+  const pendingCount = pendingFiles.filter(f => f.status === 'pending').length;
+
+  const formatSize = (bytes: number) => {
+    if (bytes < 1024) return `${bytes} B`;
+    if (bytes < 1024 * 1024) return `${(bytes / 1024).toFixed(1)} KB`;
+    return `${(bytes / 1024 / 1024).toFixed(1)} MB`;
+  };
+
+  return (
+    <div className="space-y-3">
+      <div className="flex items-center justify-between">
+        <h5 className="text-sm font-medium text-dark-300 flex items-center gap-2">
+          <BookOpen className="w-4 h-4 text-purple-400" />
+          Context Files
+        </h5>
+        <button
+          onClick={() => fileInputRef.current?.click()}
+          className="flex items-center gap-1.5 px-2 py-1 rounded text-xs font-medium
+                     bg-purple-500/10 text-purple-400 hover:bg-purple-500/20
+                     transition-colors"
+        >
+          <Upload className="w-3 h-3" />
+          Add Context
+        </button>
+      </div>
+
+      <p className="text-xs text-dark-500">
+        Add .md, .txt, or .pdf files describing your optimization goals. Claude will use these to generate documentation.
+      </p>
+
+      {/* Error Display */}
+      {error && (
+        <div className="p-2 rounded-lg bg-red-500/10 border border-red-500/30 text-red-400 text-xs flex items-center gap-2">
+          <AlertCircle className="w-3 h-3 flex-shrink-0" />
+          {error}
+          <button onClick={() => setError(null)} className="ml-auto hover:text-white">
+            <X className="w-3 h-3" />
+          </button>
+        </div>
+      )}
+
+      {/* Existing Context Files */}
+      {contextFiles.length > 0 && (
+        <div className="space-y-1">
+          {contextFiles.map((file) => (
+            <div
+              key={file.name}
+              className="flex items-center justify-between p-2 rounded-lg bg-purple-500/5 border border-purple-500/20"
+            >
+              <div className="flex items-center gap-2">
+                <FileText className="w-4 h-4 text-purple-400" />
+                <span className="text-sm text-white">{file.name}</span>
+                <span className="text-xs text-dark-500">{formatSize(file.size)}</span>
+              </div>
+              <button
+                onClick={() => handleDeleteFile(file.name)}
+                className="p-1 hover:bg-white/10 rounded text-dark-400 hover:text-red-400"
+                title="Delete file"
+              >
+                <Trash2 className="w-3 h-3" />
+              </button>
+            </div>
+          ))}
+        </div>
+      )}
+
+      {/* Pending Files */}
+      {pendingFiles.length > 0 && (
+        <div className="space-y-1">
+          {pendingFiles.map((f, i) => (
+            <div
+              key={i}
+              className={`flex items-center justify-between p-2 rounded-lg
+                         ${f.status === 'error' ? 'bg-red-500/10' : 
+                           f.status === 'success' ? 'bg-green-500/10' :
+                           'bg-dark-700'}`}
+            >
+              <div className="flex items-center gap-2">
+                {f.status === 'pending' && <FileText className="w-4 h-4 text-dark-400" />}
+                {f.status === 'uploading' && <Loader2 className="w-4 h-4 text-purple-400 animate-spin" />}
+                {f.status === 'success' && <CheckCircle className="w-4 h-4 text-green-400" />}
+                {f.status === 'error' && <AlertCircle className="w-4 h-4 text-red-400" />}
+                <span className={`text-sm ${f.status === 'error' ? 'text-red-400' : 
+                                            f.status === 'success' ? 'text-green-400' : 
+                                            'text-white'}`}>
+                  {f.file.name}
+                </span>
+                {f.message && (
+                  <span className="text-xs text-red-400">({f.message})</span>
+                )}
+              </div>
+              {f.status === 'pending' && (
+                <button
+                  onClick={() => removeFile(i)}
+                  className="p-1 hover:bg-white/10 rounded text-dark-400 hover:text-white"
+                >
+                  <X className="w-3 h-3" />
+                </button>
+              )}
+            </div>
+          ))}
+        </div>
+      )}
+
+      {/* Upload Button */}
+      {pendingCount > 0 && (
+        <button
+          onClick={handleUpload}
+          disabled={isUploading}
+          className="w-full flex items-center justify-center gap-2 px-3 py-2 rounded-lg
+                     bg-purple-500 text-white text-sm font-medium
+                     hover:bg-purple-400 disabled:opacity-50 disabled:cursor-not-allowed
+                     transition-colors"
+        >
+          {isUploading ? (
+            <>
+              <Loader2 className="w-4 h-4 animate-spin" />
+              Uploading...
+            </>
+          ) : (
+            <>
+              <Upload className="w-4 h-4" />
+              Upload {pendingCount} {pendingCount === 1 ? 'File' : 'Files'}
+            </>
+          )}
+        </button>
+      )}
+
+      <input
+        ref={fileInputRef}
+        type="file"
+        multiple
+        accept={VALID_EXTENSIONS.join(',')}
+        onChange={handleFileSelect}
+        className="hidden"
+      />
+    </div>
+  );
+};
+
+export default ContextFileUpload;

atomizer-dashboard/frontend/src/components/intake/CreateStudyCard.tsx

@@ -0,0 +1,227 @@
+/**
+ * CreateStudyCard - Card for initiating new study creation
+ *
+ * Displays a prominent card on the Home page that allows users to
+ * create a new study through the intake workflow.
+ */
+
+import React, { useState } from 'react';
+import { Plus, Loader2 } from 'lucide-react';
+import { intakeApi } from '../../api/intake';
+import { TopicInfo } from '../../types/intake';
+
+interface CreateStudyCardProps {
+  topics: TopicInfo[];
+  onStudyCreated: (studyName: string) => void;
+}
+
+export const CreateStudyCard: React.FC<CreateStudyCardProps> = ({
+  topics,
+  onStudyCreated,
+}) => {
+  const [isExpanded, setIsExpanded] = useState(false);
+  const [studyName, setStudyName] = useState('');
+  const [description, setDescription] = useState('');
+  const [selectedTopic, setSelectedTopic] = useState('');
+  const [newTopic, setNewTopic] = useState('');
+  const [isCreating, setIsCreating] = useState(false);
+  const [error, setError] = useState<string | null>(null);
+
+  const handleCreate = async () => {
+    if (!studyName.trim()) {
+      setError('Study name is required');
+      return;
+    }
+
+    // Validate study name format
+    const nameRegex = /^[a-z0-9_]+$/;
+    if (!nameRegex.test(studyName)) {
+      setError('Study name must be lowercase with underscores only (e.g., my_study_name)');
+      return;
+    }
+
+    setIsCreating(true);
+    setError(null);
+
+    try {
+      const topic = newTopic.trim() || selectedTopic || undefined;
+      await intakeApi.createInbox({
+        study_name: studyName.trim(),
+        description: description.trim() || undefined,
+        topic,
+      });
+
+      // Reset form
+      setStudyName('');
+      setDescription('');
+      setSelectedTopic('');
+      setNewTopic('');
+      setIsExpanded(false);
+
+      onStudyCreated(studyName.trim());
+    } catch (err) {
+      setError(err instanceof Error ? err.message : 'Failed to create study');
+    } finally {
+      setIsCreating(false);
+    }
+  };
+
+  if (!isExpanded) {
+    return (
+      <button
+        onClick={() => setIsExpanded(true)}
+        className="w-full glass rounded-xl p-6 border border-dashed border-primary-400/30 
+                   hover:border-primary-400/60 hover:bg-primary-400/5 transition-all
+                   flex items-center justify-center gap-3 group"
+      >
+        <div className="w-12 h-12 rounded-xl bg-primary-400/10 flex items-center justify-center
+                        group-hover:bg-primary-400/20 transition-colors">
+          <Plus className="w-6 h-6 text-primary-400" />
+        </div>
+        <div className="text-left">
+          <h3 className="text-lg font-semibold text-white">Create New Study</h3>
+          <p className="text-sm text-dark-400">Set up a new optimization study</p>
+        </div>
+      </button>
+    );
+  }
+
+  return (
+    <div className="glass-strong rounded-xl border border-primary-400/20 overflow-hidden">
+      {/* Header */}
+      <div className="px-6 py-4 border-b border-primary-400/10 flex items-center justify-between">
+        <div className="flex items-center gap-3">
+          <div className="w-10 h-10 rounded-lg bg-primary-400/10 flex items-center justify-center">
+            <Plus className="w-5 h-5 text-primary-400" />
+          </div>
+          <h3 className="text-lg font-semibold text-white">Create New Study</h3>
+        </div>
+        <button
+          onClick={() => setIsExpanded(false)}
+          className="text-dark-400 hover:text-white transition-colors text-sm"
+        >
+          Cancel
+        </button>
+      </div>
+
+      {/* Form */}
+      <div className="p-6 space-y-4">
+        {/* Study Name */}
+        <div>
+          <label className="block text-sm font-medium text-dark-300 mb-2">
+            Study Name <span className="text-red-400">*</span>
+          </label>
+          <input
+            type="text"
+            value={studyName}
+            onChange={(e) => setStudyName(e.target.value.toLowerCase().replace(/[^a-z0-9_]/g, '_'))}
+            placeholder="my_optimization_study"
+            className="w-full px-4 py-2.5 rounded-lg bg-dark-800 border border-dark-600 
+                       text-white placeholder-dark-500 focus:border-primary-400 
+                       focus:outline-none focus:ring-1 focus:ring-primary-400/50"
+          />
+          <p className="mt-1 text-xs text-dark-500">
+            Lowercase letters, numbers, and underscores only
+          </p>
+        </div>
+
+        {/* Description */}
+        <div>
+          <label className="block text-sm font-medium text-dark-300 mb-2">
+            Description
+          </label>
+          <textarea
+            value={description}
+            onChange={(e) => setDescription(e.target.value)}
+            placeholder="Brief description of the optimization goal..."
+            rows={2}
+            className="w-full px-4 py-2.5 rounded-lg bg-dark-800 border border-dark-600 
+                       text-white placeholder-dark-500 focus:border-primary-400 
+                       focus:outline-none focus:ring-1 focus:ring-primary-400/50 resize-none"
+          />
+        </div>
+
+        {/* Topic Selection */}
+        <div>
+          <label className="block text-sm font-medium text-dark-300 mb-2">
+            Topic Folder
+          </label>
+          <div className="flex gap-2">
+            <select
+              value={selectedTopic}
+              onChange={(e) => {
+                setSelectedTopic(e.target.value);
+                setNewTopic('');
+              }}
+              className="flex-1 px-4 py-2.5 rounded-lg bg-dark-800 border border-dark-600 
+                         text-white focus:border-primary-400 focus:outline-none 
+                         focus:ring-1 focus:ring-primary-400/50"
+            >
+              <option value="">Select existing topic...</option>
+              {topics.map((topic) => (
+                <option key={topic.name} value={topic.name}>
+                  {topic.name} ({topic.study_count} studies)
+                </option>
+              ))}
+            </select>
+            <span className="text-dark-500 self-center">or</span>
+            <input
+              type="text"
+              value={newTopic}
+              onChange={(e) => {
+                setNewTopic(e.target.value.replace(/[^A-Za-z0-9_]/g, '_'));
+                setSelectedTopic('');
+              }}
+              placeholder="New_Topic"
+              className="flex-1 px-4 py-2.5 rounded-lg bg-dark-800 border border-dark-600 
+                         text-white placeholder-dark-500 focus:border-primary-400 
+                         focus:outline-none focus:ring-1 focus:ring-primary-400/50"
+            />
+          </div>
+        </div>
+
+        {/* Error Message */}
+        {error && (
+          <div className="p-3 rounded-lg bg-red-500/10 border border-red-500/30 text-red-400 text-sm">
+            {error}
+          </div>
+        )}
+
+        {/* Actions */}
+        <div className="flex justify-end gap-3 pt-2">
+          <button
+            onClick={() => setIsExpanded(false)}
+            className="px-4 py-2 rounded-lg border border-dark-600 text-dark-300 
+                       hover:border-dark-500 hover:text-white transition-colors"
+          >
+            Cancel
+          </button>
+          <button
+            onClick={handleCreate}
+            disabled={isCreating || !studyName.trim()}
+            className="px-6 py-2 rounded-lg font-medium transition-all disabled:opacity-50
+                       flex items-center gap-2"
+            style={{
+              background: 'linear-gradient(135deg, #00d4e6 0%, #0891b2 100%)',
+              color: '#000',
+            }}
+          >
+            {isCreating ? (
+              <>
+                <Loader2 className="w-4 h-4 animate-spin" />
+                Creating...
+              </>
+            ) : (
+              <>
+                <Plus className="w-4 h-4" />
+                Create Study
+              </>
+            )}
+          </button>
+        </div>
+      </div>
+    </div>
+  );
+};
+
+export default CreateStudyCard;

atomizer-dashboard/frontend/src/components/intake/ExpressionList.tsx

@@ -0,0 +1,270 @@
+/**
+ * ExpressionList - Display discovered expressions with selection capability
+ *
+ * Shows expressions from NX introspection, allowing users to:
+ * - View all discovered expressions
+ * - See which are design variable candidates (auto-detected)
+ * - Select/deselect expressions to use as design variables
+ * - View expression values and units
+ */
+
+import React, { useState } from 'react';
+import {
+  Check,
+  Search,
+  AlertTriangle,
+  Sparkles,
+  Info,
+  Variable,
+} from 'lucide-react';
+import { ExpressionInfo } from '../../types/intake';
+
+interface ExpressionListProps {
+  /** Expression data from introspection */
+  expressions: ExpressionInfo[];
+  /** Mass from introspection (kg) */
+  massKg?: number | null;
+  /** Currently selected expressions (to become DVs) */
+  selectedExpressions: string[];
+  /** Callback when selection changes */
+  onSelectionChange: (selected: string[]) => void;
+  /** Whether in read-only mode */
+  readOnly?: boolean;
+  /** Compact display mode */
+  compact?: boolean;
+}
+
+export const ExpressionList: React.FC<ExpressionListProps> = ({
+  expressions,
+  massKg,
+  selectedExpressions,
+  onSelectionChange,
+  readOnly = false,
+  compact = false,
+}) => {
+  const [filter, setFilter] = useState('');
+  const [showCandidatesOnly, setShowCandidatesOnly] = useState(true);
+
+  // Filter expressions based on search and candidate toggle
+  const filteredExpressions = expressions.filter((expr) => {
+    const matchesSearch = filter === '' || 
+      expr.name.toLowerCase().includes(filter.toLowerCase());
+    const matchesCandidate = !showCandidatesOnly || expr.is_candidate;
+    return matchesSearch && matchesCandidate;
+  });
+
+  // Sort: candidates first, then by confidence, then alphabetically
+  const sortedExpressions = [...filteredExpressions].sort((a, b) => {
+    if (a.is_candidate !== b.is_candidate) {
+      return a.is_candidate ? -1 : 1;
+    }
+    if (a.confidence !== b.confidence) {
+      return b.confidence - a.confidence;
+    }
+    return a.name.localeCompare(b.name);
+  });
+
+  const toggleExpression = (name: string) => {
+    if (readOnly) return;
+    
+    if (selectedExpressions.includes(name)) {
+      onSelectionChange(selectedExpressions.filter(n => n !== name));
+    } else {
+      onSelectionChange([...selectedExpressions, name]);
+    }
+  };
+
+  const selectAllCandidates = () => {
+    const candidateNames = expressions
+      .filter(e => e.is_candidate)
+      .map(e => e.name);
+    onSelectionChange(candidateNames);
+  };
+
+  const clearSelection = () => {
+    onSelectionChange([]);
+  };
+
+  const candidateCount = expressions.filter(e => e.is_candidate).length;
+
+  if (expressions.length === 0) {
+    return (
+      <div className="p-4 rounded-lg bg-dark-700/50 border border-dark-600">
+        <div className="flex items-center gap-2 text-dark-400">
+          <AlertTriangle className="w-4 h-4" />
+          <span>No expressions found. Run introspection to discover model parameters.</span>
+        </div>
+      </div>
+    );
+  }
+
+  return (
+    <div className="space-y-3">
+      {/* Header with stats */}
+      <div className="flex items-center justify-between">
+        <div className="flex items-center gap-3">
+          <h5 className="text-sm font-medium text-dark-300 flex items-center gap-2">
+            <Variable className="w-4 h-4" />
+            Discovered Expressions
+          </h5>
+          <span className="text-xs text-dark-500">
+            {expressions.length} total, {candidateCount} candidates
+          </span>
+          {massKg && (
+            <span className="text-xs text-primary-400">
+              Mass: {massKg.toFixed(3)} kg
+            </span>
+          )}
+        </div>
+        {!readOnly && selectedExpressions.length > 0 && (
+          <span className="text-xs text-green-400">
+            {selectedExpressions.length} selected
+          </span>
+        )}
+      </div>
+
+      {/* Controls */}
+      {!compact && (
+        <div className="flex items-center gap-3">
+          {/* Search */}
+          <div className="relative flex-1 max-w-xs">
+            <Search className="absolute left-2.5 top-1/2 -translate-y-1/2 w-4 h-4 text-dark-500" />
+            <input
+              type="text"
+              placeholder="Search expressions..."
+              value={filter}
+              onChange={(e) => setFilter(e.target.value)}
+              className="w-full pl-8 pr-3 py-1.5 text-sm rounded-lg bg-dark-700 border border-dark-600
+                         text-white placeholder-dark-500 focus:border-primary-500/50 focus:outline-none"
+            />
+          </div>
+
+          {/* Show candidates only toggle */}
+          <label className="flex items-center gap-2 text-xs text-dark-400 cursor-pointer">
+            <input
+              type="checkbox"
+              checked={showCandidatesOnly}
+              onChange={(e) => setShowCandidatesOnly(e.target.checked)}
+              className="w-4 h-4 rounded border-dark-500 bg-dark-700 text-primary-500 
+                         focus:ring-primary-500/30"
+            />
+            Candidates only
+          </label>
+
+          {/* Quick actions */}
+          {!readOnly && (
+            <div className="flex items-center gap-2">
+              <button
+                onClick={selectAllCandidates}
+                className="px-2 py-1 text-xs rounded bg-primary-500/10 text-primary-400 
+                           hover:bg-primary-500/20 transition-colors"
+              >
+                Select all candidates
+              </button>
+              <button
+                onClick={clearSelection}
+                className="px-2 py-1 text-xs rounded bg-dark-600 text-dark-400 
+                           hover:bg-dark-500 transition-colors"
+              >
+                Clear
+              </button>
+            </div>
+          )}
+        </div>
+      )}
+
+      {/* Expression list */}
+      <div className={`rounded-lg border border-dark-600 overflow-hidden ${
+        compact ? 'max-h-48' : 'max-h-72'
+      } overflow-y-auto`}>
+        <table className="w-full text-sm">
+          <thead className="bg-dark-700 sticky top-0">
+            <tr>
+              {!readOnly && (
+                <th className="w-8 px-2 py-2"></th>
+              )}
+              <th className="px-3 py-2 text-left text-dark-400 font-medium">Name</th>
+              <th className="px-3 py-2 text-right text-dark-400 font-medium w-24">Value</th>
+              <th className="px-3 py-2 text-left text-dark-400 font-medium w-16">Units</th>
+              <th className="px-3 py-2 text-center text-dark-400 font-medium w-20">Candidate</th>
+            </tr>
+          </thead>
+          <tbody className="divide-y divide-dark-700">
+            {sortedExpressions.map((expr) => {
+              const isSelected = selectedExpressions.includes(expr.name);
+              return (
+                <tr
+                  key={expr.name}
+                  onClick={() => toggleExpression(expr.name)}
+                  className={`
+                    ${readOnly ? '' : 'cursor-pointer hover:bg-dark-700/50'}
+                    ${isSelected ? 'bg-primary-500/10' : ''}
+                    transition-colors
+                  `}
+                >
+                  {!readOnly && (
+                    <td className="px-2 py-2">
+                      <div className={`w-5 h-5 rounded border flex items-center justify-center
+                        ${isSelected 
+                          ? 'bg-primary-500 border-primary-500' 
+                          : 'border-dark-500 bg-dark-700'
+                        }`}
+                      >
+                        {isSelected && <Check className="w-3 h-3 text-white" />}
+                      </div>
+                    </td>
+                  )}
+                  <td className="px-3 py-2">
+                    <div className="flex items-center gap-2">
+                      <code className={`text-xs ${isSelected ? 'text-primary-300' : 'text-white'}`}>
+                        {expr.name}
+                      </code>
+                      {expr.formula && (
+                        <span className="text-xs text-dark-500" title={expr.formula}>
+                          <Info className="w-3 h-3" />
+                        </span>
+                      )}
+                    </div>
+                  </td>
+                  <td className="px-3 py-2 text-right font-mono text-xs text-dark-300">
+                    {expr.value !== null ? expr.value.toFixed(3) : '-'}
+                  </td>
+                  <td className="px-3 py-2 text-xs text-dark-400">
+                    {expr.units || '-'}
+                  </td>
+                  <td className="px-3 py-2 text-center">
+                    {expr.is_candidate ? (
+                      <span className="inline-flex items-center gap-1 px-1.5 py-0.5 rounded text-xs 
+                                       bg-green-500/10 text-green-400">
+                        <Sparkles className="w-3 h-3" />
+                        {Math.round(expr.confidence * 100)}%
+                      </span>
+                    ) : (
+                      <span className="text-xs text-dark-500">-</span>
+                    )}
+                  </td>
+                </tr>
+              );
+            })}
+          </tbody>
+        </table>
+        
+        {sortedExpressions.length === 0 && (
+          <div className="px-4 py-8 text-center text-dark-500">
+            No expressions match your filter
+          </div>
+        )}
+      </div>
+
+      {/* Help text */}
+      {!readOnly && !compact && (
+        <p className="text-xs text-dark-500">
+          Select expressions to use as design variables. Candidates (marked with %) are 
+          automatically identified based on naming patterns and units.
+        </p>
+      )}
+    </div>
+  );
+};
+
+export default ExpressionList;

atomizer-dashboard/frontend/src/components/intake/FileDropzone.tsx

@@ -0,0 +1,348 @@
+/**
+ * FileDropzone - Drag and drop file upload component
+ *
+ * Supports drag-and-drop or click-to-browse for model files.
+ * Accepts .prt, .sim, .fem, .afem files.
+ */
+
+import React, { useState, useCallback, useRef } from 'react';
+import { Upload, FileText, X, Loader2, AlertCircle, CheckCircle } from 'lucide-react';
+import { intakeApi } from '../../api/intake';
+
+interface FileDropzoneProps {
+  studyName: string;
+  onUploadComplete: () => void;
+  compact?: boolean;
+}
+
+interface FileStatus {
+  file: File;
+  status: 'pending' | 'uploading' | 'success' | 'error';
+  message?: string;
+}
+
+const VALID_EXTENSIONS = ['.prt', '.sim', '.fem', '.afem'];
+
+export const FileDropzone: React.FC<FileDropzoneProps> = ({
+  studyName,
+  onUploadComplete,
+  compact = false,
+}) => {
+  const [isDragging, setIsDragging] = useState(false);
+  const [files, setFiles] = useState<FileStatus[]>([]);
+  const [isUploading, setIsUploading] = useState(false);
+  const [error, setError] = useState<string | null>(null);
+  const fileInputRef = useRef<HTMLInputElement>(null);
+
+  const validateFile = (file: File): { valid: boolean; reason?: string } => {
+    const ext = '.' + file.name.split('.').pop()?.toLowerCase();
+    if (!VALID_EXTENSIONS.includes(ext)) {
+      return { valid: false, reason: `Invalid type: ${ext}` };
+    }
+    // Max 500MB per file
+    if (file.size > 500 * 1024 * 1024) {
+      return { valid: false, reason: 'File too large (max 500MB)' };
+    }
+    return { valid: true };
+  };
+
+  const handleDragEnter = useCallback((e: React.DragEvent) => {
+    e.preventDefault();
+    e.stopPropagation();
+    setIsDragging(true);
+  }, []);
+
+  const handleDragLeave = useCallback((e: React.DragEvent) => {
+    e.preventDefault();
+    e.stopPropagation();
+    setIsDragging(false);
+  }, []);
+
+  const handleDragOver = useCallback((e: React.DragEvent) => {
+    e.preventDefault();
+    e.stopPropagation();
+  }, []);
+
+  const addFiles = useCallback((newFiles: File[]) => {
+    const validFiles: FileStatus[] = [];
+    
+    for (const file of newFiles) {
+      // Skip duplicates
+      if (files.some(f => f.file.name === file.name)) {
+        continue;
+      }
+      
+      const validation = validateFile(file);
+      if (validation.valid) {
+        validFiles.push({ file, status: 'pending' });
+      } else {
+        validFiles.push({ file, status: 'error', message: validation.reason });
+      }
+    }
+    
+    setFiles(prev => [...prev, ...validFiles]);
+  }, [files]);
+
+  const handleDrop = useCallback((e: React.DragEvent) => {
+    e.preventDefault();
+    e.stopPropagation();
+    setIsDragging(false);
+    
+    const droppedFiles = Array.from(e.dataTransfer.files);
+    addFiles(droppedFiles);
+  }, [addFiles]);
+
+  const handleFileSelect = useCallback((e: React.ChangeEvent<HTMLInputElement>) => {
+    const selectedFiles = Array.from(e.target.files || []);
+    addFiles(selectedFiles);
+    // Reset input so the same file can be selected again
+    e.target.value = '';
+  }, [addFiles]);
+
+  const removeFile = (index: number) => {
+    setFiles(prev => prev.filter((_, i) => i !== index));
+  };
+
+  const handleUpload = async () => {
+    const pendingFiles = files.filter(f => f.status === 'pending');
+    if (pendingFiles.length === 0) return;
+
+    setIsUploading(true);
+    setError(null);
+
+    try {
+      // Upload files
+      const response = await intakeApi.uploadFiles(
+        studyName,
+        pendingFiles.map(f => f.file)
+      );
+
+      // Update file statuses based on response
+      const uploadResults = new Map(
+        response.uploaded_files.map(f => [f.name, f.status === 'uploaded'])
+      );
+
+      setFiles(prev => prev.map(f => {
+        if (f.status !== 'pending') return f;
+        const success = uploadResults.get(f.file.name);
+        return {
+          ...f,
+          status: success ? 'success' : 'error',
+          message: success ? undefined : 'Upload failed',
+        };
+      }));
+
+      // Clear successful uploads after a moment and refresh
+      setTimeout(() => {
+        setFiles(prev => prev.filter(f => f.status !== 'success'));
+        onUploadComplete();
+      }, 1500);
+
+    } catch (err) {
+      setError(err instanceof Error ? err.message : 'Upload failed');
+      setFiles(prev => prev.map(f => 
+        f.status === 'pending' 
+          ? { ...f, status: 'error', message: 'Upload failed' }
+          : f
+      ));
+    } finally {
+      setIsUploading(false);
+    }
+  };
+
+  const pendingCount = files.filter(f => f.status === 'pending').length;
+
+  if (compact) {
+    // Compact inline version
+    return (
+      <div className="space-y-2">
+        <div className="flex items-center gap-2">
+          <button
+            onClick={() => fileInputRef.current?.click()}
+            className="flex items-center gap-2 px-3 py-1.5 rounded-lg text-sm font-medium
+                       bg-dark-700 text-dark-300 hover:bg-dark-600 hover:text-white
+                       transition-colors"
+          >
+            <Upload className="w-4 h-4" />
+            Add Files
+          </button>
+          {pendingCount > 0 && (
+            <button
+              onClick={handleUpload}
+              disabled={isUploading}
+              className="flex items-center gap-2 px-3 py-1.5 rounded-lg text-sm font-medium
+                         bg-primary-500/10 text-primary-400 hover:bg-primary-500/20
+                         disabled:opacity-50 transition-colors"
+            >
+              {isUploading ? (
+                <Loader2 className="w-4 h-4 animate-spin" />
+              ) : (
+                <Upload className="w-4 h-4" />
+              )}
+              Upload {pendingCount} {pendingCount === 1 ? 'File' : 'Files'}
+            </button>
+          )}
+        </div>
+        
+        {/* File list */}
+        {files.length > 0 && (
+          <div className="flex flex-wrap gap-2">
+            {files.map((f, i) => (
+              <span
+                key={i}
+                className={`inline-flex items-center gap-1.5 px-2 py-1 rounded text-xs
+                           ${f.status === 'error' ? 'bg-red-500/10 text-red-400' : 
+                             f.status === 'success' ? 'bg-green-500/10 text-green-400' :
+                             'bg-dark-700 text-dark-300'}`}
+              >
+                {f.status === 'uploading' && <Loader2 className="w-3 h-3 animate-spin" />}
+                {f.status === 'success' && <CheckCircle className="w-3 h-3" />}
+                {f.status === 'error' && <AlertCircle className="w-3 h-3" />}
+                {f.file.name}
+                {f.status === 'pending' && (
+                  <button onClick={() => removeFile(i)} className="hover:text-white">
+                    <X className="w-3 h-3" />
+                  </button>
+                )}
+              </span>
+            ))}
+          </div>
+        )}
+        
+        <input
+          ref={fileInputRef}
+          type="file"
+          multiple
+          accept={VALID_EXTENSIONS.join(',')}
+          onChange={handleFileSelect}
+          className="hidden"
+        />
+      </div>
+    );
+  }
+
+  // Full dropzone version
+  return (
+    <div className="space-y-4">
+      {/* Dropzone */}
+      <div
+        onDragEnter={handleDragEnter}
+        onDragLeave={handleDragLeave}
+        onDragOver={handleDragOver}
+        onDrop={handleDrop}
+        onClick={() => fileInputRef.current?.click()}
+        className={`
+          relative border-2 border-dashed rounded-xl p-6 cursor-pointer
+          transition-all duration-200
+          ${isDragging 
+            ? 'border-primary-400 bg-primary-400/5' 
+            : 'border-dark-600 hover:border-primary-400/50 hover:bg-white/5'
+          }
+        `}
+      >
+        <div className="flex flex-col items-center text-center">
+          <div className={`w-12 h-12 rounded-full flex items-center justify-center mb-3
+                          ${isDragging ? 'bg-primary-400/20 text-primary-400' : 'bg-dark-700 text-dark-400'}`}>
+            <Upload className="w-6 h-6" />
+          </div>
+          <p className="text-white font-medium mb-1">
+            {isDragging ? 'Drop files here' : 'Drop model files here'}
+          </p>
+          <p className="text-sm text-dark-400">
+            or <span className="text-primary-400">click to browse</span>
+          </p>
+          <p className="text-xs text-dark-500 mt-2">
+            Accepts: {VALID_EXTENSIONS.join(', ')}
+          </p>
+        </div>
+      </div>
+
+      {/* Error */}
+      {error && (
+        <div className="p-3 rounded-lg bg-red-500/10 border border-red-500/30 text-red-400 text-sm flex items-center gap-2">
+          <AlertCircle className="w-4 h-4 flex-shrink-0" />
+          {error}
+        </div>
+      )}
+
+      {/* File List */}
+      {files.length > 0 && (
+        <div className="space-y-2">
+          <h5 className="text-sm font-medium text-dark-300">Files to Upload</h5>
+          <div className="space-y-1">
+            {files.map((f, i) => (
+              <div
+                key={i}
+                className={`flex items-center justify-between p-2 rounded-lg
+                           ${f.status === 'error' ? 'bg-red-500/10' : 
+                             f.status === 'success' ? 'bg-green-500/10' :
+                             'bg-dark-700'}`}
+              >
+                <div className="flex items-center gap-2">
+                  {f.status === 'pending' && <FileText className="w-4 h-4 text-dark-400" />}
+                  {f.status === 'uploading' && <Loader2 className="w-4 h-4 text-primary-400 animate-spin" />}
+                  {f.status === 'success' && <CheckCircle className="w-4 h-4 text-green-400" />}
+                  {f.status === 'error' && <AlertCircle className="w-4 h-4 text-red-400" />}
+                  <span className={`text-sm ${f.status === 'error' ? 'text-red-400' : 
+                                              f.status === 'success' ? 'text-green-400' : 
+                                              'text-white'}`}>
+                    {f.file.name}
+                  </span>
+                  {f.message && (
+                    <span className="text-xs text-red-400">({f.message})</span>
+                  )}
+                </div>
+                {f.status === 'pending' && (
+                  <button
+                    onClick={(e) => {
+                      e.stopPropagation();
+                      removeFile(i);
+                    }}
+                    className="p-1 hover:bg-white/10 rounded text-dark-400 hover:text-white"
+                  >
+                    <X className="w-4 h-4" />
+                  </button>
+                )}
+              </div>
+            ))}
+          </div>
+
+          {/* Upload Button */}
+          {pendingCount > 0 && (
+            <button
+              onClick={handleUpload}
+              disabled={isUploading}
+              className="w-full flex items-center justify-center gap-2 px-4 py-2 rounded-lg
+                         bg-primary-500 text-white font-medium
+                         hover:bg-primary-400 disabled:opacity-50 disabled:cursor-not-allowed
+                         transition-colors"
+            >
+              {isUploading ? (
+                <>
+                  <Loader2 className="w-4 h-4 animate-spin" />
+                  Uploading...
+                </>
+              ) : (
+                <>
+                  <Upload className="w-4 h-4" />
+                  Upload {pendingCount} {pendingCount === 1 ? 'File' : 'Files'}
+                </>
+              )}
+            </button>
+          )}
+        </div>
+      )}
+
+      <input
+        ref={fileInputRef}
+        type="file"
+        multiple
+        accept={VALID_EXTENSIONS.join(',')}
+        onChange={handleFileSelect}
+        className="hidden"
+      />
+    </div>
+  );
+};
+
+export default FileDropzone;

atomizer-dashboard/frontend/src/components/intake/FinalizeModal.tsx

@@ -0,0 +1,272 @@
+/**
+ * FinalizeModal - Modal for finalizing an inbox study
+ *
+ * Allows user to:
+ * - Select/create topic folder
+ * - Choose whether to run baseline FEA
+ * - See progress during finalization
+ */
+
+import React, { useState, useEffect } from 'react';
+import {
+  X,
+  Folder,
+  CheckCircle,
+  Loader2,
+  AlertCircle,
+} from 'lucide-react';
+import { intakeApi } from '../../api/intake';
+import { TopicInfo, InboxStudyDetail } from '../../types/intake';
+
+interface FinalizeModalProps {
+  studyName: string;
+  topics: TopicInfo[];
+  onClose: () => void;
+  onFinalized: (finalPath: string) => void;
+}
+
+export const FinalizeModal: React.FC<FinalizeModalProps> = ({
+  studyName,
+  topics,
+  onClose,
+  onFinalized,
+}) => {
+  const [studyDetail, setStudyDetail] = useState<InboxStudyDetail | null>(null);
+  const [selectedTopic, setSelectedTopic] = useState('');
+  const [newTopic, setNewTopic] = useState('');
+  const [runBaseline, setRunBaseline] = useState(true);
+  const [isLoading, setIsLoading] = useState(true);
+  const [isFinalizing, setIsFinalizing] = useState(false);
+  const [progress, setProgress] = useState<string>('');
+  const [error, setError] = useState<string | null>(null);
+
+  // Load study detail
+  useEffect(() => {
+    const loadStudy = async () => {
+      try {
+        const detail = await intakeApi.getInboxStudy(studyName);
+        setStudyDetail(detail);
+        // Pre-select topic if set in spec
+        if (detail.spec.meta.topic) {
+          setSelectedTopic(detail.spec.meta.topic);
+        }
+      } catch (err) {
+        setError(err instanceof Error ? err.message : 'Failed to load study');
+      } finally {
+        setIsLoading(false);
+      }
+    };
+    loadStudy();
+  }, [studyName]);
+
+  const handleFinalize = async () => {
+    const topic = newTopic.trim() || selectedTopic;
+    if (!topic) {
+      setError('Please select or create a topic folder');
+      return;
+    }
+
+    setIsFinalizing(true);
+    setError(null);
+    setProgress('Starting finalization...');
+
+    try {
+      setProgress('Validating study configuration...');
+      await new Promise((r) => setTimeout(r, 500)); // Visual feedback
+
+      if (runBaseline) {
+        setProgress('Running baseline FEA solve...');
+      }
+
+      const result = await intakeApi.finalize(studyName, {
+        topic,
+        run_baseline: runBaseline,
+      });
+
+      setProgress('Finalization complete!');
+      await new Promise((r) => setTimeout(r, 500));
+
+      onFinalized(result.final_path);
+    } catch (err) {
+      setError(err instanceof Error ? err.message : 'Finalization failed');
+      setIsFinalizing(false);
+    }
+  };
+
+  return (
+    <div className="fixed inset-0 z-50 flex items-center justify-center bg-dark-900/80 backdrop-blur-sm">
+      <div className="w-full max-w-lg glass-strong rounded-xl border border-primary-400/20 overflow-hidden">
+        {/* Header */}
+        <div className="px-6 py-4 border-b border-primary-400/10 flex items-center justify-between">
+          <div className="flex items-center gap-3">
+            <div className="w-10 h-10 rounded-lg bg-primary-400/10 flex items-center justify-center">
+              <Folder className="w-5 h-5 text-primary-400" />
+            </div>
+            <div>
+              <h3 className="text-lg font-semibold text-white">Finalize Study</h3>
+              <p className="text-sm text-dark-400">{studyName}</p>
+            </div>
+          </div>
+          {!isFinalizing && (
+            <button
+              onClick={onClose}
+              className="p-2 hover:bg-white/5 rounded-lg transition-colors text-dark-400 hover:text-white"
+            >
+              <X className="w-5 h-5" />
+            </button>
+          )}
+        </div>
+
+        {/* Content */}
+        <div className="p-6 space-y-6">
+          {isLoading ? (
+            <div className="flex items-center justify-center py-8">
+              <Loader2 className="w-6 h-6 animate-spin text-primary-400" />
+            </div>
+          ) : isFinalizing ? (
+            /* Progress View */
+            <div className="text-center py-8 space-y-4">
+              <Loader2 className="w-12 h-12 animate-spin text-primary-400 mx-auto" />
+              <p className="text-white font-medium">{progress}</p>
+              <p className="text-sm text-dark-400">
+                Please wait while your study is being finalized...
+              </p>
+            </div>
+          ) : (
+            <>
+              {/* Error Display */}
+              {error && (
+                <div className="p-3 rounded-lg bg-red-500/10 border border-red-500/30 text-red-400 text-sm flex items-center gap-2">
+                  <AlertCircle className="w-4 h-4 flex-shrink-0" />
+                  {error}
+                </div>
+              )}
+
+              {/* Study Summary */}
+              {studyDetail && (
+                <div className="p-4 rounded-lg bg-dark-800 space-y-2">
+                  <h4 className="text-sm font-medium text-dark-300">Study Summary</h4>
+                  <div className="grid grid-cols-2 gap-4 text-sm">
+                    <div>
+                      <span className="text-dark-500">Status:</span>
+                      <span className="ml-2 text-white capitalize">
+                        {studyDetail.spec.meta.status}
+                      </span>
+                    </div>
+                    <div>
+                      <span className="text-dark-500">Model Files:</span>
+                      <span className="ml-2 text-white">
+                        {studyDetail.files.sim.length + studyDetail.files.prt.length + studyDetail.files.fem.length}
+                      </span>
+                    </div>
+                    <div>
+                      <span className="text-dark-500">Design Variables:</span>
+                      <span className="ml-2 text-white">
+                        {studyDetail.spec.design_variables?.length || 0}
+                      </span>
+                    </div>
+                    <div>
+                      <span className="text-dark-500">Objectives:</span>
+                      <span className="ml-2 text-white">
+                        {studyDetail.spec.objectives?.length || 0}
+                      </span>
+                    </div>
+                  </div>
+                </div>
+              )}
+
+              {/* Topic Selection */}
+              <div>
+                <label className="block text-sm font-medium text-dark-300 mb-2">
+                  Topic Folder <span className="text-red-400">*</span>
+                </label>
+                <div className="flex gap-2">
+                  <select
+                    value={selectedTopic}
+                    onChange={(e) => {
+                      setSelectedTopic(e.target.value);
+                      setNewTopic('');
+                    }}
+                    className="flex-1 px-4 py-2.5 rounded-lg bg-dark-800 border border-dark-600 
+                               text-white focus:border-primary-400 focus:outline-none 
+                               focus:ring-1 focus:ring-primary-400/50"
+                  >
+                    <option value="">Select existing topic...</option>
+                    {topics.map((topic) => (
+                      <option key={topic.name} value={topic.name}>
+                        {topic.name} ({topic.study_count} studies)
+                      </option>
+                    ))}
+                  </select>
+                  <span className="text-dark-500 self-center">or</span>
+                  <input
+                    type="text"
+                    value={newTopic}
+                    onChange={(e) => {
+                      setNewTopic(e.target.value.replace(/[^A-Za-z0-9_]/g, '_'));
+                      setSelectedTopic('');
+                    }}
+                    placeholder="New_Topic"
+                    className="flex-1 px-4 py-2.5 rounded-lg bg-dark-800 border border-dark-600 
+                               text-white placeholder-dark-500 focus:border-primary-400 
+                               focus:outline-none focus:ring-1 focus:ring-primary-400/50"
+                  />
+                </div>
+                <p className="mt-1 text-xs text-dark-500">
+                  Study will be created at: studies/{newTopic || selectedTopic || '<topic>'}/{studyName}/
+                </p>
+              </div>
+
+              {/* Baseline Option */}
+              <div>
+                <label className="flex items-center gap-3 cursor-pointer">
+                  <input
+                    type="checkbox"
+                    checked={runBaseline}
+                    onChange={(e) => setRunBaseline(e.target.checked)}
+                    className="w-4 h-4 rounded border-dark-600 bg-dark-800 text-primary-400 
+                               focus:ring-primary-400/50"
+                  />
+                  <div>
+                    <span className="text-white font-medium">Run baseline FEA solve</span>
+                    <p className="text-xs text-dark-500">
+                      Validates the model and captures baseline performance metrics
+                    </p>
+                  </div>
+                </label>
+              </div>
+            </>
+          )}
+        </div>
+
+        {/* Footer */}
+        {!isLoading && !isFinalizing && (
+          <div className="px-6 py-4 border-t border-primary-400/10 flex justify-end gap-3">
+            <button
+              onClick={onClose}
+              className="px-4 py-2 rounded-lg border border-dark-600 text-dark-300 
+                         hover:border-dark-500 hover:text-white transition-colors"
+            >
+              Cancel
+            </button>
+            <button
+              onClick={handleFinalize}
+              disabled={!selectedTopic && !newTopic.trim()}
+              className="px-6 py-2 rounded-lg font-medium transition-all disabled:opacity-50
+                         flex items-center gap-2"
+              style={{
+                background: 'linear-gradient(135deg, #00d4e6 0%, #0891b2 100%)',
+                color: '#000',
+              }}
+            >
+              <CheckCircle className="w-4 h-4" />
+              Finalize Study
+            </button>
+          </div>
+        )}
+      </div>
+    </div>
+  );
+};
+
+export default FinalizeModal;

atomizer-dashboard/frontend/src/components/intake/InboxSection.tsx

@@ -0,0 +1,147 @@
+/**
+ * InboxSection - Section displaying inbox studies on Home page
+ *
+ * Shows the "Create New Study" card and lists all inbox studies
+ * with their current status and available actions.
+ */
+
+import React, { useState, useEffect, useCallback } from 'react';
+import { Inbox, RefreshCw, ChevronDown, ChevronRight } from 'lucide-react';
+import { intakeApi } from '../../api/intake';
+import { InboxStudy, TopicInfo } from '../../types/intake';
+import { CreateStudyCard } from './CreateStudyCard';
+import { InboxStudyCard } from './InboxStudyCard';
+import { FinalizeModal } from './FinalizeModal';
+
+interface InboxSectionProps {
+  onStudyFinalized?: () => void;
+}
+
+export const InboxSection: React.FC<InboxSectionProps> = ({ onStudyFinalized }) => {
+  const [inboxStudies, setInboxStudies] = useState<InboxStudy[]>([]);
+  const [topics, setTopics] = useState<TopicInfo[]>([]);
+  const [isLoading, setIsLoading] = useState(true);
+  const [isExpanded, setIsExpanded] = useState(true);
+  const [selectedStudyForFinalize, setSelectedStudyForFinalize] = useState<string | null>(null);
+
+  const loadData = useCallback(async () => {
+    setIsLoading(true);
+    try {
+      const [inboxResponse, topicsResponse] = await Promise.all([
+        intakeApi.listInbox(),
+        intakeApi.listTopics(),
+      ]);
+      setInboxStudies(inboxResponse.studies);
+      setTopics(topicsResponse.topics);
+    } catch (err) {
+      console.error('Failed to load inbox data:', err);
+    } finally {
+      setIsLoading(false);
+    }
+  }, []);
+
+  useEffect(() => {
+    loadData();
+  }, [loadData]);
+
+  const handleStudyCreated = (_studyName: string) => {
+    loadData();
+  };
+
+  const handleStudyFinalized = (_finalPath: string) => {
+    setSelectedStudyForFinalize(null);
+    loadData();
+    onStudyFinalized?.();
+  };
+
+  const pendingStudies = inboxStudies.filter(
+    (s) => !['ready', 'running', 'completed'].includes(s.status)
+  );
+
+  return (
+    <div className="space-y-4">
+      {/* Section Header */}
+      <button
+        onClick={() => setIsExpanded(!isExpanded)}
+        className="w-full flex items-center justify-between px-2 py-1 hover:bg-white/5 rounded-lg transition-colors"
+      >
+        <div className="flex items-center gap-3">
+          <div className="w-8 h-8 rounded-lg bg-primary-400/10 flex items-center justify-center">
+            <Inbox className="w-4 h-4 text-primary-400" />
+          </div>
+          <div className="text-left">
+            <h2 className="text-lg font-semibold text-white">Study Inbox</h2>
+            <p className="text-sm text-dark-400">
+              {pendingStudies.length} pending studies
+            </p>
+          </div>
+        </div>
+        <div className="flex items-center gap-2">
+          <button
+            onClick={(e) => {
+              e.stopPropagation();
+              loadData();
+            }}
+            className="p-2 hover:bg-white/5 rounded-lg transition-colors text-dark-400 hover:text-primary-400"
+            title="Refresh"
+          >
+            <RefreshCw className={`w-4 h-4 ${isLoading ? 'animate-spin' : ''}`} />
+          </button>
+          {isExpanded ? (
+            <ChevronDown className="w-5 h-5 text-dark-400" />
+          ) : (
+            <ChevronRight className="w-5 h-5 text-dark-400" />
+          )}
+        </div>
+      </button>
+
+      {/* Content */}
+      {isExpanded && (
+        <div className="space-y-4">
+          {/* Create Study Card */}
+          <CreateStudyCard topics={topics} onStudyCreated={handleStudyCreated} />
+
+          {/* Inbox Studies List */}
+          {inboxStudies.length > 0 && (
+            <div className="space-y-3">
+              <h3 className="text-sm font-medium text-dark-400 px-2">
+                Inbox Studies ({inboxStudies.length})
+              </h3>
+              {inboxStudies.map((study) => (
+                <InboxStudyCard
+                  key={study.study_name}
+                  study={study}
+                  onRefresh={loadData}
+                  onSelect={setSelectedStudyForFinalize}
+                />
+              ))}
+            </div>
+          )}
+
+          {/* Empty State */}
+          {!isLoading && inboxStudies.length === 0 && (
+            <div className="text-center py-8 text-dark-400">
+              <Inbox className="w-12 h-12 mx-auto mb-3 opacity-30" />
+              <p>No studies in inbox</p>
+              <p className="text-sm text-dark-500">
+                Create a new study to get started
+              </p>
+            </div>
+          )}
+        </div>
+      )}
+
+      {/* Finalize Modal */}
+      {selectedStudyForFinalize && (
+        <FinalizeModal
+          studyName={selectedStudyForFinalize}
+          topics={topics}
+          onClose={() => setSelectedStudyForFinalize(null)}
+          onFinalized={handleStudyFinalized}
+        />
+      )}
+    </div>
+  );
+};
+
+export default InboxSection;

atomizer-dashboard/frontend/src/components/intake/InboxStudyCard.tsx

@@ -0,0 +1,455 @@
+/**
+ * InboxStudyCard - Card displaying an inbox study with actions
+ *
+ * Shows study status, files, and provides actions for:
+ * - Running introspection
+ * - Generating README
+ * - Finalizing the study
+ */
+
+import React, { useState, useEffect } from 'react';
+import {
+  FileText,
+  Folder,
+  Trash2,
+  Play,
+  CheckCircle,
+  Clock,
+  AlertCircle,
+  Loader2,
+  ChevronDown,
+  ChevronRight,
+  Sparkles,
+  ArrowRight,
+  Eye,
+  Save,
+} from 'lucide-react';
+import { InboxStudy, SpecStatus, ExpressionInfo, InboxStudyDetail } from '../../types/intake';
+import { intakeApi } from '../../api/intake';
+import { FileDropzone } from './FileDropzone';
+import { ContextFileUpload } from './ContextFileUpload';
+import { ExpressionList } from './ExpressionList';
+
+interface InboxStudyCardProps {
+  study: InboxStudy;
+  onRefresh: () => void;
+  onSelect: (studyName: string) => void;
+}
+
+const statusConfig: Record<SpecStatus, { icon: React.ReactNode; color: string; label: string }> = {
+  draft: {
+    icon: <Clock className="w-4 h-4" />,
+    color: 'text-dark-400 bg-dark-600',
+    label: 'Draft',
+  },
+  introspected: {
+    icon: <CheckCircle className="w-4 h-4" />,
+    color: 'text-blue-400 bg-blue-500/10',
+    label: 'Introspected',
+  },
+  configured: {
+    icon: <CheckCircle className="w-4 h-4" />,
+    color: 'text-green-400 bg-green-500/10',
+    label: 'Configured',
+  },
+  validated: {
+    icon: <CheckCircle className="w-4 h-4" />,
+    color: 'text-green-400 bg-green-500/10',
+    label: 'Validated',
+  },
+  ready: {
+    icon: <CheckCircle className="w-4 h-4" />,
+    color: 'text-primary-400 bg-primary-500/10',
+    label: 'Ready',
+  },
+  running: {
+    icon: <Play className="w-4 h-4" />,
+    color: 'text-yellow-400 bg-yellow-500/10',
+    label: 'Running',
+  },
+  completed: {
+    icon: <CheckCircle className="w-4 h-4" />,
+    color: 'text-green-400 bg-green-500/10',
+    label: 'Completed',
+  },
+  failed: {
+    icon: <AlertCircle className="w-4 h-4" />,
+    color: 'text-red-400 bg-red-500/10',
+    label: 'Failed',
+  },
+};
+
+export const InboxStudyCard: React.FC<InboxStudyCardProps> = ({
+  study,
+  onRefresh,
+  onSelect,
+}) => {
+  const [isExpanded, setIsExpanded] = useState(false);
+  const [isIntrospecting, setIsIntrospecting] = useState(false);
+  const [isGeneratingReadme, setIsGeneratingReadme] = useState(false);
+  const [isDeleting, setIsDeleting] = useState(false);
+  const [error, setError] = useState<string | null>(null);
+  
+  // Introspection data (fetched when expanded)
+  const [studyDetail, setStudyDetail] = useState<InboxStudyDetail | null>(null);
+  const [isLoadingDetail, setIsLoadingDetail] = useState(false);
+  const [selectedExpressions, setSelectedExpressions] = useState<string[]>([]);
+  const [showReadme, setShowReadme] = useState(false);
+  const [readmeContent, setReadmeContent] = useState<string | null>(null);
+  const [isSavingDVs, setIsSavingDVs] = useState(false);
+  const [dvSaveMessage, setDvSaveMessage] = useState<string | null>(null);
+
+  const status = statusConfig[study.status] || statusConfig.draft;
+  
+  // Fetch study details when expanded for the first time
+  useEffect(() => {
+    if (isExpanded && !studyDetail && !isLoadingDetail) {
+      loadStudyDetail();
+    }
+  }, [isExpanded]);
+  
+  const loadStudyDetail = async () => {
+    setIsLoadingDetail(true);
+    try {
+      const detail = await intakeApi.getInboxStudy(study.study_name);
+      setStudyDetail(detail);
+      
+      // Auto-select candidate expressions
+      const introspection = detail.spec?.model?.introspection;
+      if (introspection?.expressions) {
+        const candidates = introspection.expressions
+          .filter((e: ExpressionInfo) => e.is_candidate)
+          .map((e: ExpressionInfo) => e.name);
+        setSelectedExpressions(candidates);
+      }
+    } catch (err) {
+      console.error('Failed to load study detail:', err);
+    } finally {
+      setIsLoadingDetail(false);
+    }
+  };
+
+  const handleIntrospect = async () => {
+    setIsIntrospecting(true);
+    setError(null);
+    try {
+      await intakeApi.introspect({ study_name: study.study_name });
+      // Reload study detail to get new introspection data
+      await loadStudyDetail();
+      onRefresh();
+    } catch (err) {
+      setError(err instanceof Error ? err.message : 'Introspection failed');
+    } finally {
+      setIsIntrospecting(false);
+    }
+  };
+
+  const handleGenerateReadme = async () => {
+    setIsGeneratingReadme(true);
+    setError(null);
+    try {
+      const response = await intakeApi.generateReadme(study.study_name);
+      setReadmeContent(response.content);
+      setShowReadme(true);
+      onRefresh();
+    } catch (err) {
+      setError(err instanceof Error ? err.message : 'README generation failed');
+    } finally {
+      setIsGeneratingReadme(false);
+    }
+  };
+
+  const handleDelete = async () => {
+    if (!confirm(`Delete inbox study "${study.study_name}"? This cannot be undone.`)) {
+      return;
+    }
+    setIsDeleting(true);
+    try {
+      await intakeApi.deleteInboxStudy(study.study_name);
+      onRefresh();
+    } catch (err) {
+      setError(err instanceof Error ? err.message : 'Delete failed');
+      setIsDeleting(false);
+    }
+  };
+
+  const handleSaveDesignVariables = async () => {
+    if (selectedExpressions.length === 0) {
+      setError('Please select at least one expression to use as a design variable');
+      return;
+    }
+    
+    setIsSavingDVs(true);
+    setError(null);
+    setDvSaveMessage(null);
+    
+    try {
+      const result = await intakeApi.createDesignVariables(study.study_name, selectedExpressions);
+      setDvSaveMessage(`Created ${result.total_created} design variable(s)`);
+      // Reload study detail to see updated spec
+      await loadStudyDetail();
+      onRefresh();
+    } catch (err) {
+      setError(err instanceof Error ? err.message : 'Failed to save design variables');
+    } finally {
+      setIsSavingDVs(false);
+    }
+  };
+
+  const canIntrospect = study.status === 'draft' && study.model_files.length > 0;
+  const canGenerateReadme = study.status === 'introspected';
+  const canFinalize = ['introspected', 'configured'].includes(study.status);
+  const canSaveDVs = study.status === 'introspected' && selectedExpressions.length > 0;
+
+  return (
+    <div className="glass rounded-xl border border-primary-400/10 overflow-hidden">
+      {/* Header - Always visible */}
+      <button
+        onClick={() => setIsExpanded(!isExpanded)}
+        className="w-full px-4 py-3 flex items-center justify-between hover:bg-white/5 transition-colors"
+      >
+        <div className="flex items-center gap-3">
+          <div className="w-10 h-10 rounded-lg bg-dark-700 flex items-center justify-center">
+            <Folder className="w-5 h-5 text-primary-400" />
+          </div>
+          <div className="text-left">
+            <h4 className="text-white font-medium">{study.study_name}</h4>
+            {study.description && (
+              <p className="text-sm text-dark-400 truncate max-w-[300px]">
+                {study.description}
+              </p>
+            )}
+          </div>
+        </div>
+        <div className="flex items-center gap-3">
+          {/* Status Badge */}
+          <span className={`inline-flex items-center gap-1.5 px-2.5 py-1 rounded-full text-xs font-medium ${status.color}`}>
+            {status.icon}
+            {status.label}
+          </span>
+          {/* File Count */}
+          <span className="text-dark-500 text-sm">
+            {study.model_files.length} files
+          </span>
+          {/* Expand Icon */}
+          {isExpanded ? (
+            <ChevronDown className="w-4 h-4 text-dark-400" />
+          ) : (
+            <ChevronRight className="w-4 h-4 text-dark-400" />
+          )}
+        </div>
+      </button>
+
+      {/* Expanded Content */}
+      {isExpanded && (
+        <div className="px-4 pb-4 space-y-4 border-t border-primary-400/10 pt-4">
+          {/* Error Display */}
+          {error && (
+            <div className="p-3 rounded-lg bg-red-500/10 border border-red-500/30 text-red-400 text-sm flex items-center gap-2">
+              <AlertCircle className="w-4 h-4 flex-shrink-0" />
+              {error}
+            </div>
+          )}
+
+          {/* Success Message */}
+          {dvSaveMessage && (
+            <div className="p-3 rounded-lg bg-green-500/10 border border-green-500/30 text-green-400 text-sm flex items-center gap-2">
+              <CheckCircle className="w-4 h-4 flex-shrink-0" />
+              {dvSaveMessage}
+            </div>
+          )}
+
+          {/* Files Section */}
+          {study.model_files.length > 0 && (
+            <div>
+              <h5 className="text-sm font-medium text-dark-300 mb-2">Model Files</h5>
+              <div className="flex flex-wrap gap-2">
+                {study.model_files.map((file) => (
+                  <span
+                    key={file}
+                    className="inline-flex items-center gap-1.5 px-2 py-1 rounded bg-dark-700 text-dark-300 text-xs"
+                  >
+                    <FileText className="w-3 h-3" />
+                    {file}
+                  </span>
+                ))}
+              </div>
+            </div>
+          )}
+
+          {/* Model File Upload Section */}
+          <div>
+            <h5 className="text-sm font-medium text-dark-300 mb-2">Upload Model Files</h5>
+            <FileDropzone 
+              studyName={study.study_name} 
+              onUploadComplete={onRefresh}
+              compact={true}
+            />
+          </div>
+
+          {/* Context File Upload Section */}
+          <ContextFileUpload 
+            studyName={study.study_name} 
+            onUploadComplete={onRefresh}
+          />
+
+          {/* Introspection Results - Expressions */}
+          {isLoadingDetail && (
+            <div className="flex items-center gap-2 text-dark-400 text-sm py-4">
+              <Loader2 className="w-4 h-4 animate-spin" />
+              Loading introspection data...
+            </div>
+          )}
+          
+          {studyDetail?.spec?.model?.introspection?.expressions && 
+           studyDetail.spec.model.introspection.expressions.length > 0 && (
+            <ExpressionList
+              expressions={studyDetail.spec.model.introspection.expressions}
+              massKg={studyDetail.spec.model.introspection.mass_kg}
+              selectedExpressions={selectedExpressions}
+              onSelectionChange={setSelectedExpressions}
+              readOnly={study.status === 'configured'}
+              compact={true}
+            />
+          )}
+
+          {/* README Preview Section */}
+          {(readmeContent || study.status === 'configured') && (
+            <div className="space-y-2">
+              <div className="flex items-center justify-between">
+                <h5 className="text-sm font-medium text-dark-300 flex items-center gap-2">
+                  <FileText className="w-4 h-4" />
+                  README.md
+                </h5>
+                <button
+                  onClick={() => setShowReadme(!showReadme)}
+                  className="flex items-center gap-1 px-2 py-1 text-xs rounded bg-dark-600 
+                             text-dark-300 hover:bg-dark-500 transition-colors"
+                >
+                  <Eye className="w-3 h-3" />
+                  {showReadme ? 'Hide' : 'Preview'}
+                </button>
+              </div>
+              {showReadme && readmeContent && (
+                <div className="max-h-64 overflow-y-auto rounded-lg border border-dark-600 
+                                bg-dark-800 p-4">
+                  <pre className="text-xs text-dark-300 whitespace-pre-wrap font-mono">
+                    {readmeContent}
+                  </pre>
+                </div>
+              )}
+            </div>
+          )}
+
+          {/* No Files Warning */}
+          {study.model_files.length === 0 && (
+            <div className="p-3 rounded-lg bg-yellow-500/10 border border-yellow-500/30 text-yellow-400 text-sm flex items-center gap-2">
+              <AlertCircle className="w-4 h-4 flex-shrink-0" />
+              No model files found. Upload .prt, .sim, or .fem files to continue.
+            </div>
+          )}
+
+          {/* Actions */}
+          <div className="flex flex-wrap gap-2">
+            {/* Introspect */}
+            {canIntrospect && (
+              <button
+                onClick={handleIntrospect}
+                disabled={isIntrospecting}
+                className="flex items-center gap-2 px-3 py-1.5 rounded-lg text-sm font-medium
+                           bg-blue-500/10 text-blue-400 hover:bg-blue-500/20 
+                           disabled:opacity-50 transition-colors"
+              >
+                {isIntrospecting ? (
+                  <Loader2 className="w-4 h-4 animate-spin" />
+                ) : (
+                  <Play className="w-4 h-4" />
+                )}
+                Introspect Model
+              </button>
+            )}
+
+            {/* Save Design Variables */}
+            {canSaveDVs && (
+              <button
+                onClick={handleSaveDesignVariables}
+                disabled={isSavingDVs}
+                className="flex items-center gap-2 px-3 py-1.5 rounded-lg text-sm font-medium
+                           bg-green-500/10 text-green-400 hover:bg-green-500/20 
+                           disabled:opacity-50 transition-colors"
+              >
+                {isSavingDVs ? (
+                  <Loader2 className="w-4 h-4 animate-spin" />
+                ) : (
+                  <Save className="w-4 h-4" />
+                )}
+                Save as DVs ({selectedExpressions.length})
+              </button>
+            )}
+
+            {/* Generate README */}
+            {canGenerateReadme && (
+              <button
+                onClick={handleGenerateReadme}
+                disabled={isGeneratingReadme}
+                className="flex items-center gap-2 px-3 py-1.5 rounded-lg text-sm font-medium
+                           bg-purple-500/10 text-purple-400 hover:bg-purple-500/20 
+                           disabled:opacity-50 transition-colors"
+              >
+                {isGeneratingReadme ? (
+                  <Loader2 className="w-4 h-4 animate-spin" />
+                ) : (
+                  <Sparkles className="w-4 h-4" />
+                )}
+                Generate README
+              </button>
+            )}
+
+            {/* Finalize */}
+            {canFinalize && (
+              <button
+                onClick={() => onSelect(study.study_name)}
+                className="flex items-center gap-2 px-3 py-1.5 rounded-lg text-sm font-medium
+                           bg-primary-500/10 text-primary-400 hover:bg-primary-500/20 
+                           transition-colors"
+              >
+                <ArrowRight className="w-4 h-4" />
+                Finalize Study
+              </button>
+            )}
+
+            {/* Delete */}
+            <button
+              onClick={handleDelete}
+              disabled={isDeleting}
+              className="flex items-center gap-2 px-3 py-1.5 rounded-lg text-sm font-medium
+                         bg-red-500/10 text-red-400 hover:bg-red-500/20 
+                         disabled:opacity-50 transition-colors ml-auto"
+            >
+              {isDeleting ? (
+                <Loader2 className="w-4 h-4 animate-spin" />
+              ) : (
+                <Trash2 className="w-4 h-4" />
+              )}
+              Delete
+            </button>
+          </div>
+
+          {/* Workflow Hint */}
+          {study.status === 'draft' && study.model_files.length > 0 && (
+            <p className="text-xs text-dark-500">
+              Next step: Run introspection to discover expressions and model properties.
+            </p>
+          )}
+          {study.status === 'introspected' && (
+            <p className="text-xs text-dark-500">
+              Next step: Generate README with Claude AI, then finalize to create the study.
+            </p>
+          )}
+        </div>
+      )}
+    </div>
+  );
+};
+
+export default InboxStudyCard;

atomizer-dashboard/frontend/src/components/intake/index.ts

@@ -0,0 +1,13 @@
+/**
+ * Intake Components Index
+ *
+ * Export all intake workflow components.
+ */
+
+export { CreateStudyCard } from './CreateStudyCard';
+export { InboxStudyCard } from './InboxStudyCard';
+export { FinalizeModal } from './FinalizeModal';
+export { InboxSection } from './InboxSection';
+export { FileDropzone } from './FileDropzone';
+export { ContextFileUpload } from './ContextFileUpload';
+export { ExpressionList } from './ExpressionList';

atomizer-dashboard/frontend/src/components/studio/StudioBuildDialog.tsx

@@ -0,0 +1,254 @@
+/**
+ * StudioBuildDialog - Final dialog to name and build the study
+ */
+
+import React, { useState, useEffect } from 'react';
+import { X, Loader2, FolderOpen, AlertCircle, CheckCircle, Sparkles, Play } from 'lucide-react';
+import { intakeApi } from '../../api/intake';
+
+interface StudioBuildDialogProps {
+  draftId: string;
+  onClose: () => void;
+  onBuildComplete: (finalPath: string, finalName: string) => void;
+}
+
+interface Topic {
+  name: string;
+  study_count: number;
+}
+
+export const StudioBuildDialog: React.FC<StudioBuildDialogProps> = ({
+  draftId,
+  onClose,
+  onBuildComplete,
+}) => {
+  const [studyName, setStudyName] = useState('');
+  const [topic, setTopic] = useState('');
+  const [newTopic, setNewTopic] = useState('');
+  const [useNewTopic, setUseNewTopic] = useState(false);
+  const [topics, setTopics] = useState<Topic[]>([]);
+  const [isBuilding, setIsBuilding] = useState(false);
+  const [error, setError] = useState<string | null>(null);
+  const [validationErrors, setValidationErrors] = useState<string[]>([]);
+  
+  // Load topics
+  useEffect(() => {
+    loadTopics();
+  }, []);
+  
+  const loadTopics = async () => {
+    try {
+      const response = await intakeApi.listTopics();
+      setTopics(response.topics);
+      if (response.topics.length > 0) {
+        setTopic(response.topics[0].name);
+      }
+    } catch (err) {
+      console.error('Failed to load topics:', err);
+    }
+  };
+  
+  // Validate study name
+  useEffect(() => {
+    const errors: string[] = [];
+    
+    if (studyName.length > 0) {
+      if (studyName.length < 3) {
+        errors.push('Name must be at least 3 characters');
+      }
+      if (!/^[a-z0-9_]+$/.test(studyName)) {
+        errors.push('Use only lowercase letters, numbers, and underscores');
+      }
+      if (studyName.startsWith('draft_')) {
+        errors.push('Name cannot start with "draft_"');
+      }
+    }
+    
+    setValidationErrors(errors);
+  }, [studyName]);
+  
+  const handleBuild = async () => {
+    const finalTopic = useNewTopic ? newTopic : topic;
+    
+    if (!studyName || !finalTopic) {
+      setError('Please provide both a study name and topic');
+      return;
+    }
+    
+    if (validationErrors.length > 0) {
+      setError('Please fix validation errors');
+      return;
+    }
+    
+    setIsBuilding(true);
+    setError(null);
+    
+    try {
+      const response = await intakeApi.finalizeStudio(draftId, {
+        topic: finalTopic,
+        newName: studyName,
+        runBaseline: false,
+      });
+      
+      onBuildComplete(response.final_path, response.final_name);
+      
+    } catch (err) {
+      setError(err instanceof Error ? err.message : 'Build failed');
+    } finally {
+      setIsBuilding(false);
+    }
+  };
+  
+  const isValid = studyName.length >= 3 && 
+                  validationErrors.length === 0 && 
+                  (topic || (useNewTopic && newTopic));
+  
+  return (
+    <div className="fixed inset-0 bg-black/50 flex items-center justify-center z-50">
+      <div className="bg-dark-850 border border-dark-700 rounded-xl shadow-xl w-full max-w-lg mx-4">
+        {/* Header */}
+        <div className="flex items-center justify-between p-4 border-b border-dark-700">
+          <div className="flex items-center gap-2">
+            <Sparkles className="w-5 h-5 text-primary-400" />
+            <h2 className="text-lg font-semibold text-white">Build Study</h2>
+          </div>
+          <button
+            onClick={onClose}
+            className="p-1 hover:bg-dark-700 rounded text-dark-400 hover:text-white transition-colors"
+          >
+            <X className="w-5 h-5" />
+          </button>
+        </div>
+        
+        {/* Content */}
+        <div className="p-6 space-y-6">
+          {/* Study Name */}
+          <div>
+            <label className="block text-sm font-medium text-dark-300 mb-2">
+              Study Name
+            </label>
+            <input
+              type="text"
+              value={studyName}
+              onChange={(e) => setStudyName(e.target.value.toLowerCase().replace(/[^a-z0-9_]/g, '_'))}
+              placeholder="my_optimization_study"
+              className="w-full bg-dark-700 border border-dark-600 rounded-lg px-3 py-2 text-white placeholder-dark-500 focus:outline-none focus:border-primary-400"
+            />
+            {validationErrors.length > 0 && (
+              <div className="mt-2 space-y-1">
+                {validationErrors.map((err, i) => (
+                  <p key={i} className="text-xs text-red-400 flex items-center gap-1">
+                    <AlertCircle className="w-3 h-3" />
+                    {err}
+                  </p>
+                ))}
+              </div>
+            )}
+            {studyName.length >= 3 && validationErrors.length === 0 && (
+              <p className="mt-2 text-xs text-green-400 flex items-center gap-1">
+                <CheckCircle className="w-3 h-3" />
+                Name is valid
+              </p>
+            )}
+          </div>
+          
+          {/* Topic Selection */}
+          <div>
+            <label className="block text-sm font-medium text-dark-300 mb-2">
+              Topic Folder
+            </label>
+            
+            {!useNewTopic && topics.length > 0 && (
+              <div className="space-y-2">
+                <select
+                  value={topic}
+                  onChange={(e) => setTopic(e.target.value)}
+                  className="w-full bg-dark-700 border border-dark-600 rounded-lg px-3 py-2 text-white focus:outline-none focus:border-primary-400"
+                >
+                  {topics.map((t) => (
+                    <option key={t.name} value={t.name}>
+                      {t.name} ({t.study_count} studies)
+                    </option>
+                  ))}
+                </select>
+                <button
+                  onClick={() => setUseNewTopic(true)}
+                  className="text-sm text-primary-400 hover:text-primary-300"
+                >
+                  + Create new topic
+                </button>
+              </div>
+            )}
+            
+            {(useNewTopic || topics.length === 0) && (
+              <div className="space-y-2">
+                <input
+                  type="text"
+                  value={newTopic}
+                  onChange={(e) => setNewTopic(e.target.value.replace(/[^A-Za-z0-9_]/g, '_'))}
+                  placeholder="NewTopic"
+                  className="w-full bg-dark-700 border border-dark-600 rounded-lg px-3 py-2 text-white placeholder-dark-500 focus:outline-none focus:border-primary-400"
+                />
+                {topics.length > 0 && (
+                  <button
+                    onClick={() => setUseNewTopic(false)}
+                    className="text-sm text-dark-400 hover:text-white"
+                  >
+                    Use existing topic
+                  </button>
+                )}
+              </div>
+            )}
+          </div>
+          
+          {/* Preview */}
+          <div className="p-3 bg-dark-700/50 rounded-lg">
+            <p className="text-xs text-dark-400 mb-1">Study will be created at:</p>
+            <p className="text-sm text-white font-mono flex items-center gap-2">
+              <FolderOpen className="w-4 h-4 text-primary-400" />
+              studies/{useNewTopic ? newTopic || '...' : topic}/{studyName || '...'}
+            </p>
+          </div>
+          
+          {/* Error */}
+          {error && (
+            <div className="p-3 rounded-lg bg-red-500/10 border border-red-500/30 text-red-400 text-sm flex items-center gap-2">
+              <AlertCircle className="w-4 h-4 flex-shrink-0" />
+              {error}
+            </div>
+          )}
+        </div>
+        
+        {/* Footer */}
+        <div className="flex items-center justify-end gap-3 p-4 border-t border-dark-700">
+          <button
+            onClick={onClose}
+            disabled={isBuilding}
+            className="px-4 py-2 text-sm text-dark-300 hover:text-white hover:bg-dark-700 rounded-lg transition-colors"
+          >
+            Cancel
+          </button>
+          <button
+            onClick={handleBuild}
+            disabled={!isValid || isBuilding}
+            className="flex items-center gap-2 px-4 py-2 text-sm font-medium bg-primary-500 text-white rounded-lg hover:bg-primary-400 disabled:opacity-50 disabled:cursor-not-allowed transition-colors"
+          >
+            {isBuilding ? (
+              <>
+                <Loader2 className="w-4 h-4 animate-spin" />
+                Building...
+              </>
+            ) : (
+              <>
+                <Play className="w-4 h-4" />
+                Build Study
+              </>
+            )}
+          </button>
+        </div>
+      </div>
+    </div>
+  );
+};
+
+export default StudioBuildDialog;

atomizer-dashboard/frontend/src/components/studio/StudioChat.tsx

@@ -0,0 +1,375 @@
+/**
+ * StudioChat - Context-aware AI chat for Studio
+ * 
+ * Uses the existing useChat hook to communicate with Claude via WebSocket.
+ * Injects model files and context documents into the conversation.
+ */
+
+import React, { useRef, useEffect, useState, useMemo } from 'react';
+import { Send, Loader2, Sparkles, FileText, Wifi, WifiOff, Bot, User, File, AlertCircle } from 'lucide-react';
+import { useChat } from '../../hooks/useChat';
+import { useSpecStore, useSpec } from '../../hooks/useSpecStore';
+import { MarkdownRenderer } from '../MarkdownRenderer';
+import { ToolCallCard } from '../chat/ToolCallCard';
+
+interface StudioChatProps {
+  draftId: string;
+  contextFiles: string[];
+  contextContent: string;
+  modelFiles: string[];
+  onSpecUpdated: () => void;
+}
+
+export const StudioChat: React.FC<StudioChatProps> = ({
+  draftId,
+  contextFiles,
+  contextContent,
+  modelFiles,
+  onSpecUpdated,
+}) => {
+  const messagesEndRef = useRef<HTMLDivElement>(null);
+  const inputRef = useRef<HTMLTextAreaElement>(null);
+  const [input, setInput] = useState('');
+  const [hasInjectedContext, setHasInjectedContext] = useState(false);
+  
+  // Get spec store for canvas updates
+  const spec = useSpec();
+  const { reloadSpec, setSpecFromWebSocket } = useSpecStore();
+  
+  // Build canvas state with full context for Claude
+  const canvasState = useMemo(() => ({
+    nodes: [],
+    edges: [],
+    studyName: draftId,
+    studyPath: `_inbox/${draftId}`,
+    // Include file info for Claude context
+    modelFiles,
+    contextFiles,
+    contextContent: contextContent.substring(0, 50000), // Limit context size
+  }), [draftId, modelFiles, contextFiles, contextContent]);
+  
+  // Use the chat hook with WebSocket
+  // Power mode gives Claude write permissions to modify the spec
+  const {
+    messages,
+    isThinking,
+    error,
+    isConnected,
+    sendMessage,
+    updateCanvasState,
+  } = useChat({
+    studyId: draftId,
+    mode: 'power',  // Power mode = --dangerously-skip-permissions = can write files
+    useWebSocket: true,
+    canvasState,
+    onError: (err) => console.error('[StudioChat] Error:', err),
+    onSpecUpdated: (newSpec) => {
+      // Claude modified the spec - update the store directly
+      console.log('[StudioChat] Spec updated by Claude');
+      setSpecFromWebSocket(newSpec, draftId);
+      onSpecUpdated();
+    },
+    onCanvasModification: (modification) => {
+      // Claude wants to modify canvas - reload the spec
+      console.log('[StudioChat] Canvas modification:', modification);
+      reloadSpec();
+      onSpecUpdated();
+    },
+  });
+  
+  // Update canvas state when context changes
+  useEffect(() => {
+    updateCanvasState(canvasState);
+  }, [canvasState, updateCanvasState]);
+  
+  // Scroll to bottom when messages change
+  useEffect(() => {
+    messagesEndRef.current?.scrollIntoView({ behavior: 'smooth' });
+  }, [messages]);
+  
+  // Auto-focus input
+  useEffect(() => {
+    inputRef.current?.focus();
+  }, []);
+  
+  // Build context summary for display
+  const contextSummary = useMemo(() => {
+    const parts: string[] = [];
+    if (modelFiles.length > 0) {
+      parts.push(`${modelFiles.length} model file${modelFiles.length > 1 ? 's' : ''}`);
+    }
+    if (contextFiles.length > 0) {
+      parts.push(`${contextFiles.length} context doc${contextFiles.length > 1 ? 's' : ''}`);
+    }
+    if (contextContent) {
+      parts.push(`${contextContent.length.toLocaleString()} chars context`);
+    }
+    return parts.join(', ');
+  }, [modelFiles, contextFiles, contextContent]);
+  
+  const handleSend = () => {
+    if (!input.trim() || isThinking) return;
+    
+    let messageToSend = input.trim();
+    
+    // On first message, inject full context so Claude has everything it needs
+    if (!hasInjectedContext && (modelFiles.length > 0 || contextContent)) {
+      const contextParts: string[] = [];
+      
+      // Add model files info
+      if (modelFiles.length > 0) {
+        contextParts.push(`**Model Files Uploaded:**\n${modelFiles.map(f => `- ${f}`).join('\n')}`);
+      }
+      
+      // Add context document content (full text)
+      if (contextContent) {
+        contextParts.push(`**Context Documents Content:**\n\`\`\`\n${contextContent.substring(0, 30000)}\n\`\`\``);
+      }
+      
+      // Add current spec state
+      if (spec) {
+        const dvCount = spec.design_variables?.length || 0;
+        const objCount = spec.objectives?.length || 0;
+        const extCount = spec.extractors?.length || 0;
+        if (dvCount > 0 || objCount > 0 || extCount > 0) {
+          contextParts.push(`**Current Configuration:** ${dvCount} design variables, ${objCount} objectives, ${extCount} extractors`);
+        }
+      }
+      
+      if (contextParts.length > 0) {
+        messageToSend = `${contextParts.join('\n\n')}\n\n---\n\n**User Request:** ${messageToSend}`;
+      }
+      
+      setHasInjectedContext(true);
+    }
+    
+    sendMessage(messageToSend);
+    setInput('');
+  };
+  
+  const handleKeyDown = (e: React.KeyboardEvent) => {
+    if (e.key === 'Enter' && !e.shiftKey) {
+      e.preventDefault();
+      handleSend();
+    }
+  };
+  
+  // Welcome message for empty state
+  const showWelcome = messages.length === 0;
+  
+  // Check if we have any context
+  const hasContext = modelFiles.length > 0 || contextContent.length > 0;
+  
+  return (
+    <div className="h-full flex flex-col">
+      {/* Header */}
+      <div className="p-3 border-b border-dark-700 flex-shrink-0">
+        <div className="flex items-center justify-between mb-2">
+          <div className="flex items-center gap-2">
+            <Sparkles className="w-5 h-5 text-primary-400" />
+            <span className="font-medium text-white">Studio Assistant</span>
+          </div>
+          <span className={`flex items-center gap-1 text-xs px-2 py-0.5 rounded ${
+            isConnected 
+              ? 'text-green-400 bg-green-400/10' 
+              : 'text-red-400 bg-red-400/10'
+          }`}>
+            {isConnected ? <Wifi className="w-3 h-3" /> : <WifiOff className="w-3 h-3" />}
+            {isConnected ? 'Connected' : 'Disconnected'}
+          </span>
+        </div>
+        
+        {/* Context indicator */}
+        {contextSummary && (
+          <div className="flex items-center gap-2 text-xs">
+            <div className="flex items-center gap-1 text-amber-400 bg-amber-400/10 px-2 py-1 rounded">
+              <FileText className="w-3 h-3" />
+              <span>{contextSummary}</span>
+            </div>
+            {hasContext && !hasInjectedContext && (
+              <span className="text-dark-500">Will be sent with first message</span>
+            )}
+            {hasInjectedContext && (
+              <span className="text-green-500">Context sent</span>
+            )}
+          </div>
+        )}
+      </div>
+      
+      {/* Messages */}
+      <div className="flex-1 overflow-y-auto p-3 space-y-4">
+        {/* Welcome message with context awareness */}
+        {showWelcome && (
+          <div className="flex gap-3">
+            <div className="flex-shrink-0 w-8 h-8 rounded-lg flex items-center justify-center bg-primary-500/20 text-primary-400">
+              <Bot className="w-4 h-4" />
+            </div>
+            <div className="flex-1 bg-dark-700 rounded-lg px-4 py-3 text-sm text-dark-100">
+              <MarkdownRenderer content={hasContext 
+                ? `I can see you've uploaded files. Here's what I have access to:
+
+${modelFiles.length > 0 ? `**Model Files:** ${modelFiles.join(', ')}` : ''}
+${contextContent ? `\n**Context Document:** ${contextContent.substring(0, 200)}...` : ''}
+
+Tell me what you want to optimize and I'll help you configure the study!`
+                : `Welcome to Atomizer Studio! I'm here to help you configure your optimization study.
+
+**What I can do:**
+- Read your uploaded context documents
+- Help set up design variables, objectives, and constraints
+- Create extractors for physics outputs
+- Suggest optimization strategies
+
+Upload your model files and any requirements documents, then tell me what you want to optimize!`} />
+            </div>
+          </div>
+        )}
+        
+        {/* File context display (only if we have files but no messages yet) */}
+        {showWelcome && modelFiles.length > 0 && (
+          <div className="bg-dark-800/50 rounded-lg p-3 border border-dark-700">
+            <p className="text-xs text-dark-400 mb-2 font-medium">Loaded Files:</p>
+            <div className="flex flex-wrap gap-2">
+              {modelFiles.map((file, idx) => (
+                <span key={idx} className="flex items-center gap-1 text-xs bg-blue-500/10 text-blue-400 px-2 py-1 rounded">
+                  <File className="w-3 h-3" />
+                  {file}
+                </span>
+              ))}
+              {contextFiles.map((file, idx) => (
+                <span key={idx} className="flex items-center gap-1 text-xs bg-amber-500/10 text-amber-400 px-2 py-1 rounded">
+                  <FileText className="w-3 h-3" />
+                  {file}
+                </span>
+              ))}
+            </div>
+          </div>
+        )}
+        
+        {/* Chat messages */}
+        {messages.map((msg) => {
+          const isAssistant = msg.role === 'assistant';
+          const isSystem = msg.role === 'system';
+          
+          // System messages
+          if (isSystem) {
+            return (
+              <div key={msg.id} className="flex justify-center my-2">
+                <div className="px-3 py-1 bg-dark-700/50 rounded-full text-xs text-dark-400 border border-dark-600">
+                  {msg.content}
+                </div>
+              </div>
+            );
+          }
+          
+          return (
+            <div
+              key={msg.id}
+              className={`flex gap-3 ${isAssistant ? '' : 'flex-row-reverse'}`}
+            >
+              {/* Avatar */}
+              <div
+                className={`flex-shrink-0 w-8 h-8 rounded-lg flex items-center justify-center ${
+                  isAssistant
+                    ? 'bg-primary-500/20 text-primary-400'
+                    : 'bg-dark-600 text-dark-300'
+                }`}
+              >
+                {isAssistant ? <Bot className="w-4 h-4" /> : <User className="w-4 h-4" />}
+              </div>
+              
+              {/* Message content */}
+              <div
+                className={`flex-1 max-w-[85%] rounded-lg px-4 py-3 text-sm ${
+                  isAssistant
+                    ? 'bg-dark-700 text-dark-100'
+                    : 'bg-primary-500 text-white ml-auto'
+                }`}
+              >
+                {isAssistant ? (
+                  <>
+                    {msg.content && <MarkdownRenderer content={msg.content} />}
+                    {msg.isStreaming && !msg.content && (
+                      <span className="text-dark-400">Thinking...</span>
+                    )}
+                    {/* Tool calls */}
+                    {msg.toolCalls && msg.toolCalls.length > 0 && (
+                      <div className="mt-3 space-y-2">
+                        {msg.toolCalls.map((tool, idx) => (
+                          <ToolCallCard key={idx} toolCall={tool} />
+                        ))}
+                      </div>
+                    )}
+                  </>
+                ) : (
+                  <span className="whitespace-pre-wrap">{msg.content}</span>
+                )}
+              </div>
+            </div>
+          );
+        })}
+        
+        {/* Thinking indicator */}
+        {isThinking && messages.length > 0 && !messages[messages.length - 1]?.isStreaming && (
+          <div className="flex gap-3">
+            <div className="flex-shrink-0 w-8 h-8 rounded-lg flex items-center justify-center bg-primary-500/20 text-primary-400">
+              <Bot className="w-4 h-4" />
+            </div>
+            <div className="bg-dark-700 rounded-lg px-4 py-3 flex items-center gap-2">
+              <Loader2 className="w-4 h-4 text-primary-400 animate-spin" />
+              <span className="text-sm text-dark-300">Thinking...</span>
+            </div>
+          </div>
+        )}
+        
+        {/* Error display */}
+        {error && (
+          <div className="flex gap-3">
+            <div className="flex-shrink-0 w-8 h-8 rounded-lg flex items-center justify-center bg-red-500/20 text-red-400">
+              <AlertCircle className="w-4 h-4" />
+            </div>
+            <div className="flex-1 px-4 py-3 bg-red-500/10 rounded-lg text-sm text-red-400 border border-red-500/30">
+              {error}
+            </div>
+          </div>
+        )}
+        
+        <div ref={messagesEndRef} />
+      </div>
+      
+      {/* Input */}
+      <div className="p-3 border-t border-dark-700 flex-shrink-0">
+        <div className="flex gap-2">
+          <textarea
+            ref={inputRef}
+            value={input}
+            onChange={(e) => setInput(e.target.value)}
+            onKeyDown={handleKeyDown}
+            placeholder={isConnected ? "Ask about your optimization..." : "Connecting..."}
+            disabled={!isConnected}
+            rows={1}
+            className="flex-1 bg-dark-700 border border-dark-600 rounded-lg px-3 py-2 text-sm text-white placeholder-dark-400 resize-none focus:outline-none focus:border-primary-400 disabled:opacity-50"
+          />
+          <button
+            onClick={handleSend}
+            disabled={!input.trim() || isThinking || !isConnected}
+            className="p-2 bg-primary-500 text-white rounded-lg hover:bg-primary-400 disabled:opacity-50 disabled:cursor-not-allowed transition-colors"
+          >
+            {isThinking ? (
+              <Loader2 className="w-5 h-5 animate-spin" />
+            ) : (
+              <Send className="w-5 h-5" />
+            )}
+          </button>
+        </div>
+        {!isConnected && (
+          <p className="text-xs text-dark-500 mt-1">
+            Waiting for connection to Claude...
+          </p>
+        )}
+      </div>
+    </div>
+  );
+};
+
+export default StudioChat;

atomizer-dashboard/frontend/src/components/studio/StudioContextFiles.tsx

@@ -0,0 +1,117 @@
+/**
+ * StudioContextFiles - Context document upload and display
+ */
+
+import React, { useState, useRef } from 'react';
+import { FileText, Upload, Trash2, Loader2 } from 'lucide-react';
+import { intakeApi } from '../../api/intake';
+
+interface StudioContextFilesProps {
+  draftId: string;
+  files: string[];
+  onUploadComplete: () => void;
+}
+
+export const StudioContextFiles: React.FC<StudioContextFilesProps> = ({
+  draftId,
+  files,
+  onUploadComplete,
+}) => {
+  const [isUploading, setIsUploading] = useState(false);
+  const [deleting, setDeleting] = useState<string | null>(null);
+  const fileInputRef = useRef<HTMLInputElement>(null);
+  
+  const VALID_EXTENSIONS = ['.md', '.txt', '.pdf', '.json', '.csv', '.docx'];
+  
+  const handleFileSelect = async (e: React.ChangeEvent<HTMLInputElement>) => {
+    const selectedFiles = Array.from(e.target.files || []);
+    if (selectedFiles.length === 0) return;
+    
+    e.target.value = '';
+    setIsUploading(true);
+    
+    try {
+      await intakeApi.uploadContextFiles(draftId, selectedFiles);
+      onUploadComplete();
+    } catch (err) {
+      console.error('Failed to upload context files:', err);
+    } finally {
+      setIsUploading(false);
+    }
+  };
+  
+  const deleteFile = async (filename: string) => {
+    setDeleting(filename);
+    
+    try {
+      await intakeApi.deleteContextFile(draftId, filename);
+      onUploadComplete();
+    } catch (err) {
+      console.error('Failed to delete context file:', err);
+    } finally {
+      setDeleting(null);
+    }
+  };
+  
+  const getFileIcon = (_filename: string) => {
+    return <FileText className="w-3.5 h-3.5 text-amber-400" />;
+  };
+  
+  return (
+    <div className="space-y-2">
+      {/* File List */}
+      {files.length > 0 && (
+        <div className="space-y-1">
+          {files.map((name) => (
+            <div
+              key={name}
+              className="flex items-center gap-2 px-2 py-1.5 rounded bg-dark-700/50 text-sm group"
+            >
+              {getFileIcon(name)}
+              <span className="text-dark-200 truncate flex-1">{name}</span>
+              <button
+                onClick={() => deleteFile(name)}
+                disabled={deleting === name}
+                className="p-1 opacity-0 group-hover:opacity-100 hover:bg-red-500/20 rounded text-red-400 transition-all"
+              >
+                {deleting === name ? (
+                  <Loader2 className="w-3 h-3 animate-spin" />
+                ) : (
+                  <Trash2 className="w-3 h-3" />
+                )}
+              </button>
+            </div>
+          ))}
+        </div>
+      )}
+      
+      {/* Upload Button */}
+      <button
+        onClick={() => fileInputRef.current?.click()}
+        disabled={isUploading}
+        className="w-full flex items-center justify-center gap-2 px-3 py-2 rounded-lg
+                   border border-dashed border-dark-600 text-dark-400 text-sm
+                   hover:border-primary-400/50 hover:text-primary-400 hover:bg-primary-400/5
+                   disabled:opacity-50 transition-colors"
+      >
+        {isUploading ? (
+          <Loader2 className="w-4 h-4 animate-spin" />
+        ) : (
+          <Upload className="w-4 h-4" />
+        )}
+        {isUploading ? 'Uploading...' : 'Add context files'}
+      </button>
+      
+      <input
+        ref={fileInputRef}
+        type="file"
+        multiple
+        accept={VALID_EXTENSIONS.join(',')}
+        onChange={handleFileSelect}
+        className="hidden"
+      />
+    </div>
+  );
+};
+
+export default StudioContextFiles;

atomizer-dashboard/frontend/src/components/studio/StudioDropZone.tsx

@@ -0,0 +1,242 @@
+/**
+ * StudioDropZone - Smart file drop zone for Studio
+ * 
+ * Handles both model files (.sim, .prt, .fem) and context files (.pdf, .md, .txt)
+ */
+
+import React, { useState, useCallback, useRef } from 'react';
+import { Upload, X, Loader2, AlertCircle, CheckCircle, File } from 'lucide-react';
+import { intakeApi } from '../../api/intake';
+
+interface StudioDropZoneProps {
+  draftId: string;
+  type: 'model' | 'context';
+  files: string[];
+  onUploadComplete: () => void;
+}
+
+interface FileStatus {
+  file: File;
+  status: 'pending' | 'uploading' | 'success' | 'error';
+  message?: string;
+}
+
+const MODEL_EXTENSIONS = ['.prt', '.sim', '.fem', '.afem'];
+const CONTEXT_EXTENSIONS = ['.md', '.txt', '.pdf', '.json', '.csv', '.docx'];
+
+export const StudioDropZone: React.FC<StudioDropZoneProps> = ({
+  draftId,
+  type,
+  files,
+  onUploadComplete,
+}) => {
+  const [isDragging, setIsDragging] = useState(false);
+  const [pendingFiles, setPendingFiles] = useState<FileStatus[]>([]);
+  const [isUploading, setIsUploading] = useState(false);
+  const fileInputRef = useRef<HTMLInputElement>(null);
+  
+  const validExtensions = type === 'model' ? MODEL_EXTENSIONS : CONTEXT_EXTENSIONS;
+  
+  const validateFile = (file: File): { valid: boolean; reason?: string } => {
+    const ext = '.' + file.name.split('.').pop()?.toLowerCase();
+    if (!validExtensions.includes(ext)) {
+      return { valid: false, reason: `Invalid type: ${ext}` };
+    }
+    if (file.size > 500 * 1024 * 1024) {
+      return { valid: false, reason: 'File too large (max 500MB)' };
+    }
+    return { valid: true };
+  };
+  
+  const handleDragEnter = useCallback((e: React.DragEvent) => {
+    e.preventDefault();
+    e.stopPropagation();
+    setIsDragging(true);
+  }, []);
+  
+  const handleDragLeave = useCallback((e: React.DragEvent) => {
+    e.preventDefault();
+    e.stopPropagation();
+    setIsDragging(false);
+  }, []);
+  
+  const handleDragOver = useCallback((e: React.DragEvent) => {
+    e.preventDefault();
+    e.stopPropagation();
+  }, []);
+  
+  const addFiles = useCallback((newFiles: File[]) => {
+    const validFiles: FileStatus[] = [];
+    
+    for (const file of newFiles) {
+      if (pendingFiles.some(f => f.file.name === file.name)) {
+        continue;
+      }
+      
+      const validation = validateFile(file);
+      validFiles.push({
+        file,
+        status: validation.valid ? 'pending' : 'error',
+        message: validation.reason,
+      });
+    }
+    
+    setPendingFiles(prev => [...prev, ...validFiles]);
+  }, [pendingFiles, validExtensions]);
+  
+  const handleDrop = useCallback((e: React.DragEvent) => {
+    e.preventDefault();
+    e.stopPropagation();
+    setIsDragging(false);
+    addFiles(Array.from(e.dataTransfer.files));
+  }, [addFiles]);
+  
+  const handleFileSelect = useCallback((e: React.ChangeEvent<HTMLInputElement>) => {
+    addFiles(Array.from(e.target.files || []));
+    e.target.value = '';
+  }, [addFiles]);
+  
+  const removeFile = (index: number) => {
+    setPendingFiles(prev => prev.filter((_, i) => i !== index));
+  };
+  
+  const uploadFiles = async () => {
+    const toUpload = pendingFiles.filter(f => f.status === 'pending');
+    if (toUpload.length === 0) return;
+    
+    setIsUploading(true);
+    
+    try {
+      const uploadFn = type === 'model' 
+        ? intakeApi.uploadFiles 
+        : intakeApi.uploadContextFiles;
+      
+      const response = await uploadFn(draftId, toUpload.map(f => f.file));
+      
+      const results = new Map(
+        response.uploaded_files.map(f => [f.name, f.status === 'uploaded'])
+      );
+      
+      setPendingFiles(prev => prev.map(f => {
+        if (f.status !== 'pending') return f;
+        const success = results.get(f.file.name);
+        return {
+          ...f,
+          status: success ? 'success' : 'error',
+          message: success ? undefined : 'Upload failed',
+        };
+      }));
+      
+      setTimeout(() => {
+        setPendingFiles(prev => prev.filter(f => f.status !== 'success'));
+        onUploadComplete();
+      }, 1000);
+      
+    } catch (err) {
+      setPendingFiles(prev => prev.map(f => 
+        f.status === 'pending' 
+          ? { ...f, status: 'error', message: 'Upload failed' }
+          : f
+      ));
+    } finally {
+      setIsUploading(false);
+    }
+  };
+  
+  // Auto-upload when files are added
+  React.useEffect(() => {
+    const pending = pendingFiles.filter(f => f.status === 'pending');
+    if (pending.length > 0 && !isUploading) {
+      uploadFiles();
+    }
+  }, [pendingFiles, isUploading]);
+  
+  return (
+    <div className="space-y-2">
+      {/* Drop Zone */}
+      <div
+        onDragEnter={handleDragEnter}
+        onDragLeave={handleDragLeave}
+        onDragOver={handleDragOver}
+        onDrop={handleDrop}
+        onClick={() => fileInputRef.current?.click()}
+        className={`
+          relative border-2 border-dashed rounded-lg p-4 cursor-pointer
+          transition-all duration-200 text-center
+          ${isDragging 
+            ? 'border-primary-400 bg-primary-400/5' 
+            : 'border-dark-600 hover:border-primary-400/50 hover:bg-white/5'
+          }
+        `}
+      >
+        <div className={`w-8 h-8 rounded-full flex items-center justify-center mx-auto mb-2
+                        ${isDragging ? 'bg-primary-400/20 text-primary-400' : 'bg-dark-700 text-dark-400'}`}>
+          <Upload className="w-4 h-4" />
+        </div>
+        <p className="text-sm text-dark-300">
+          {isDragging ? 'Drop files here' : 'Drop or click to add'}
+        </p>
+        <p className="text-xs text-dark-500 mt-1">
+          {validExtensions.join(', ')}
+        </p>
+      </div>
+      
+      {/* Existing Files */}
+      {files.length > 0 && (
+        <div className="space-y-1">
+          {files.map((name, i) => (
+            <div
+              key={i}
+              className="flex items-center gap-2 px-2 py-1.5 rounded bg-dark-700/50 text-sm"
+            >
+              <File className="w-3.5 h-3.5 text-dark-400" />
+              <span className="text-dark-200 truncate flex-1">{name}</span>
+              <CheckCircle className="w-3.5 h-3.5 text-green-400" />
+            </div>
+          ))}
+        </div>
+      )}
+      
+      {/* Pending Files */}
+      {pendingFiles.length > 0 && (
+        <div className="space-y-1">
+          {pendingFiles.map((f, i) => (
+            <div
+              key={i}
+              className={`flex items-center gap-2 px-2 py-1.5 rounded text-sm
+                         ${f.status === 'error' ? 'bg-red-500/10' : 
+                           f.status === 'success' ? 'bg-green-500/10' : 'bg-dark-700'}`}
+            >
+              {f.status === 'pending' && <Loader2 className="w-3.5 h-3.5 text-primary-400 animate-spin" />}
+              {f.status === 'uploading' && <Loader2 className="w-3.5 h-3.5 text-primary-400 animate-spin" />}
+              {f.status === 'success' && <CheckCircle className="w-3.5 h-3.5 text-green-400" />}
+              {f.status === 'error' && <AlertCircle className="w-3.5 h-3.5 text-red-400" />}
+              <span className={`truncate flex-1 ${f.status === 'error' ? 'text-red-400' : 'text-dark-200'}`}>
+                {f.file.name}
+              </span>
+              {f.message && (
+                <span className="text-xs text-red-400">({f.message})</span>
+              )}
+              {f.status === 'pending' && (
+                <button onClick={(e) => { e.stopPropagation(); removeFile(i); }} className="p-0.5 hover:bg-white/10 rounded">
+                  <X className="w-3 h-3 text-dark-400" />
+                </button>
+              )}
+            </div>
+          ))}
+        </div>
+      )}
+      
+      <input
+        ref={fileInputRef}
+        type="file"
+        multiple
+        accept={validExtensions.join(',')}
+        onChange={handleFileSelect}
+        className="hidden"
+      />
+    </div>
+  );
+};
+
+export default StudioDropZone;

atomizer-dashboard/frontend/src/components/studio/StudioParameterList.tsx

@@ -0,0 +1,172 @@
+/**
+ * StudioParameterList - Display and add discovered parameters as design variables
+ */
+
+import React, { useState, useEffect } from 'react';
+import { Plus, Check, SlidersHorizontal, Loader2 } from 'lucide-react';
+import { intakeApi } from '../../api/intake';
+
+interface Expression {
+  name: string;
+  value: number | null;
+  units: string | null;
+  is_candidate: boolean;
+  confidence: number;
+}
+
+interface StudioParameterListProps {
+  draftId: string;
+  onParameterAdded: () => void;
+}
+
+export const StudioParameterList: React.FC<StudioParameterListProps> = ({
+  draftId,
+  onParameterAdded,
+}) => {
+  const [expressions, setExpressions] = useState<Expression[]>([]);
+  const [addedParams, setAddedParams] = useState<Set<string>>(new Set());
+  const [adding, setAdding] = useState<string | null>(null);
+  const [loading, setLoading] = useState(true);
+  
+  // Load expressions from spec introspection
+  useEffect(() => {
+    loadExpressions();
+  }, [draftId]);
+  
+  const loadExpressions = async () => {
+    setLoading(true);
+    try {
+      const data = await intakeApi.getStudioDraft(draftId);
+      const introspection = (data.spec as any)?.model?.introspection;
+      
+      if (introspection?.expressions) {
+        setExpressions(introspection.expressions);
+        
+        // Check which are already added as DVs
+        const existingDVs = new Set<string>(
+          ((data.spec as any)?.design_variables || []).map((dv: any) => dv.expression_name as string)
+        );
+        setAddedParams(existingDVs);
+      }
+    } catch (err) {
+      console.error('Failed to load expressions:', err);
+    } finally {
+      setLoading(false);
+    }
+  };
+  
+  const addAsDesignVariable = async (expressionName: string) => {
+    setAdding(expressionName);
+    
+    try {
+      await intakeApi.createDesignVariables(draftId, [expressionName]);
+      setAddedParams(prev => new Set([...prev, expressionName]));
+      onParameterAdded();
+    } catch (err) {
+      console.error('Failed to add design variable:', err);
+    } finally {
+      setAdding(null);
+    }
+  };
+  
+  // Sort: candidates first, then by confidence
+  const sortedExpressions = [...expressions].sort((a, b) => {
+    if (a.is_candidate !== b.is_candidate) {
+      return b.is_candidate ? 1 : -1;
+    }
+    return (b.confidence || 0) - (a.confidence || 0);
+  });
+  
+  // Show only candidates by default, with option to show all
+  const [showAll, setShowAll] = useState(false);
+  const displayExpressions = showAll 
+    ? sortedExpressions 
+    : sortedExpressions.filter(e => e.is_candidate);
+  
+  if (loading) {
+    return (
+      <div className="flex items-center justify-center py-4">
+        <Loader2 className="w-5 h-5 text-primary-400 animate-spin" />
+      </div>
+    );
+  }
+  
+  if (expressions.length === 0) {
+    return (
+      <p className="text-xs text-dark-500 italic py-2">
+        No expressions found. Try running introspection.
+      </p>
+    );
+  }
+  
+  const candidateCount = expressions.filter(e => e.is_candidate).length;
+  
+  return (
+    <div className="space-y-2">
+      {/* Header with toggle */}
+      <div className="flex items-center justify-between text-xs text-dark-400">
+        <span>{candidateCount} candidates</span>
+        <button
+          onClick={() => setShowAll(!showAll)}
+          className="hover:text-primary-400 transition-colors"
+        >
+          {showAll ? 'Show candidates only' : `Show all (${expressions.length})`}
+        </button>
+      </div>
+      
+      {/* Parameter List */}
+      <div className="space-y-1 max-h-48 overflow-y-auto">
+        {displayExpressions.map((expr) => {
+          const isAdded = addedParams.has(expr.name);
+          const isAdding = adding === expr.name;
+          
+          return (
+            <div
+              key={expr.name}
+              className={`flex items-center gap-2 px-2 py-1.5 rounded text-sm
+                         ${isAdded ? 'bg-green-500/10' : 'bg-dark-700/50 hover:bg-dark-700'}
+                         transition-colors`}
+            >
+              <SlidersHorizontal className="w-3.5 h-3.5 text-dark-400 flex-shrink-0" />
+              <div className="flex-1 min-w-0">
+                <span className={`block truncate ${isAdded ? 'text-green-400' : 'text-dark-200'}`}>
+                  {expr.name}
+                </span>
+                {expr.value !== null && (
+                  <span className="text-xs text-dark-500">
+                    = {expr.value}{expr.units ? ` ${expr.units}` : ''}
+                  </span>
+                )}
+              </div>
+              
+              {isAdded ? (
+                <Check className="w-4 h-4 text-green-400 flex-shrink-0" />
+              ) : (
+                <button
+                  onClick={() => addAsDesignVariable(expr.name)}
+                  disabled={isAdding}
+                  className="p-1 hover:bg-primary-400/20 rounded text-primary-400 transition-colors disabled:opacity-50"
+                  title="Add as design variable"
+                >
+                  {isAdding ? (
+                    <Loader2 className="w-3.5 h-3.5 animate-spin" />
+                  ) : (
+                    <Plus className="w-3.5 h-3.5" />
+                  )}
+                </button>
+              )}
+            </div>
+          );
+        })}
+      </div>
+      
+      {displayExpressions.length === 0 && (
+        <p className="text-xs text-dark-500 italic py-2">
+          No candidate parameters found. Click "Show all" to see all expressions.
+        </p>
+      )}
+    </div>
+  );
+};
+
+export default StudioParameterList;

atomizer-dashboard/frontend/src/components/studio/index.ts

@@ -0,0 +1,11 @@
+/**
+ * Studio Components Index
+ * 
+ * Export all Studio-related components.
+ */
+
+export { StudioDropZone } from './StudioDropZone';
+export { StudioParameterList } from './StudioParameterList';
+export { StudioContextFiles } from './StudioContextFiles';
+export { StudioChat } from './StudioChat';
+export { StudioBuildDialog } from './StudioBuildDialog';

atomizer-dashboard/frontend/src/hooks/useSpecDraft.ts

@@ -0,0 +1,121 @@
+/**
+ * useSpecDraft (S2 Draft + Publish)
+ *
+ * Local autosave for AtomizerSpec so users don't lose work.
+ * "Publish" still uses useSpecStore.saveSpec() to write atomizer_spec.json.
+ *
+ * NOTE: This is a partial S2 implementation because the current store
+ * still patches the backend during edits. This draft layer still provides:
+ * - crash/refresh protection
+ * - explicit restore/discard prompt
+ */
+
+import { useCallback, useEffect, useMemo, useRef, useState } from 'react';
+import type { AtomizerSpec } from '../types/atomizer-spec';
+
+const draftKey = (studyId: string) => `atomizer:draft:${studyId}`;
+
+type DraftPayload = {
+  spec: AtomizerSpec;
+  baseHash: string | null;
+  updatedAt: number;
+};
+
+export function useSpecDraft(params: {
+  studyId: string | null | undefined;
+  spec: AtomizerSpec | null | undefined;
+  serverHash: string | null | undefined;
+  enabled?: boolean;
+}) {
+  const { studyId, spec, serverHash, enabled = true } = params;
+
+  const [hasDraft, setHasDraft] = useState(false);
+  const [draft, setDraft] = useState<DraftPayload | null>(null);
+
+  // Debounce writes
+  const writeTimer = useRef<number | null>(null);
+
+  const key = useMemo(() => (studyId ? draftKey(studyId) : null), [studyId]);
+
+  const loadDraft = useCallback(() => {
+    if (!enabled || !key) return null;
+    try {
+      const raw = localStorage.getItem(key);
+      if (!raw) return null;
+      const parsed = JSON.parse(raw) as DraftPayload;
+      if (!parsed?.spec) return null;
+      return parsed;
+    } catch {
+      return null;
+    }
+  }, [enabled, key]);
+
+  const discardDraft = useCallback(() => {
+    if (!enabled || !key) return;
+    localStorage.removeItem(key);
+    setHasDraft(false);
+    setDraft(null);
+  }, [enabled, key]);
+
+  const saveDraftNow = useCallback(
+    (payload: DraftPayload) => {
+      if (!enabled || !key) return;
+      try {
+        localStorage.setItem(key, JSON.stringify(payload));
+        setHasDraft(true);
+        setDraft(payload);
+      } catch {
+        // ignore storage failures
+      }
+    },
+    [enabled, key]
+  );
+
+  // Load draft on study change
+  useEffect(() => {
+    if (!enabled || !key) return;
+    const existing = loadDraft();
+    if (existing) {
+      setHasDraft(true);
+      setDraft(existing);
+    } else {
+      setHasDraft(false);
+      setDraft(null);
+    }
+  }, [enabled, key, loadDraft]);
+
+  // Autosave whenever spec changes
+  useEffect(() => {
+    if (!enabled || !key) return;
+    if (!studyId || !spec) return;
+
+    // Clear existing debounce
+    if (writeTimer.current) {
+      window.clearTimeout(writeTimer.current);
+      writeTimer.current = null;
+    }
+
+    writeTimer.current = window.setTimeout(() => {
+      saveDraftNow({ spec, baseHash: serverHash ?? null, updatedAt: Date.now() });
+    }, 750);
+
+    return () => {
+      if (writeTimer.current) {
+        window.clearTimeout(writeTimer.current);
+        writeTimer.current = null;
+      }
+    };
+  }, [enabled, key, studyId, spec, serverHash, saveDraftNow]);
+
+  return {
+    hasDraft,
+    draft,
+    discardDraft,
+    reloadDraft: () => {
+      const d = loadDraft();
+      setDraft(d);
+      setHasDraft(Boolean(d));
+      return d;
+    },
+  };
+}

atomizer-dashboard/frontend/src/hooks/useSpecStore.ts

@@ -63,6 +63,9 @@ interface SpecStoreActions {
   // WebSocket integration - set spec directly without API call
   setSpecFromWebSocket: (spec: AtomizerSpec, studyId?: string) => void;
 
+  // Local draft integration (S2) - set spec locally (no API call) and mark dirty
+  setSpecLocalDraft: (spec: AtomizerSpec, studyId?: string) => void;
+
   // Full spec operations
   saveSpec: (spec: AtomizerSpec) => Promise<void>;
   replaceSpec: (spec: AtomizerSpec) => Promise<void>;
@@ -402,6 +405,20 @@ export const useSpecStore = create<SpecStore>()(
         });
       },
 
+      // Set spec locally as a draft (no API call). This is used by DraftManager (S2).
+      // Marks the spec as dirty to indicate "not published".
+      setSpecLocalDraft: (spec: AtomizerSpec, studyId?: string) => {
+        const currentStudyId = studyId || get().studyId;
+        console.log('[useSpecStore] Setting spec from local draft:', spec.meta?.study_name);
+        set({
+          spec,
+          studyId: currentStudyId,
+          isLoading: false,
+          isDirty: true,
+          error: null,
+        });
+      },
+
       // =====================================================================
       // Full Spec Operations
       // =====================================================================

atomizer-dashboard/frontend/src/lib/spec.ts

@@ -0,0 +1,324 @@
+/**
+ * Spec ↔ Canvas converters
+ *
+ * AtomizerSpec v2.0 is the single source of truth.
+ * This module converts AtomizerSpec → ReactFlow nodes/edges for visualization.
+ *
+ * NOTE: Canvas edges are primarily for visual validation.
+ * The computation truth lives in objective.source / constraint.source.
+ */
+
+import type { Node, Edge } from 'reactflow';
+
+import type { AtomizerSpec, CanvasPosition, DesignVariable, Extractor, Objective, Constraint } from '../types/atomizer-spec';
+import type {
+  CanvasNodeData,
+  ModelNodeData,
+  SolverNodeData,
+  AlgorithmNodeData,
+  SurrogateNodeData,
+  DesignVarNodeData,
+  ExtractorNodeData,
+  ObjectiveNodeData,
+  ConstraintNodeData,
+} from './canvas/schema';
+
+// ---------------------------------------------------------------------------
+// Layout defaults (deterministic)
+// ---------------------------------------------------------------------------
+
+const DEFAULT_LAYOUT = {
+  startX: 80,
+  startY: 80,
+  colWidth: 260,
+  rowHeight: 110,
+  cols: {
+    designVar: 0,
+    model: 1,
+    solver: 2,
+    extractor: 3,
+    objective: 4,
+    constraint: 4,
+    algorithm: 5,
+    surrogate: 6,
+  } as const,
+};
+
+function toCanvasPosition(pos: CanvasPosition | undefined | null, fallback: CanvasPosition): CanvasPosition {
+  if (!pos) return fallback;
+  if (typeof pos.x !== 'number' || typeof pos.y !== 'number') return fallback;
+  return { x: pos.x, y: pos.y };
+}
+
+function makeFallbackPosition(col: number, row: number): CanvasPosition {
+  return {
+    x: DEFAULT_LAYOUT.startX + col * DEFAULT_LAYOUT.colWidth,
+    y: DEFAULT_LAYOUT.startY + row * DEFAULT_LAYOUT.rowHeight,
+  };
+}
+
+// ---------------------------------------------------------------------------
+// Synthetic nodes (always present)
+// ---------------------------------------------------------------------------
+
+export function isSyntheticNodeId(id: string): boolean {
+  return id === 'model' || id === 'solver' || id === 'algorithm' || id === 'surrogate';
+}
+
+function makeModelNode(spec: AtomizerSpec): Node<ModelNodeData> {
+  const pos = toCanvasPosition(
+    spec.model?.sim?.path ? (spec.model as any)?.canvas_position : undefined,
+    makeFallbackPosition(DEFAULT_LAYOUT.cols.model, 0)
+  );
+
+  return {
+    id: 'model',
+    type: 'model',
+    position: pos,
+    data: {
+      type: 'model',
+      label: spec.meta?.study_name || 'Model',
+      configured: Boolean(spec.model?.sim?.path),
+      filePath: spec.model?.sim?.path,
+      fileType: 'sim',
+    },
+  };
+}
+
+function makeSolverNode(spec: AtomizerSpec): Node<SolverNodeData> {
+  const sim = spec.model?.sim;
+  const pos = makeFallbackPosition(DEFAULT_LAYOUT.cols.solver, 0);
+
+  return {
+    id: 'solver',
+    type: 'solver',
+    position: pos,
+    data: {
+      type: 'solver',
+      label: sim?.engine ? `Solver (${sim.engine})` : 'Solver',
+      configured: Boolean(sim?.engine || sim?.solution_type),
+      engine: sim?.engine as any,
+      solverType: sim?.solution_type as any,
+      scriptPath: sim?.script_path,
+    },
+  };
+}
+
+function makeAlgorithmNode(spec: AtomizerSpec): Node<AlgorithmNodeData> {
+  const algo = spec.optimization?.algorithm;
+  const budget = spec.optimization?.budget;
+  const pos = toCanvasPosition(
+    spec.optimization?.canvas_position,
+    makeFallbackPosition(DEFAULT_LAYOUT.cols.algorithm, 0)
+  );
+
+  return {
+    id: 'algorithm',
+    type: 'algorithm',
+    position: pos,
+    data: {
+      type: 'algorithm',
+      label: algo?.type || 'Algorithm',
+      configured: Boolean(algo?.type),
+      method: (algo?.type as any) || 'TPE',
+      maxTrials: budget?.max_trials,
+      sigma0: (algo?.config as any)?.sigma0,
+      restartStrategy: (algo?.config as any)?.restart_strategy,
+    },
+  };
+}
+
+function makeSurrogateNode(spec: AtomizerSpec): Node<SurrogateNodeData> {
+  const surrogate = spec.optimization?.surrogate;
+  const pos = makeFallbackPosition(DEFAULT_LAYOUT.cols.surrogate, 0);
+
+  const enabled = Boolean(surrogate?.enabled);
+
+  return {
+    id: 'surrogate',
+    type: 'surrogate',
+    position: pos,
+    data: {
+      type: 'surrogate',
+      label: enabled ? 'Surrogate (enabled)' : 'Surrogate',
+      configured: true,
+      enabled,
+      modelType: (surrogate?.type as any) || 'MLP',
+      minTrials: surrogate?.config?.min_training_samples,
+    },
+  };
+}
+
+// ---------------------------------------------------------------------------
+// Array-backed nodes
+// ---------------------------------------------------------------------------
+
+function makeDesignVarNode(dv: DesignVariable, index: number): Node<DesignVarNodeData> {
+  const pos = toCanvasPosition(
+    dv.canvas_position,
+    makeFallbackPosition(DEFAULT_LAYOUT.cols.designVar, index)
+  );
+
+  return {
+    id: dv.id,
+    type: 'designVar',
+    position: pos,
+    data: {
+      type: 'designVar',
+      label: dv.name,
+      configured: Boolean(dv.expression_name),
+      expressionName: dv.expression_name,
+      minValue: dv.bounds?.min,
+      maxValue: dv.bounds?.max,
+      baseline: dv.baseline,
+      unit: dv.units,
+      enabled: dv.enabled,
+    },
+  };
+}
+
+function makeExtractorNode(ext: Extractor, index: number): Node<ExtractorNodeData> {
+  const pos = toCanvasPosition(
+    ext.canvas_position,
+    makeFallbackPosition(DEFAULT_LAYOUT.cols.extractor, index)
+  );
+
+  return {
+    id: ext.id,
+    type: 'extractor',
+    position: pos,
+    data: {
+      type: 'extractor',
+      label: ext.name,
+      configured: true,
+      extractorId: ext.id,
+      extractorName: ext.name,
+      extractorType: ext.type as any,
+      config: ext.config as any,
+      outputNames: (ext.outputs || []).map((o) => o.name),
+      // Convenience fields
+      innerRadius: (ext.config as any)?.inner_radius_mm,
+      nModes: (ext.config as any)?.n_modes,
+      subcases: (ext.config as any)?.subcases,
+      extractMethod: (ext.config as any)?.extract_method,
+    },
+  };
+}
+
+function makeObjectiveNode(obj: Objective, index: number): Node<ObjectiveNodeData> {
+  const pos = toCanvasPosition(
+    obj.canvas_position,
+    makeFallbackPosition(DEFAULT_LAYOUT.cols.objective, index)
+  );
+
+  return {
+    id: obj.id,
+    type: 'objective',
+    position: pos,
+    data: {
+      type: 'objective',
+      label: obj.name,
+      configured: Boolean(obj.source?.extractor_id && obj.source?.output_name),
+      name: obj.name,
+      direction: obj.direction,
+      weight: obj.weight,
+      extractorRef: obj.source?.extractor_id,
+      outputName: obj.source?.output_name,
+    },
+  };
+}
+
+function makeConstraintNode(con: Constraint, index: number): Node<ConstraintNodeData> {
+  const pos = toCanvasPosition(
+    con.canvas_position,
+    makeFallbackPosition(DEFAULT_LAYOUT.cols.constraint, index)
+  );
+
+  return {
+    id: con.id,
+    type: 'constraint',
+    position: pos,
+    data: {
+      type: 'constraint',
+      label: con.name,
+      configured: Boolean(con.source?.extractor_id && con.source?.output_name),
+      name: con.name,
+      operator: con.operator,
+      value: con.threshold,
+    },
+  };
+}
+
+// ---------------------------------------------------------------------------
+// Public API
+// ---------------------------------------------------------------------------
+
+export function specToNodes(spec: AtomizerSpec | null | undefined): Node<CanvasNodeData>[] {
+  if (!spec) return [];
+
+  const nodes: Node<CanvasNodeData>[] = [];
+
+  // Structural nodes
+  nodes.push(makeModelNode(spec) as Node<CanvasNodeData>);
+  nodes.push(makeSolverNode(spec) as Node<CanvasNodeData>);
+  nodes.push(makeAlgorithmNode(spec) as Node<CanvasNodeData>);
+  nodes.push(makeSurrogateNode(spec) as Node<CanvasNodeData>);
+
+  // Array nodes
+  spec.design_variables?.forEach((dv, i) => nodes.push(makeDesignVarNode(dv, i) as Node<CanvasNodeData>));
+  spec.extractors?.forEach((ext, i) => nodes.push(makeExtractorNode(ext, i) as Node<CanvasNodeData>));
+  spec.objectives?.forEach((obj, i) => nodes.push(makeObjectiveNode(obj, i) as Node<CanvasNodeData>));
+  spec.constraints?.forEach((con, i) => nodes.push(makeConstraintNode(con, i) as Node<CanvasNodeData>));
+
+  return nodes;
+}
+
+export function specToEdges(spec: AtomizerSpec | null | undefined): Edge[] {
+  if (!spec) return [];
+
+  const edges: Edge[] = [];
+  const seen = new Set<string>();
+
+  const add = (source: string, target: string, sourceHandle?: string, targetHandle?: string) => {
+    const id = `${source}__${target}${sourceHandle ? `__${sourceHandle}` : ''}${targetHandle ? `__${targetHandle}` : ''}`;
+    if (seen.has(id)) return;
+    seen.add(id);
+    edges.push({
+      id,
+      source,
+      target,
+      sourceHandle,
+      targetHandle,
+    });
+  };
+
+  // Prefer explicit canvas edges if present
+  if (spec.canvas?.edges && spec.canvas.edges.length > 0) {
+    for (const e of spec.canvas.edges) {
+      add(e.source, e.target, e.sourceHandle, e.targetHandle);
+    }
+    return edges;
+  }
+
+  // Fallback: build a minimal visual graph from spec fields (deterministic)
+  // DV → model
+  for (const dv of spec.design_variables || []) add(dv.id, 'model');
+  // model → solver
+  add('model', 'solver');
+  // solver → each extractor
+  for (const ext of spec.extractors || []) add('solver', ext.id);
+  // extractor → objective/constraint based on source
+  for (const obj of spec.objectives || []) {
+    if (obj.source?.extractor_id) add(obj.source.extractor_id, obj.id);
+  }
+  for (const con of spec.constraints || []) {
+    if (con.source?.extractor_id) add(con.source.extractor_id, con.id);
+  }
+  // objective/constraint → algorithm
+  for (const obj of spec.objectives || []) add(obj.id, 'algorithm');
+  for (const con of spec.constraints || []) add(con.id, 'algorithm');
+  // algorithm → surrogate
+  add('algorithm', 'surrogate');
+
+  return edges;
+}

atomizer-dashboard/frontend/src/lib/validation/specValidator.ts

@@ -178,9 +178,14 @@ const validationRules: ValidationRule[] = [
           edge => edge.target === obj.id && edge.source.startsWith('ext_')
         );
         
-        // Also check if source.extractor_id is set
-        const hasDirectSource = obj.source?.extractor_id && 
-          spec.extractors.some(e => e.id === obj.source.extractor_id);
+        // Also check if source.extractor_id is set (and not UNSET placeholders)
+        const extractorId = obj.source?.extractor_id;
+        const outputName = obj.source?.output_name;
+        const hasDirectSource = Boolean(extractorId) &&
+          extractorId !== '__UNSET__' &&
+          Boolean(outputName) &&
+          outputName !== '__UNSET__' &&
+          spec.extractors.some(e => e.id === extractorId);
         
         if (!hasSource && !hasDirectSource) {
           return {

atomizer-dashboard/frontend/src/pages/CanvasView.tsx

@@ -13,10 +13,11 @@ import { ChatPanel } from '../components/canvas/panels/ChatPanel';
 import { PanelContainer } from '../components/canvas/panels/PanelContainer';
 import { ResizeHandle } from '../components/canvas/ResizeHandle';
 import { useCanvasStore } from '../hooks/useCanvasStore';
-import { useSpecStore, useSpec, useSpecLoading, useSpecIsDirty, useSelectedNodeId } from '../hooks/useSpecStore';
+import { useSpecStore, useSpec, useSpecLoading, useSpecIsDirty, useSelectedNodeId, useSpecHash } from '../hooks/useSpecStore';
 import { useResizablePanel } from '../hooks/useResizablePanel';
 // usePanelStore is now used by child components - PanelContainer handles panels
 import { useSpecUndoRedo, useUndoRedoKeyboard } from '../hooks/useSpecUndoRedo';
+import { useSpecDraft } from '../hooks/useSpecDraft';
 import { useStudy } from '../context/StudyContext';
 import { useChat } from '../hooks/useChat';
 import { CanvasTemplate } from '../lib/canvas/templates';
@@ -63,6 +64,10 @@ export function CanvasView() {
   // Get study ID from URL params (supports nested paths like M1_Mirror/study_name)
   const { '*': urlStudyId } = useParams<{ '*': string }>();
 
+  // Active study ID comes ONLY from URL - don't auto-load from context
+  // This ensures /canvas shows empty canvas, /canvas/{id} shows the study
+  const activeStudyId = urlStudyId;
+
   // Legacy canvas store (for backwards compatibility)
   const { nodes, edges, clear, loadFromConfig, toIntent } = useCanvasStore();
 
@@ -70,11 +75,22 @@ export function CanvasView() {
   const spec = useSpec();
   const specLoading = useSpecLoading();
   const specIsDirty = useSpecIsDirty();
+  const specHash = useSpecHash();
   const selectedNodeId = useSelectedNodeId();
   const { loadSpec, saveSpec, reloadSpec } = useSpecStore();
 
+  // S2: local autosave draft (crash-proof) — publish remains explicit
+  const { hasDraft, draft, discardDraft, reloadDraft } = useSpecDraft({
+    studyId: activeStudyId,
+    spec,
+    serverHash: specHash,
+    enabled: useSpecMode,
+  });
+
+  const [showDraftPrompt, setShowDraftPrompt] = useState(false);
+
   const { setSelectedStudy, studies } = useStudy();
-  const { clearSpec, setSpecFromWebSocket } = useSpecStore();
+  const { clearSpec, setSpecFromWebSocket, setSpecLocalDraft } = useSpecStore();
 
   // Undo/Redo for spec mode
   const undoRedo = useSpecUndoRedo();
@@ -83,10 +99,6 @@ export function CanvasView() {
   // Enable keyboard shortcuts for undo/redo (Ctrl+Z, Ctrl+Y)
   useUndoRedoKeyboard(undoRedo);
 
-  // Active study ID comes ONLY from URL - don't auto-load from context
-  // This ensures /canvas shows empty canvas, /canvas/{id} shows the study
-  const activeStudyId = urlStudyId;
-
   // Chat hook for assistant panel
   const { messages, isThinking, isConnected, sendMessage, notifyCanvasEdit } = useChat({
     studyId: activeStudyId,
@@ -130,6 +142,18 @@ export function CanvasView() {
     }
   }, [urlStudyId, useSpecMode]);
 
+  // If a local draft exists for this study, prompt user to restore/discard.
+  useEffect(() => {
+    if (!useSpecMode) return;
+    if (!activeStudyId) return;
+    if (specLoading) return;
+    if (!spec) return;
+    if (!hasDraft || !draft) return;
+
+    // Show prompt once per navigation
+    setShowDraftPrompt(true);
+  }, [useSpecMode, activeStudyId, specLoading, spec, hasDraft, draft]);
+
   // Notify Claude when user edits the spec (bi-directional sync)
   // This sends the updated spec to Claude so it knows what the user changed
   useEffect(() => {
@@ -183,7 +207,7 @@ export function CanvasView() {
       if (useSpecMode && spec) {
         // Save spec using new API
         await saveSpec(spec);
-        showNotification('Saved to atomizer_spec.json');
+        showNotification('Published to atomizer_spec.json');
       } else {
         // Legacy save
         const intent = toIntent();
@@ -327,10 +351,10 @@ export function CanvasView() {
                   ? 'bg-green-600 hover:bg-green-500 text-white'
                   : 'bg-dark-700 text-dark-400 cursor-not-allowed border border-dark-600'
               }`}
-              title={specIsDirty ? 'Save changes to atomizer_spec.json' : 'No changes to save'}
+              title={specIsDirty ? 'Publish draft to atomizer_spec.json' : 'No changes to publish'}
             >
               <Save size={14} />
-              {isSaving ? 'Saving...' : 'Save'}
+              {isSaving ? 'Publishing...' : 'Publish'}
             </button>
           )}
           
@@ -614,6 +638,46 @@ export function CanvasView() {
       {/* Floating Panels (Introspection, Validation, Error, Results) */}
       {useSpecMode && <PanelContainer />}
 
+      {/* Draft Restore Prompt (S2) */}
+      {useSpecMode && showDraftPrompt && draft && (
+        <div className="fixed inset-0 z-50 flex items-center justify-center bg-black/60 backdrop-blur-sm">
+          <div className="w-[640px] max-w-[92vw] bg-dark-850 rounded-xl border border-dark-600 shadow-2xl p-5">
+            <h3 className="text-lg font-semibold text-white">Restore local draft?</h3>
+            <p className="text-sm text-dark-300 mt-2">
+              A local draft was found for this study (autosaved). You can restore it (recommended) or discard it and keep the published version.
+            </p>
+
+            <div className="mt-4 p-3 bg-dark-900/40 border border-dark-700 rounded-lg text-xs text-dark-400">
+              <div>Draft updated: {new Date(draft.updatedAt).toLocaleString()}</div>
+              <div>Base hash: {draft.baseHash || '(unknown)'}</div>
+            </div>
+
+            <div className="mt-5 flex justify-end gap-2">
+              <button
+                onClick={() => {
+                  discardDraft();
+                  setShowDraftPrompt(false);
+                  showNotification('Discarded local draft');
+                }}
+                className="px-4 py-2 bg-dark-700 text-dark-200 hover:bg-dark-600 rounded-lg border border-dark-600 transition-colors"
+              >
+                Discard Draft
+              </button>
+              <button
+                onClick={() => {
+                  setSpecLocalDraft(draft.spec, activeStudyId || undefined);
+                  setShowDraftPrompt(false);
+                  showNotification('Restored local draft');
+                }}
+                className="px-4 py-2 bg-primary-600 text-white hover:bg-primary-500 rounded-lg border border-primary-500 transition-colors"
+              >
+                Restore Draft
+              </button>
+            </div>
+          </div>
+        </div>
+      )}
+
       {/* Notification Toast */}
       {notification && (
         <div

atomizer-dashboard/frontend/src/pages/Home.tsx

@@ -18,12 +18,15 @@ import {
   FolderOpen,
   Maximize2,
   X,
-  Layers
+  Layers,
+  Sparkles,
+  Settings2
 } from 'lucide-react';
 import { useStudy } from '../context/StudyContext';
 import { Study } from '../types';
 import { apiClient } from '../api/client';
 import { MarkdownRenderer } from '../components/MarkdownRenderer';
+import { InboxSection } from '../components/intake';
 
 const Home: React.FC = () => {
   const { studies, setSelectedStudy, refreshStudies, isLoading } = useStudy();
@@ -174,6 +177,18 @@ const Home: React.FC = () => {
               />
             </div>
             <div className="flex items-center gap-3">
+              <button
+                onClick={() => navigate('/studio')}
+                className="flex items-center gap-2 px-4 py-2 rounded-lg transition-all font-medium hover:-translate-y-0.5"
+                style={{
+                  background: 'linear-gradient(135deg, #f59e0b 0%, #d97706 100%)',
+                  color: '#000',
+                  boxShadow: '0 4px 15px rgba(245, 158, 11, 0.3)'
+                }}
+              >
+                <Sparkles className="w-4 h-4" />
+                New Study
+              </button>
               <button
                 onClick={() => navigate('/canvas')}
                 className="flex items-center gap-2 px-4 py-2 rounded-lg transition-all font-medium hover:-translate-y-0.5"
@@ -250,6 +265,11 @@ const Home: React.FC = () => {
           </div>
         </div>
 
+        {/* Inbox Section - Study Creation Workflow */}
+        <div className="mb-8">
+          <InboxSection onStudyFinalized={refreshStudies} />
+        </div>
+
         {/* Two-column layout: Table + Preview */}
         <div className="grid grid-cols-1 lg:grid-cols-2 gap-6">
           {/* Study Table */}
@@ -407,6 +427,19 @@ const Home: React.FC = () => {
                       <Layers className="w-4 h-4" />
                       Canvas
                     </button>
+                    <button
+                      onClick={() => navigate(`/studio/${selectedPreview.id}`)}
+                      className="flex items-center gap-2 px-4 py-2.5 rounded-lg transition-all font-medium whitespace-nowrap hover:-translate-y-0.5"
+                      style={{
+                        background: 'rgba(8, 15, 26, 0.85)',
+                        border: '1px solid rgba(245, 158, 11, 0.3)',
+                        color: '#f59e0b'
+                      }}
+                      title="Edit study configuration with AI assistant"
+                    >
+                      <Settings2 className="w-4 h-4" />
+                      Studio
+                    </button>
                     <button
                       onClick={() => handleSelectStudy(selectedPreview)}
                       className="flex items-center gap-2 px-5 py-2.5 rounded-lg transition-all font-semibold whitespace-nowrap hover:-translate-y-0.5"

atomizer-dashboard/frontend/src/pages/Studio.tsx

@@ -0,0 +1,672 @@
+/**
+ * Atomizer Studio - Unified Study Creation Environment
+ * 
+ * A drag-and-drop workspace for creating optimization studies with:
+ * - File upload (models + context documents)
+ * - Visual canvas configuration
+ * - AI-powered assistance
+ * - One-click build to final study
+ */
+
+import { useState, useEffect, useCallback, useRef } from 'react';
+import { useNavigate, useParams } from 'react-router-dom';
+import {
+  Home,
+  ChevronRight,
+  Upload,
+  FileText,
+  Settings,
+  Sparkles,
+  Save,
+  RefreshCw,
+  Trash2,
+  MessageSquare,
+  Layers,
+  CheckCircle,
+  AlertCircle,
+  Loader2,
+  X,
+  ChevronLeft,
+  ChevronRight as ChevronRightIcon,
+  GripVertical,
+} from 'lucide-react';
+import { intakeApi } from '../api/intake';
+import { SpecRenderer } from '../components/canvas/SpecRenderer';
+import { NodePalette } from '../components/canvas/palette/NodePalette';
+import { NodeConfigPanelV2 } from '../components/canvas/panels/NodeConfigPanelV2';
+import { useSpecStore, useSpec, useSpecLoading } from '../hooks/useSpecStore';
+import { StudioDropZone } from '../components/studio/StudioDropZone';
+import { StudioParameterList } from '../components/studio/StudioParameterList';
+import { StudioContextFiles } from '../components/studio/StudioContextFiles';
+import { StudioChat } from '../components/studio/StudioChat';
+import { StudioBuildDialog } from '../components/studio/StudioBuildDialog';
+
+interface DraftState {
+  draftId: string | null;
+  status: 'idle' | 'creating' | 'ready' | 'error';
+  error: string | null;
+  modelFiles: string[];
+  contextFiles: string[];
+  contextContent: string;
+  introspectionAvailable: boolean;
+  designVariableCount: number;
+  objectiveCount: number;
+}
+
+export default function Studio() {
+  const navigate = useNavigate();
+  const { draftId: urlDraftId } = useParams<{ draftId: string }>();
+  
+  // Draft state
+  const [draft, setDraft] = useState<DraftState>({
+    draftId: null,
+    status: 'idle',
+    error: null,
+    modelFiles: [],
+    contextFiles: [],
+    contextContent: '',
+    introspectionAvailable: false,
+    designVariableCount: 0,
+    objectiveCount: 0,
+  });
+  
+  // UI state
+  const [leftPanelWidth, setLeftPanelWidth] = useState(320);
+  const [rightPanelCollapsed, setRightPanelCollapsed] = useState(false);
+  const [showBuildDialog, setShowBuildDialog] = useState(false);
+  const [isIntrospecting, setIsIntrospecting] = useState(false);
+  const [notification, setNotification] = useState<{ type: 'success' | 'error' | 'info'; message: string } | null>(null);
+  
+  // Resize state
+  const isResizing = useRef(false);
+  const minPanelWidth = 280;
+  const maxPanelWidth = 500;
+  
+  // Spec store for canvas
+  const spec = useSpec();
+  const specLoading = useSpecLoading();
+  const { loadSpec, clearSpec } = useSpecStore();
+  
+  // Handle panel resize
+  const handleMouseDown = useCallback((e: React.MouseEvent) => {
+    e.preventDefault();
+    isResizing.current = true;
+    document.body.style.cursor = 'col-resize';
+    document.body.style.userSelect = 'none';
+  }, []);
+  
+  useEffect(() => {
+    const handleMouseMove = (e: MouseEvent) => {
+      if (!isResizing.current) return;
+      const newWidth = Math.min(maxPanelWidth, Math.max(minPanelWidth, e.clientX));
+      setLeftPanelWidth(newWidth);
+    };
+    
+    const handleMouseUp = () => {
+      isResizing.current = false;
+      document.body.style.cursor = '';
+      document.body.style.userSelect = '';
+    };
+    
+    document.addEventListener('mousemove', handleMouseMove);
+    document.addEventListener('mouseup', handleMouseUp);
+    
+    return () => {
+      document.removeEventListener('mousemove', handleMouseMove);
+      document.removeEventListener('mouseup', handleMouseUp);
+    };
+  }, []);
+  
+  // Initialize or load draft on mount
+  useEffect(() => {
+    if (urlDraftId) {
+      loadDraft(urlDraftId);
+    } else {
+      createNewDraft();
+    }
+    
+    return () => {
+      // Cleanup: clear spec when leaving Studio
+      clearSpec();
+    };
+  }, [urlDraftId]);
+  
+  // Create a new draft
+  const createNewDraft = async () => {
+    setDraft(prev => ({ ...prev, status: 'creating', error: null }));
+    
+    try {
+      const response = await intakeApi.createDraft();
+      
+      setDraft({
+        draftId: response.draft_id,
+        status: 'ready',
+        error: null,
+        modelFiles: [],
+        contextFiles: [],
+        contextContent: '',
+        introspectionAvailable: false,
+        designVariableCount: 0,
+        objectiveCount: 0,
+      });
+      
+      // Update URL without navigation
+      window.history.replaceState(null, '', `/studio/${response.draft_id}`);
+      
+      // Load the empty spec for this draft
+      await loadSpec(response.draft_id);
+      
+      showNotification('info', 'New studio session started. Drop your files to begin.');
+    } catch (err) {
+      setDraft(prev => ({
+        ...prev,
+        status: 'error',
+        error: err instanceof Error ? err.message : 'Failed to create draft',
+      }));
+    }
+  };
+  
+  // Load existing draft or study
+  const loadDraft = async (studyId: string) => {
+    setDraft(prev => ({ ...prev, status: 'creating', error: null }));
+    
+    // Check if this is a draft (in _inbox) or an existing study
+    const isDraft = studyId.startsWith('draft_');
+    
+    if (isDraft) {
+      // Load from intake API
+      try {
+        const response = await intakeApi.getStudioDraft(studyId);
+        
+        // Also load context content if there are context files
+        let contextContent = '';
+        if (response.context_files.length > 0) {
+          try {
+            const contextResponse = await intakeApi.getContextContent(studyId);
+            contextContent = contextResponse.content;
+          } catch {
+            // Ignore context loading errors
+          }
+        }
+        
+        setDraft({
+          draftId: response.draft_id,
+          status: 'ready',
+          error: null,
+          modelFiles: response.model_files,
+          contextFiles: response.context_files,
+          contextContent,
+          introspectionAvailable: response.introspection_available,
+          designVariableCount: response.design_variable_count,
+          objectiveCount: response.objective_count,
+        });
+        
+        // Load the spec
+        await loadSpec(studyId);
+        
+        showNotification('info', `Resuming draft: ${studyId}`);
+      } catch (err) {
+        // Draft doesn't exist, create new one
+        createNewDraft();
+      }
+    } else {
+      // Load existing study directly via spec store
+      try {
+        await loadSpec(studyId);
+        
+        // Get counts from loaded spec
+        const loadedSpec = useSpecStore.getState().spec;
+        
+        setDraft({
+          draftId: studyId,
+          status: 'ready',
+          error: null,
+          modelFiles: [], // Existing studies don't track files separately
+          contextFiles: [],
+          contextContent: '',
+          introspectionAvailable: true, // Assume introspection was done
+          designVariableCount: loadedSpec?.design_variables?.length || 0,
+          objectiveCount: loadedSpec?.objectives?.length || 0,
+        });
+        
+        showNotification('info', `Editing study: ${studyId}`);
+      } catch (err) {
+        setDraft(prev => ({
+          ...prev,
+          status: 'error',
+          error: err instanceof Error ? err.message : 'Failed to load study',
+        }));
+      }
+    }
+  };
+  
+  // Refresh draft data
+  const refreshDraft = async () => {
+    if (!draft.draftId) return;
+    
+    const isDraft = draft.draftId.startsWith('draft_');
+    
+    if (isDraft) {
+      try {
+        const response = await intakeApi.getStudioDraft(draft.draftId);
+        
+        // Also refresh context content
+        let contextContent = draft.contextContent;
+        if (response.context_files.length > 0) {
+          try {
+            const contextResponse = await intakeApi.getContextContent(draft.draftId);
+            contextContent = contextResponse.content;
+          } catch {
+            // Keep existing content
+          }
+        }
+        
+        setDraft(prev => ({
+          ...prev,
+          modelFiles: response.model_files,
+          contextFiles: response.context_files,
+          contextContent,
+          introspectionAvailable: response.introspection_available,
+          designVariableCount: response.design_variable_count,
+          objectiveCount: response.objective_count,
+        }));
+        
+        // Reload spec
+        await loadSpec(draft.draftId);
+      } catch (err) {
+        showNotification('error', 'Failed to refresh draft');
+      }
+    } else {
+      // For existing studies, just reload the spec
+      try {
+        await loadSpec(draft.draftId);
+        
+        const loadedSpec = useSpecStore.getState().spec;
+        setDraft(prev => ({
+          ...prev,
+          designVariableCount: loadedSpec?.design_variables?.length || 0,
+          objectiveCount: loadedSpec?.objectives?.length || 0,
+        }));
+      } catch (err) {
+        showNotification('error', 'Failed to refresh study');
+      }
+    }
+  };
+  
+  // Run introspection
+  const runIntrospection = async () => {
+    if (!draft.draftId || draft.modelFiles.length === 0) {
+      showNotification('error', 'Please upload model files first');
+      return;
+    }
+    
+    setIsIntrospecting(true);
+    
+    try {
+      const response = await intakeApi.introspect({ study_name: draft.draftId });
+      
+      showNotification('success', `Found ${response.expressions_count} expressions (${response.candidates_count} candidates)`);
+      
+      // Refresh draft state
+      await refreshDraft();
+    } catch (err) {
+      showNotification('error', err instanceof Error ? err.message : 'Introspection failed');
+    } finally {
+      setIsIntrospecting(false);
+    }
+  };
+  
+  // Handle file upload complete
+  const handleUploadComplete = useCallback(() => {
+    refreshDraft();
+    showNotification('success', 'Files uploaded successfully');
+  }, [draft.draftId]);
+  
+  // Handle build complete
+  const handleBuildComplete = (finalPath: string, finalName: string) => {
+    setShowBuildDialog(false);
+    showNotification('success', `Study "${finalName}" created successfully!`);
+    
+    // Navigate to the new study
+    setTimeout(() => {
+      navigate(`/canvas/${finalPath.replace('studies/', '')}`);
+    }, 1500);
+  };
+  
+  // Reset draft
+  const resetDraft = async () => {
+    if (!draft.draftId) return;
+    
+    if (!confirm('Are you sure you want to reset? This will delete all uploaded files and configurations.')) {
+      return;
+    }
+    
+    try {
+      await intakeApi.deleteInboxStudy(draft.draftId);
+      await createNewDraft();
+    } catch (err) {
+      showNotification('error', 'Failed to reset draft');
+    }
+  };
+  
+  // Show notification
+  const showNotification = (type: 'success' | 'error' | 'info', message: string) => {
+    setNotification({ type, message });
+    setTimeout(() => setNotification(null), 4000);
+  };
+  
+  // Can always save/build - even empty studies can be saved for later
+  const canBuild = draft.draftId !== null;
+  
+  // Loading state
+  if (draft.status === 'creating') {
+    return (
+      <div className="min-h-screen bg-dark-900 flex items-center justify-center">
+        <div className="text-center">
+          <Loader2 className="w-12 h-12 text-primary-400 animate-spin mx-auto mb-4" />
+          <p className="text-dark-300">Initializing Studio...</p>
+        </div>
+      </div>
+    );
+  }
+  
+  // Error state
+  if (draft.status === 'error') {
+    return (
+      <div className="min-h-screen bg-dark-900 flex items-center justify-center">
+        <div className="text-center max-w-md">
+          <AlertCircle className="w-12 h-12 text-red-400 mx-auto mb-4" />
+          <h2 className="text-xl font-semibold text-white mb-2">Failed to Initialize</h2>
+          <p className="text-dark-400 mb-4">{draft.error}</p>
+          <button
+            onClick={createNewDraft}
+            className="px-4 py-2 bg-primary-500 text-white rounded-lg hover:bg-primary-400 transition-colors"
+          >
+            Try Again
+          </button>
+        </div>
+      </div>
+    );
+  }
+  
+  return (
+    <div className="min-h-screen bg-dark-900 flex flex-col">
+      {/* Header */}
+      <header className="h-14 bg-dark-850 border-b border-dark-700 flex items-center justify-between px-4 flex-shrink-0">
+        {/* Left: Navigation */}
+        <div className="flex items-center gap-3">
+          <button
+            onClick={() => navigate('/')}
+            className="p-2 hover:bg-dark-700 rounded-lg text-dark-400 hover:text-white transition-colors"
+          >
+            <Home className="w-5 h-5" />
+          </button>
+          <ChevronRight className="w-4 h-4 text-dark-600" />
+          <div className="flex items-center gap-2">
+            <Sparkles className="w-5 h-5 text-primary-400" />
+            <span className="text-white font-medium">Atomizer Studio</span>
+          </div>
+          {draft.draftId && (
+            <>
+              <ChevronRight className="w-4 h-4 text-dark-600" />
+              <span className="text-dark-400 text-sm font-mono">{draft.draftId}</span>
+            </>
+          )}
+        </div>
+        
+        {/* Right: Actions */}
+        <div className="flex items-center gap-2">
+          <button
+            onClick={resetDraft}
+            className="flex items-center gap-2 px-3 py-1.5 text-sm text-dark-400 hover:text-white hover:bg-dark-700 rounded-lg transition-colors"
+          >
+            <Trash2 className="w-4 h-4" />
+            Reset
+          </button>
+          <button
+            onClick={() => setShowBuildDialog(true)}
+            disabled={!canBuild}
+            className="flex items-center gap-2 px-4 py-1.5 text-sm font-medium bg-primary-500 text-white rounded-lg hover:bg-primary-400 disabled:opacity-50 disabled:cursor-not-allowed transition-colors"
+          >
+            <Save className="w-4 h-4" />
+            Save & Name Study
+          </button>
+        </div>
+      </header>
+      
+      {/* Main Content */}
+      <div className="flex-1 flex overflow-hidden">
+        {/* Left Panel: Resources (Resizable) */}
+        <div
+          className="bg-dark-850 border-r border-dark-700 flex flex-col flex-shrink-0 relative"
+          style={{ width: leftPanelWidth }}
+        >
+          <div className="flex-1 overflow-y-auto p-4 space-y-6">
+            {/* Drop Zone */}
+            <section>
+              <h3 className="text-sm font-medium text-dark-300 mb-3 flex items-center gap-2">
+                <Upload className="w-4 h-4" />
+                Model Files
+              </h3>
+              {draft.draftId && (
+                <StudioDropZone
+                  draftId={draft.draftId}
+                  type="model"
+                  files={draft.modelFiles}
+                  onUploadComplete={handleUploadComplete}
+                />
+              )}
+            </section>
+            
+            {/* Introspection */}
+            {draft.modelFiles.length > 0 && (
+              <section>
+                <div className="flex items-center justify-between mb-3">
+                  <h3 className="text-sm font-medium text-dark-300 flex items-center gap-2">
+                    <Settings className="w-4 h-4" />
+                    Parameters
+                  </h3>
+                  <button
+                    onClick={runIntrospection}
+                    disabled={isIntrospecting}
+                    className="flex items-center gap-1 px-2 py-1 text-xs text-primary-400 hover:bg-primary-400/10 rounded transition-colors disabled:opacity-50"
+                  >
+                    {isIntrospecting ? (
+                      <Loader2 className="w-3 h-3 animate-spin" />
+                    ) : (
+                      <RefreshCw className="w-3 h-3" />
+                    )}
+                    {isIntrospecting ? 'Scanning...' : 'Scan'}
+                  </button>
+                </div>
+                {draft.draftId && draft.introspectionAvailable && (
+                  <StudioParameterList
+                    draftId={draft.draftId}
+                    onParameterAdded={refreshDraft}
+                  />
+                )}
+                {!draft.introspectionAvailable && (
+                  <p className="text-xs text-dark-500 italic">
+                    Click "Scan" to discover parameters from your model.
+                  </p>
+                )}
+              </section>
+            )}
+            
+            {/* Context Files */}
+            <section>
+              <h3 className="text-sm font-medium text-dark-300 mb-3 flex items-center gap-2">
+                <FileText className="w-4 h-4" />
+                Context Documents
+              </h3>
+              {draft.draftId && (
+                <StudioContextFiles
+                  draftId={draft.draftId}
+                  files={draft.contextFiles}
+                  onUploadComplete={handleUploadComplete}
+                />
+              )}
+              <p className="text-xs text-dark-500 mt-2">
+                Upload requirements, goals, or specs. The AI will read these.
+              </p>
+              
+              {/* Show context preview if loaded */}
+              {draft.contextContent && (
+                <div className="mt-3 p-2 bg-dark-700/50 rounded-lg border border-dark-600">
+                  <p className="text-xs text-amber-400 mb-1 font-medium">Context Loaded:</p>
+                  <p className="text-xs text-dark-400 line-clamp-3">
+                    {draft.contextContent.substring(0, 200)}...
+                  </p>
+                </div>
+              )}
+            </section>
+            
+            {/* Node Palette - EXPANDED, not collapsed */}
+            <section>
+              <h3 className="text-sm font-medium text-dark-300 mb-3 flex items-center gap-2">
+                <Layers className="w-4 h-4" />
+                Components
+              </h3>
+              <NodePalette 
+                collapsed={false} 
+                showToggle={false}
+                className="!w-full !border-0 !bg-transparent"
+              />
+            </section>
+          </div>
+          
+          {/* Resize Handle */}
+          <div
+            className="absolute right-0 top-0 bottom-0 w-1 cursor-col-resize hover:bg-primary-500/50 transition-colors group"
+            onMouseDown={handleMouseDown}
+          >
+            <div className="absolute right-0 top-1/2 -translate-y-1/2 w-4 h-8 flex items-center justify-center opacity-0 group-hover:opacity-100 transition-opacity">
+              <GripVertical className="w-3 h-3 text-dark-400" />
+            </div>
+          </div>
+        </div>
+        
+        {/* Center: Canvas */}
+        <div className="flex-1 relative bg-dark-900">
+          {draft.draftId && (
+            <SpecRenderer
+              studyId={draft.draftId}
+              editable={true}
+              showLoadingOverlay={false}
+            />
+          )}
+          
+          {/* Empty state */}
+          {!specLoading && (!spec || Object.keys(spec).length === 0) && (
+            <div className="absolute inset-0 flex items-center justify-center pointer-events-none">
+              <div className="text-center max-w-md p-8">
+                <div className="w-20 h-20 rounded-full bg-dark-800 flex items-center justify-center mx-auto mb-6">
+                  <Sparkles className="w-10 h-10 text-primary-400" />
+                </div>
+                <h2 className="text-2xl font-semibold text-white mb-3">
+                  Welcome to Atomizer Studio
+                </h2>
+                <p className="text-dark-400 mb-6">
+                  Drop your model files on the left, or drag components from the palette to start building your optimization study.
+                </p>
+                <div className="flex flex-col gap-2 text-sm text-dark-500">
+                  <div className="flex items-center gap-2">
+                    <CheckCircle className="w-4 h-4 text-green-400" />
+                    <span>Upload .sim, .prt, .fem files</span>
+                  </div>
+                  <div className="flex items-center gap-2">
+                    <CheckCircle className="w-4 h-4 text-green-400" />
+                    <span>Add context documents (PDF, MD, TXT)</span>
+                  </div>
+                  <div className="flex items-center gap-2">
+                    <CheckCircle className="w-4 h-4 text-green-400" />
+                    <span>Configure with AI assistance</span>
+                  </div>
+                </div>
+              </div>
+            </div>
+          )}
+        </div>
+        
+        {/* Right Panel: Assistant + Config - wider for better chat UX */}
+        <div
+          className={`bg-dark-850 border-l border-dark-700 flex flex-col transition-all duration-300 flex-shrink-0 ${
+            rightPanelCollapsed ? 'w-12' : 'w-[480px]'
+          }`}
+        >
+          {/* Collapse toggle */}
+          <button
+            onClick={() => setRightPanelCollapsed(!rightPanelCollapsed)}
+            className="absolute right-0 top-1/2 -translate-y-1/2 z-10 p-1 bg-dark-700 border border-dark-600 rounded-l-lg hover:bg-dark-600 transition-colors"
+            style={{ marginRight: rightPanelCollapsed ? '48px' : '480px' }}
+          >
+            {rightPanelCollapsed ? (
+              <ChevronLeft className="w-4 h-4 text-dark-400" />
+            ) : (
+              <ChevronRightIcon className="w-4 h-4 text-dark-400" />
+            )}
+          </button>
+          
+          {!rightPanelCollapsed && (
+            <div className="flex-1 flex flex-col overflow-hidden">
+              {/* Chat */}
+              <div className="flex-1 overflow-hidden">
+                {draft.draftId && (
+                  <StudioChat
+                    draftId={draft.draftId}
+                    contextFiles={draft.contextFiles}
+                    contextContent={draft.contextContent}
+                    modelFiles={draft.modelFiles}
+                    onSpecUpdated={refreshDraft}
+                  />
+                )}
+              </div>
+              
+              {/* Config Panel (when node selected) */}
+              <NodeConfigPanelV2 />
+            </div>
+          )}
+          
+          {rightPanelCollapsed && (
+            <div className="flex flex-col items-center py-4 gap-4">
+              <MessageSquare className="w-5 h-5 text-dark-400" />
+            </div>
+          )}
+        </div>
+      </div>
+      
+      {/* Notification Toast */}
+      {notification && (
+        <div
+          className={`fixed bottom-4 right-4 flex items-center gap-3 px-4 py-3 rounded-lg shadow-lg z-50 animate-slide-up ${
+            notification.type === 'success'
+              ? 'bg-green-500/10 border border-green-500/30 text-green-400'
+              : notification.type === 'error'
+              ? 'bg-red-500/10 border border-red-500/30 text-red-400'
+              : 'bg-primary-500/10 border border-primary-500/30 text-primary-400'
+          }`}
+        >
+          {notification.type === 'success' && <CheckCircle className="w-5 h-5" />}
+          {notification.type === 'error' && <AlertCircle className="w-5 h-5" />}
+          {notification.type === 'info' && <Sparkles className="w-5 h-5" />}
+          <span>{notification.message}</span>
+          <button
+            onClick={() => setNotification(null)}
+            className="p-1 hover:bg-white/10 rounded"
+          >
+            <X className="w-4 h-4" />
+          </button>
+        </div>
+      )}
+      
+      {/* Build Dialog */}
+      {showBuildDialog && draft.draftId && (
+        <StudioBuildDialog
+          draftId={draft.draftId}
+          onClose={() => setShowBuildDialog(false)}
+          onBuildComplete={handleBuildComplete}
+        />
+      )}
+    </div>
+  );
+}

atomizer-dashboard/frontend/src/types/intake.ts

@@ -0,0 +1,201 @@
+/**
+ * Intake Workflow TypeScript Types
+ * 
+ * Types for the study intake/creation workflow.
+ */
+
+// ============================================================================
+// Status Types
+// ============================================================================
+
+export type SpecStatus = 
+  | 'draft'
+  | 'introspected'
+  | 'configured'
+  | 'validated'
+  | 'ready'
+  | 'running'
+  | 'completed'
+  | 'failed';
+
+// ============================================================================
+// Expression/Introspection Types
+// ============================================================================
+
+export interface ExpressionInfo {
+  /** Expression name in NX */
+  name: string;
+  /** Current value */
+  value: number | null;
+  /** Physical units */
+  units: string | null;
+  /** Expression formula if any */
+  formula: string | null;
+  /** Whether this is a design variable candidate */
+  is_candidate: boolean;
+  /** Confidence that this is a DV (0-1) */
+  confidence: number;
+}
+
+export interface BaselineData {
+  /** When baseline was run */
+  timestamp: string;
+  /** How long the solve took */
+  solve_time_seconds: number;
+  /** Computed mass from BDF/FEM */
+  mass_kg: number | null;
+  /** Max displacement result */
+  max_displacement_mm: number | null;
+  /** Max von Mises stress */
+  max_stress_mpa: number | null;
+  /** Whether baseline solve succeeded */
+  success: boolean;
+  /** Error message if failed */
+  error: string | null;
+}
+
+export interface IntrospectionData {
+  /** When introspection was run */
+  timestamp: string;
+  /** Detected solver type */
+  solver_type: string | null;
+  /** Mass from expressions or properties */
+  mass_kg: number | null;
+  /** Volume from mass properties */
+  volume_mm3: number | null;
+  /** Discovered expressions */
+  expressions: ExpressionInfo[];
+  /** Baseline solve results */
+  baseline: BaselineData | null;
+  /** Warnings from introspection */
+  warnings: string[];
+}
+
+// ============================================================================
+// Request/Response Types
+// ============================================================================
+
+export interface CreateInboxRequest {
+  study_name: string;
+  description?: string;
+  topic?: string;
+}
+
+export interface CreateInboxResponse {
+  success: boolean;
+  study_name: string;
+  inbox_path: string;
+  spec_path: string;
+  status: SpecStatus;
+}
+
+export interface IntrospectRequest {
+  study_name: string;
+  model_file?: string;
+}
+
+export interface IntrospectResponse {
+  success: boolean;
+  study_name: string;
+  status: SpecStatus;
+  expressions_count: number;
+  candidates_count: number;
+  mass_kg: number | null;
+  warnings: string[];
+}
+
+export interface InboxStudy {
+  study_name: string;
+  status: SpecStatus;
+  description: string | null;
+  topic: string | null;
+  created: string | null;
+  modified: string | null;
+  model_files: string[];
+  has_context: boolean;
+}
+
+export interface ListInboxResponse {
+  studies: InboxStudy[];
+  total: number;
+}
+
+export interface TopicInfo {
+  name: string;
+  study_count: number;
+  path: string;
+}
+
+export interface ListTopicsResponse {
+  topics: TopicInfo[];
+  total: number;
+}
+
+export interface InboxStudyDetail {
+  study_name: string;
+  inbox_path: string;
+  spec: import('./atomizer-spec').AtomizerSpec;
+  files: {
+    sim: string[];
+    prt: string[];
+    fem: string[];
+  };
+  context_files: string[];
+}
+
+// ============================================================================
+// Finalize Types
+// ============================================================================
+
+export interface FinalizeRequest {
+  topic: string;
+  run_baseline?: boolean;
+}
+
+export interface FinalizeProgress {
+  step: string;
+  progress: number;
+  message: string;
+  completed: boolean;
+  error?: string;
+}
+
+export interface FinalizeResponse {
+  success: boolean;
+  study_name: string;
+  final_path: string;
+  status: SpecStatus;
+  baseline?: BaselineData;
+  readme_generated: boolean;
+}
+
+// ============================================================================
+// README Generation Types
+// ============================================================================
+
+export interface GenerateReadmeRequest {
+  study_name: string;
+}
+
+export interface GenerateReadmeResponse {
+  success: boolean;
+  content: string;
+  path: string;
+}
+
+// ============================================================================
+// Upload Types
+// ============================================================================
+
+export interface UploadFilesResponse {
+  success: boolean;
+  study_name: string;
+  uploaded_files: Array<{
+    name: string;
+    status: 'uploaded' | 'rejected' | 'skipped';
+    path?: string;
+    size?: number;
+    reason?: string;
+  }>;
+  total_uploaded: number;
+}

atomizer-dashboard/frontend/test-results/.last-run.json

@@ -0,0 +1,4 @@
+{
+  "status": "passed",
+  "failedTests": []
+}

atomizer-dashboard/frontend/tests/e2e/home.spec.ts

@@ -0,0 +1,171 @@
+import { test, expect } from '@playwright/test';
+
+/**
+ * Home Page E2E Tests
+ * 
+ * Tests the study list page at /
+ * Covers: study loading, topic expansion, navigation
+ */
+
+test.describe('Home Page - Study List', () => {
+  
+  test.beforeEach(async ({ page }) => {
+    // Navigate to home page
+    await page.goto('/');
+  });
+
+  test('displays page header', async ({ page }) => {
+    // Check header is visible
+    await expect(page.locator('header')).toBeVisible();
+    
+    // Check for key header elements - Studies heading (exact match to avoid Inbox Studies)
+    await expect(page.getByRole('heading', { name: 'Studies', exact: true })).toBeVisible({ timeout: 10000 });
+  });
+
+  test('shows aggregate statistics cards', async ({ page }) => {
+    // Wait for stats to load
+    await expect(page.getByText('Total Studies')).toBeVisible();
+    await expect(page.getByText('Running')).toBeVisible();
+    await expect(page.getByText('Total Trials')).toBeVisible();
+    await expect(page.getByText('Best Overall')).toBeVisible();
+  });
+
+  test('loads studies table with topic folders', async ({ page }) => {
+    // Wait for studies section (exact match to avoid Inbox Studies)
+    await expect(page.getByRole('heading', { name: 'Studies', exact: true })).toBeVisible();
+    
+    // Wait for loading to complete - either see folders or empty state
+    // Folders have "trials" text in them
+    const folderLocator = page.locator('button:has-text("trials")');
+    const emptyStateLocator = page.getByText('No studies found');
+    
+    // Wait for either studies loaded or empty state (10s timeout)
+    await expect(folderLocator.first().or(emptyStateLocator)).toBeVisible({ timeout: 10000 });
+  });
+
+  test('expands topic folder to show studies', async ({ page }) => {
+    // Wait for folders to load
+    const folderButton = page.locator('button:has-text("trials")').first();
+    
+    // Wait for folder to be visible (studies loaded)
+    await expect(folderButton).toBeVisible({ timeout: 10000 });
+    
+    // Click to expand
+    await folderButton.click();
+    
+    // After expansion, study rows should be visible (they have status badges)
+    // Status badges contain: running, completed, idle, paused, not_started
+    const statusBadges = page.locator('span:has-text("running"), span:has-text("completed"), span:has-text("idle"), span:has-text("paused"), span:has-text("not_started")');
+    await expect(statusBadges.first()).toBeVisible({ timeout: 5000 });
+  });
+
+  test('clicking study shows preview panel', async ({ page }) => {
+    // Wait for and expand first folder
+    const folderButton = page.locator('button:has-text("trials")').first();
+    await expect(folderButton).toBeVisible({ timeout: 10000 });
+    await folderButton.click();
+    
+    // Wait for expanded content and click first study row
+    const studyRow = page.locator('.bg-dark-850\\/50 > div').first();
+    await expect(studyRow).toBeVisible({ timeout: 5000 });
+    await studyRow.click();
+    
+    // Preview panel should show with buttons - use exact match to avoid header nav button
+    await expect(page.getByRole('button', { name: 'Canvas', exact: true })).toBeVisible({ timeout: 5000 });
+    await expect(page.getByRole('button', { name: 'Open' })).toBeVisible();
+  });
+
+  test('Open button navigates to dashboard', async ({ page }) => {
+    // Wait for and expand first folder
+    const folderButton = page.locator('button:has-text("trials")').first();
+    await expect(folderButton).toBeVisible({ timeout: 10000 });
+    await folderButton.click();
+    
+    // Wait for and click study row
+    const studyRow = page.locator('.bg-dark-850\\/50 > div').first();
+    await expect(studyRow).toBeVisible({ timeout: 5000 });
+    await studyRow.click();
+    
+    // Wait for and click Open button
+    const openButton = page.getByRole('button', { name: 'Open' });
+    await expect(openButton).toBeVisible({ timeout: 5000 });
+    await openButton.click();
+    
+    // Should navigate to dashboard
+    await expect(page).toHaveURL(/\/dashboard/);
+  });
+
+  test('Canvas button navigates to canvas view', async ({ page }) => {
+    // Wait for and expand first folder
+    const folderButton = page.locator('button:has-text("trials")').first();
+    await expect(folderButton).toBeVisible({ timeout: 10000 });
+    await folderButton.click();
+    
+    // Wait for and click study row
+    const studyRow = page.locator('.bg-dark-850\\/50 > div').first();
+    await expect(studyRow).toBeVisible({ timeout: 5000 });
+    await studyRow.click();
+    
+    // Wait for and click Canvas button (exact match to avoid header nav)
+    const canvasButton = page.getByRole('button', { name: 'Canvas', exact: true });
+    await expect(canvasButton).toBeVisible({ timeout: 5000 });
+    await canvasButton.click();
+    
+    // Should navigate to canvas
+    await expect(page).toHaveURL(/\/canvas\//);
+  });
+
+  test('refresh button reloads studies', async ({ page }) => {
+    // Find the main studies section refresh button (the one with visible text "Refresh")
+    const refreshButton = page.getByText('Refresh');
+    await expect(refreshButton).toBeVisible({ timeout: 5000 });
+    
+    // Click refresh
+    await refreshButton.click();
+    
+    // Should show loading state or complete quickly
+    // Just verify no errors occurred (exact match to avoid Inbox Studies)
+    await expect(page.getByRole('heading', { name: 'Studies', exact: true })).toBeVisible();
+  });
+});
+
+/**
+ * Inbox Section Tests
+ * 
+ * Tests the new study intake workflow
+ */
+test.describe('Home Page - Inbox Section', () => {
+  
+  test.beforeEach(async ({ page }) => {
+    await page.goto('/');
+  });
+
+  test('displays inbox section with header', async ({ page }) => {
+    // Check for Study Inbox heading (section is expanded by default)
+    const inboxHeading = page.getByRole('heading', { name: 'Study Inbox' });
+    await expect(inboxHeading).toBeVisible({ timeout: 10000 });
+  });
+
+  test('inbox section shows pending count', async ({ page }) => {
+    // Section should show pending studies count
+    const pendingText = page.getByText(/\d+ pending studies/);
+    await expect(pendingText).toBeVisible({ timeout: 10000 });
+  });
+
+  test('inbox has new study button', async ({ page }) => {
+    // Section is expanded by default, look for the New Study button
+    const newStudyButton = page.getByRole('button', { name: /New Study/ });
+    await expect(newStudyButton).toBeVisible({ timeout: 10000 });
+  });
+
+  test('clicking new study shows create form', async ({ page }) => {
+    // Click the New Study button
+    const newStudyButton = page.getByRole('button', { name: /New Study/ });
+    await expect(newStudyButton).toBeVisible({ timeout: 10000 });
+    await newStudyButton.click();
+    
+    // Form should expand with input fields
+    const studyNameInput = page.getByPlaceholder(/my_study/i).or(page.locator('input[type="text"]').first());
+    await expect(studyNameInput).toBeVisible({ timeout: 5000 });
+  });
+});

atomizer-field/.gitignore

@@ -1,56 +0,0 @@
-# Python
-__pycache__/
-*.py[cod]
-*$py.class
-*.so
-.Python
-env/
-venv/
-ENV/
-*.egg-info/
-dist/
-build/
-
-# Jupyter Notebooks
-.ipynb_checkpoints/
-*.ipynb
-
-# IDEs
-.vscode/
-.idea/
-*.swp
-*.swo
-*~
-
-# OS
-.DS_Store
-Thumbs.db
-
-# Data files (large)
-*.op2
-*.bdf
-*.dat
-*.f06
-*.pch
-*.h5
-*.hdf5
-
-# Training data
-training_data/
-checkpoints/
-runs/
-logs/
-
-# Test outputs
-test_case_*/
-visualization_images/
-
-# Temporary files
-*.tmp
-*.log
-*.bak
-*.orig
-
-# Environment
-atomizer_env/
-.conda/

atomizer-field/ATOMIZER_FIELD_STATUS_REPORT.md

@@ -1,635 +0,0 @@
-# AtomizerField - Complete Status Report
-
-**Date:** November 24, 2025
-**Version:** 1.0
-**Status:** ✅ Core System Operational, Unit Issues Resolved
-
----
-
-## Executive Summary
-
-**AtomizerField** is a neural field learning system that replaces traditional FEA simulations with graph neural networks, providing **1000× faster predictions** for structural optimization.
-
-### Current Status
-- ✅ **Core pipeline working**: BDF/OP2 → Neural format → GNN inference
-- ✅ **Test case validated**: Simple Beam (5,179 nodes, 4,866 elements)
-- ✅ **Unit system understood**: MN-MM system (kPa stress, N forces, mm length)
-- ⚠️ **Not yet trained**: Neural network has random weights
-- 🔜 **Next step**: Generate training data and train model
-
----
-
-## What AtomizerField Does
-
-### 1. Data Pipeline ✅ WORKING
-
-**Purpose:** Convert Nastran FEA results into neural network training data
-
-**Input:**
-- BDF file (geometry, materials, loads, BCs)
-- OP2 file (FEA results: displacement, stress, reactions)
-
-**Output:**
-- JSON metadata (mesh, materials, loads, statistics)
-- HDF5 arrays (coordinates, displacement, stress fields)
-
-**What's Extracted:**
-- ✅ Mesh: 5,179 nodes, 4,866 CQUAD4 shell elements
-- ✅ Materials: Young's modulus, Poisson's ratio, density
-- ✅ Boundary conditions: SPCs, MPCs (if present)
-- ✅ Loads: 35 point forces with directions
-- ✅ Displacement field: 6 DOF per node (Tx, Ty, Tz, Rx, Ry, Rz)
-- ✅ Stress field: 8 components per element (σxx, σyy, τxy, principals, von Mises)
-- ✅ Reaction forces: 6 DOF per node
-
-**Performance:**
-- Parse time: 1.27 seconds
-- Data size: JSON 1.7 MB, HDF5 546 KB
-
-### 2. Graph Neural Network ✅ ARCHITECTURE WORKING
-
-**Purpose:** Learn FEA physics to predict displacement/stress from geometry/loads
-
-**Architecture:**
-- Type: Graph Neural Network (PyTorch Geometric)
-- Parameters: 128,589 (small model for testing)
-- Layers: 6 message passing layers
-- Hidden dimension: 64
-
-**Input Features:**
-- Node features (12D): position (3D), BCs (6 DOF), loads (3D)
-- Edge features (5D): E, ν, ρ, G, α (material properties)
-
-**Output Predictions:**
-- Displacement: (N_nodes, 6) - full 6 DOF per node
-- Stress: (N_elements, 6) - stress tensor components
-- Von Mises: (N_elements,) - scalar stress measure
-
-**Current State:**
-- ✅ Model instantiates successfully
-- ✅ Forward pass works
-- ✅ Inference time: 95.94 ms (< 100 ms target)
-- ⚠️ Predictions are random (untrained weights)
-
-### 3. Visualization ✅ WORKING
-
-**Purpose:** Visualize mesh, displacement, and stress fields
-
-**Capabilities:**
-- ✅ 3D mesh rendering (nodes + elements)
-- ✅ Displacement visualization (original + deformed)
-- ✅ Stress field coloring (von Mises)
-- ✅ Automatic report generation (markdown + images)
-
-**Generated Outputs:**
-- mesh.png (227 KB)
-- displacement.png (335 KB)
-- stress.png (215 KB)
-- Markdown report with embedded images
-
-### 4. Unit System ✅ UNDERSTOOD
-
-**Nastran UNITSYS: MN-MM**
-
-Despite the name, actual units are:
-- Length: **mm** (millimeter)
-- Force: **N** (Newton) - NOT MegaNewton!
-- Stress: **kPa** (kiloPascal = N/mm²) - NOT MPa!
-- Mass: **kg** (kilogram)
-- Young's modulus: **kPa** (200,000,000 kPa = 200 GPa for steel)
-
-**Validated Values:**
-- Max stress: 117,000 kPa = **117 MPa** ✓ (reasonable for steel)
-- Max displacement: **19.5 mm** ✓
-- Applied forces: **~2.73 MN each** ✓ (large beam structure)
-- Young's modulus: 200,000,000 kPa = **200 GPa** ✓ (steel)
-
-### 5. Direction Handling ✅ FULLY VECTORIAL
-
-**All fields preserve directional information:**
-
-**Displacement (6 DOF):**
-```
-[Tx, Ty, Tz, Rx, Ry, Rz]
-```
-- Stored as (5179, 6) array
-- Full translation + rotation at each node
-
-**Forces/Reactions (6 DOF):**
-```
-[Fx, Fy, Fz, Mx, My, Mz]
-```
-- Stored as (5179, 6) array
-- Full force + moment vectors
-
-**Stress Tensor (shell elements):**
-```
-[fiber_distance, σxx, σyy, τxy, angle, σ_major, σ_minor, von_mises]
-```
-- Stored as (9732, 8) array
-- Full stress state for each element (2 per CQUAD4)
-
-**Coordinate System:**
-- Global XYZ coordinates
-- Node positions: (5179, 3) array
-- Element connectivity preserves topology
-
-**Neural Network:**
-- Learns directional relationships through graph structure
-- Message passing propagates forces through mesh topology
-- Predicts full displacement vectors and stress tensors
-
----
-
-## What's Been Tested
-
-### ✅ Smoke Tests (5/5 PASS)
-
-1. **Model Creation**: GNN instantiates with 128,589 parameters
-2. **Forward Pass**: Processes dummy graph data
-3. **Loss Functions**: All 4 loss types compute correctly
-4. **Batch Processing**: Handles batched data
-5. **Gradient Flow**: Backpropagation works
-
-**Status:** All passing, system fundamentally sound
-
-### ✅ Simple Beam End-to-End Test (7/7 PASS)
-
-1. **File Existence**: BDF (1,230 KB) and OP2 (4,461 KB) found
-2. **Directory Setup**: test_case_beam/ structure created
-3. **Module Imports**: All dependencies load correctly
-4. **BDF/OP2 Parsing**: 5,179 nodes, 4,866 elements extracted
-5. **Data Validation**: No NaN values, physics consistent
-6. **Graph Conversion**: PyTorch Geometric format successful
-7. **Neural Prediction**: Inference in 95.94 ms
-
-**Status:** Complete pipeline validated with real FEA data
-
-### ✅ Visualization Test
-
-1. **Mesh Rendering**: 5,179 nodes, 4,866 elements displayed
-2. **Displacement Field**: Original + deformed (10× scale)
-3. **Stress Field**: Von Mises coloring across elements
-4. **Report Generation**: Markdown + embedded images
-
-**Status:** All visualizations working correctly
-
-### ✅ Unit Validation
-
-1. **UNITSYS Detection**: MN-MM system identified
-2. **Material Properties**: E = 200 GPa confirmed for steel
-3. **Stress Values**: 117 MPa reasonable for loaded beam
-4. **Force Values**: 2.73 MN per load point validated
-
-**Status:** Units understood, values physically realistic
-
----
-
-## What's NOT Tested Yet
-
-### ❌ Physics Validation Tests (0/4)
-
-These require **trained model**:
-
-1. **Cantilever Beam Test**: Analytical solution comparison
-   - Load known geometry/loads
-   - Compare prediction vs analytical deflection formula
-   - Target: < 5% error
-
-2. **Equilibrium Test**: ∇·σ + f = 0
-   - Check force balance at each node
-   - Ensure physics laws satisfied
-   - Target: Residual < 1% of max force
-
-3. **Constitutive Law Test**: σ = C:ε (Hooke's law)
-   - Verify stress-strain relationship
-   - Check material model accuracy
-   - Target: < 5% deviation
-
-4. **Energy Conservation Test**: Strain energy = work done
-   - Compute ∫(σ:ε)dV vs ∫(f·u)dV
-   - Ensure energy balance
-   - Target: < 5% difference
-
-**Blocker:** Model not trained yet (random weights)
-
-### ❌ Learning Tests (0/4)
-
-These require **trained model**:
-
-1. **Memorization Test**: Can model fit single example?
-   - Train on 1 case, test on same case
-   - Target: < 1% error (proves capacity)
-
-2. **Interpolation Test**: Can model predict between training cases?
-   - Train on cases A and C
-   - Test on case B (intermediate)
-   - Target: < 10% error
-
-3. **Extrapolation Test**: Can model generalize?
-   - Train on small loads
-   - Test on larger loads
-   - Target: < 20% error (harder)
-
-4. **Pattern Recognition Test**: Does model learn physics?
-   - Test on different geometry with same physics
-   - Check if physical principles transfer
-   - Target: Qualitative correctness
-
-**Blocker:** Model not trained yet
-
-### ❌ Integration Tests (0/5)
-
-These require **trained model + optimization interface**:
-
-1. **Batch Prediction**: Process multiple designs
-2. **Gradient Computation**: Analytical sensitivities
-3. **Optimization Loop**: Full design cycle
-4. **Uncertainty Quantification**: Ensemble predictions
-5. **Online Learning**: Update during optimization
-
-**Blocker:** Model not trained yet
-
-### ❌ Performance Tests (0/3)
-
-These require **trained model**:
-
-1. **Accuracy Benchmark**: < 10% error vs FEA
-2. **Speed Benchmark**: < 50 ms inference time
-3. **Scalability Test**: Larger meshes (10K+ nodes)
-
-**Blocker:** Model not trained yet
-
----
-
-## Current Capabilities Summary
-
-| Feature | Status | Notes |
-|---------|--------|-------|
-| **Data Pipeline** | ✅ Working | Parses BDF/OP2 to neural format |
-| **Unit Handling** | ✅ Understood | MN-MM system (kPa stress, N force) |
-| **Direction Handling** | ✅ Complete | Full 6 DOF + tensor components |
-| **Graph Conversion** | ✅ Working | PyTorch Geometric format |
-| **GNN Architecture** | ✅ Working | 128K params, 6 layers |
-| **Forward Pass** | ✅ Working | 95.94 ms inference |
-| **Visualization** | ✅ Working | 3D mesh, displacement, stress |
-| **Training Pipeline** | ⚠️ Ready | Code exists, not executed |
-| **Physics Compliance** | ❌ Unknown | Requires trained model |
-| **Prediction Accuracy** | ❌ Unknown | Requires trained model |
-
----
-
-## Known Issues
-
-### ⚠️ Minor Issues
-
-1. **Unit Labels**: Parser labels stress as "MPa" when it's actually "kPa"
-   - Impact: Confusing but documented
-   - Fix: Update labels in neural_field_parser.py
-   - Priority: Low (doesn't affect calculations)
-
-2. **Unicode Encoding**: Windows cp1252 codec limitations
-   - Impact: Crashes with Unicode symbols (✓, →, σ, etc.)
-   - Fix: Already replaced most with ASCII
-   - Priority: Low (cosmetic)
-
-3. **No SPCs Found**: Test beam has no explicit constraints
-   - Impact: Warning message appears
-   - Fix: Probably fixed at edges (investigate BDF)
-   - Priority: Low (analysis ran successfully)
-
-### ✅ Resolved Issues
-
-1. ~~**NumPy MINGW-W64 Crashes**~~
-   - Fixed: Created conda environment with proper NumPy
-   - Status: All tests running without crashes
-
-2. ~~**pyNastran API Compatibility**~~
-   - Fixed: Added getattr/hasattr checks for optional attributes
-   - Status: Parser handles missing 'sol' and 'temps'
-
-3. ~~**Element Connectivity Structure**~~
-   - Fixed: Discovered categorized dict structure (solid/shell/beam)
-   - Status: Visualization working correctly
-
-4. ~~**Node ID Mapping**~~
-   - Fixed: Created node_id_to_idx mapping for 1-indexed IDs
-   - Status: Element plotting correct
-
----
-
-## What's Next
-
-### Phase 1: Fix Unit Labels (30 minutes)
-
-**Goal:** Update parser to correctly label units
-
-**Changes needed:**
-```python
-# neural_field_parser.py line ~623
-"units": "kPa"  # Changed from "MPa"
-
-# metadata section
-"stress": "kPa"  # Changed from "MPa"
-```
-
-**Validation:**
-- Re-run test_simple_beam.py
-- Check reports show "117 kPa" not "117 MPa"
-- Or add conversion: stress/1000 → MPa
-
-### Phase 2: Generate Training Data (1-2 weeks)
-
-**Goal:** Create 50-500 training cases
-
-**Approach:**
-1. Vary beam dimensions (length, width, thickness)
-2. Vary loading conditions (magnitude, direction, location)
-3. Vary material properties (steel, aluminum, titanium)
-4. Vary boundary conditions (cantilever, simply supported, clamped)
-
-**Expected:**
-- 50 minimum (quick validation)
-- 200 recommended (good accuracy)
-- 500 maximum (best performance)
-
-**Tools:**
-- Use parametric FEA (NX Nastran)
-- Batch processing script
-- Quality validation for each case
-
-### Phase 3: Train Neural Network (2-6 hours)
-
-**Goal:** Train model to < 10% prediction error
-
-**Configuration:**
-```bash
-python train.py \
-  --data_dirs training_data/* \
-  --epochs 100 \
-  --batch_size 16 \
-  --lr 0.001 \
-  --loss physics \
-  --checkpoint_dir checkpoints/
-```
-
-**Expected:**
-- Training time: 2-6 hours (CPU)
-- Loss convergence: < 0.01
-- Validation error: < 10%
-
-**Monitoring:**
-- TensorBoard for loss curves
-- Validation metrics every 10 epochs
-- Early stopping if no improvement
-
-### Phase 4: Validate Performance (1-2 hours)
-
-**Goal:** Run full test suite
-
-**Tests:**
-```bash
-# Physics tests
-python test_suite.py --physics
-
-# Learning tests
-python test_suite.py --learning
-
-# Full validation
-python test_suite.py --full
-```
-
-**Expected:**
-- All 18 tests passing
-- Physics compliance < 5% error
-- Prediction accuracy < 10% error
-- Inference time < 50 ms
-
-### Phase 5: Production Deployment (1 day)
-
-**Goal:** Integrate with Atomizer
-
-**Interface:**
-```python
-from optimization_interface import NeuralFieldOptimizer
-
-optimizer = NeuralFieldOptimizer('checkpoints/best_model.pt')
-results = optimizer.evaluate(design_graph)
-sensitivities = optimizer.get_sensitivities(design_graph)
-```
-
-**Features:**
-- Fast evaluation: ~10 ms per design
-- Analytical gradients: 1M× faster than finite differences
-- Uncertainty quantification: Confidence intervals
-- Online learning: Improve during optimization
-
----
-
-## Testing Strategy
-
-### Current: Smoke Testing ✅
-
-**Status:** Completed
-- 5/5 smoke tests passing
-- 7/7 end-to-end tests passing
-- System fundamentally operational
-
-### Next: Unit Testing
-
-**What to test:**
-- Individual parser functions
-- Data validation rules
-- Unit conversion functions
-- Graph construction logic
-
-**Priority:** Medium (system working, but good for maintainability)
-
-### Future: Integration Testing
-
-**What to test:**
-- Multi-case batch processing
-- Training pipeline end-to-end
-- Optimization interface
-- Uncertainty quantification
-
-**Priority:** High (required before production)
-
-### Future: Physics Testing
-
-**What to test:**
-- Analytical solution comparison
-- Energy conservation
-- Force equilibrium
-- Constitutive laws
-
-**Priority:** Critical (validates correctness)
-
----
-
-## Performance Expectations
-
-### After Training
-
-| Metric | Target | Expected |
-|--------|--------|----------|
-| Prediction Error | < 10% | 5-10% |
-| Inference Time | < 50 ms | 10-30 ms |
-| Speedup vs FEA | 1000× | 1000-3000× |
-| Memory Usage | < 500 MB | ~300 MB |
-
-### Production Capability
-
-**Single Evaluation:**
-- FEA: 30-300 seconds
-- Neural: 10-30 ms
-- **Speedup: 1000-10,000×**
-
-**Optimization Loop (100 iterations):**
-- FEA: 50-500 minutes
-- Neural: 1-3 seconds
-- **Speedup: 3000-30,000×**
-
-**Gradient Computation:**
-- FEA (finite diff): 300-3000 seconds
-- Neural (analytical): 0.1 ms
-- **Speedup: 3,000,000-30,000,000×**
-
----
-
-## Risk Assessment
-
-### Low Risk ✅
-
-- Core pipeline working
-- Data extraction validated
-- Units understood
-- Visualization working
-
-### Medium Risk ⚠️
-
-- Model architecture untested with training
-- Physics compliance unknown
-- Generalization capability unclear
-- Need diverse training data
-
-### High Risk ❌
-
-- None identified currently
-
-### Mitigation Strategies
-
-1. **Start with small dataset** (50 cases) to validate training
-2. **Monitor physics losses** during training
-3. **Test on analytical cases** first (cantilever beam)
-4. **Gradual scaling** to larger/more complex geometries
-
----
-
-## Resource Requirements
-
-### Computational
-
-**Training:**
-- CPU: 8+ cores recommended
-- RAM: 16 GB minimum
-- GPU: Optional (10× faster, 8+ GB VRAM)
-- Time: 2-6 hours
-
-**Inference:**
-- CPU: Any (even single core works)
-- RAM: 2 GB sufficient
-- GPU: Not needed
-- Time: 10-30 ms per case
-
-### Data Storage
-
-**Per Training Case:**
-- BDF: ~1 MB
-- OP2: ~5 MB
-- Parsed (JSON): ~2 MB
-- Parsed (HDF5): ~500 KB
-- **Total: ~8.5 MB per case**
-
-**Full Training Set (200 cases):**
-- Raw: ~1.2 GB
-- Parsed: ~500 MB
-- Model: ~2 MB
-- **Total: ~1.7 GB**
-
----
-
-## Recommendations
-
-### Immediate (This Week)
-
-1. ✅ **Fix unit labels** - 30 minutes
-   - Update "MPa" → "kPa" in parser
-   - Or add /1000 conversion to match expected units
-
-2. **Document unit system** - 1 hour
-   - Add comments in parser
-   - Update user documentation
-   - Create unit conversion guide
-
-### Short-term (Next 2 Weeks)
-
-3. **Generate training data** - 1-2 weeks
-   - Start with 50 cases (minimum viable)
-   - Validate data quality
-   - Expand to 200 if needed
-
-4. **Initial training** - 1 day
-   - Train on 50 cases
-   - Validate on 10 held-out cases
-   - Check physics compliance
-
-### Medium-term (Next Month)
-
-5. **Full validation** - 1 week
-   - Run complete test suite
-   - Physics compliance tests
-   - Accuracy benchmarks
-
-6. **Production integration** - 1 week
-   - Connect to Atomizer
-   - End-to-end optimization test
-   - Performance profiling
-
----
-
-## Conclusion
-
-### ✅ What's Working
-
-AtomizerField has a **fully functional core pipeline**:
-- Parses real FEA data (5,179 nodes validated)
-- Converts to neural network format
-- GNN architecture operational (128K params)
-- Inference runs fast (95.94 ms)
-- Visualization produces publication-quality figures
-- Units understood and validated
-
-### 🔜 What's Next
-
-The system is **ready for training**:
-- All infrastructure in place
-- Test case validated
-- Neural architecture proven
-- Just needs training data
-
-### 🎯 Production Readiness
-
-**After training (2-3 weeks):**
-- Prediction accuracy: < 10% error
-- Inference speed: 1000× faster than FEA
-- Full integration with Atomizer
-- **Revolutionary optimization capability unlocked!**
-
-The hard work is done - now we train and deploy! 🚀
-
----
-
-*Report generated: November 24, 2025*
-*AtomizerField v1.0*
-*Status: Core operational, ready for training*

atomizer-field/AtomizerField_Development_Report.md

@@ -1,603 +0,0 @@
-# AtomizerField Development Report
-
-**Prepared for:** Antoine Polvé  
-**Date:** November 24, 2025  
-**Status:** Core System Complete → Ready for Training Phase
-
----
-
-## Executive Summary
-
-AtomizerField is **fully implemented and validated** at the architectural level. The project has achieved approximately **~7,000 lines of production code** across all phases, with a complete data pipeline, neural network architecture, physics-informed training system, and optimization interface. 
-
-**Current Position:** You're at the transition point between "building" and "training/deploying."
-
-**Critical Insight:** The system works—now it needs data to learn from.
-
----
-
-## Part 1: Current Development Status
-
-### What's Built ✅
-
-| Component | Status | Lines of Code | Validation |
-|-----------|--------|---------------|------------|
-| **BDF/OP2 Parser** | ✅ Complete | ~1,400 | Tested with Simple Beam |
-| **Graph Neural Network** | ✅ Complete | ~490 | 718,221 parameters, forward pass validated |
-| **Physics-Informed Losses** | ✅ Complete | ~450 | All 4 loss types tested |
-| **Data Loader** | ✅ Complete | ~420 | PyTorch Geometric integration |
-| **Training Pipeline** | ✅ Complete | ~430 | TensorBoard, checkpointing, early stopping |
-| **Inference Engine** | ✅ Complete | ~380 | 95ms inference time validated |
-| **Optimization Interface** | ✅ Complete | ~430 | Drop-in FEA replacement ready |
-| **Uncertainty Quantification** | ✅ Complete | ~380 | Ensemble-based, online learning |
-| **Test Suite** | ✅ Complete | ~2,700 | 18 automated tests |
-| **Documentation** | ✅ Complete | 10 guides | Comprehensive coverage |
-
-### Simple Beam Validation Results
-
-Your actual FEA model was successfully processed:
-
-```
-✅ Nodes parsed:        5,179
-✅ Elements parsed:     4,866 CQUAD4
-✅ Displacement field:  Complete (max: 19.56 mm)
-✅ Stress field:        Complete (9,732 values)
-✅ Graph conversion:    PyTorch Geometric format
-✅ Neural inference:    95.94 ms
-✅ All 7 tests:         PASSED
-```
-
-### What's NOT Done Yet ⏳
-
-| Gap | Impact | Effort Required |
-|-----|--------|-----------------|
-| **Training data generation** | Can't train without data | 1-2 weeks (50-500 cases) |
-| **Model training** | Model has random weights | 2-8 hours (GPU) |
-| **Physics validation** | Can't verify accuracy | After training |
-| **Atomizer integration** | Not connected yet | 1-2 weeks |
-| **Production deployment** | Not in optimization loop | After integration |
-
----
-
-## Part 2: The Physics-Neural Network Architecture
-
-### Core Innovation: Learning Fields, Not Scalars
-
-**Traditional Approach:**
-```
-Design Parameters → FEA (30 min) → max_stress = 450 MPa (1 number)
-```
-
-**AtomizerField Approach:**
-```
-Design Parameters → Neural Network (50 ms) → stress_field[5,179 nodes × 6 components]
-                                           = 31,074 stress values!
-```
-
-This isn't just faster—it's fundamentally different. You know **WHERE** the stress is, not just **HOW MUCH**.
-
-### The Graph Neural Network Architecture
-
-```
-┌─────────────────────────────────────────────────────────────────┐
-│                    GRAPH REPRESENTATION                          │
-├─────────────────────────────────────────────────────────────────┤
-│  NODES (from FEA mesh):                                         │
-│  ├── Position (x, y, z)           → 3 features                  │
-│  ├── Boundary conditions (6 DOF)  → 6 features (0/1 mask)       │
-│  └── Applied loads (Fx, Fy, Fz)   → 3 features                  │
-│      Total: 12 features per node                                │
-│                                                                  │
-│  EDGES (from element connectivity):                              │
-│  ├── Young's modulus (E)          → Material stiffness          │
-│  ├── Poisson's ratio (ν)          → Lateral contraction         │
-│  ├── Density (ρ)                  → Mass distribution           │
-│  ├── Shear modulus (G)            → Shear behavior              │
-│  └── Thermal expansion (α)        → Thermal effects             │
-│      Total: 5 features per edge                                 │
-└─────────────────────────────────────────────────────────────────┘
-                              ↓
-┌─────────────────────────────────────────────────────────────────┐
-│                    MESSAGE PASSING (6 LAYERS)                    │
-├─────────────────────────────────────────────────────────────────┤
-│  Each layer:                                                     │
-│  1. Gather neighbor information                                  │
-│  2. Weight by material properties (edge features)                │
-│  3. Update node representation                                   │
-│  4. Residual connection + LayerNorm                             │
-│                                                                  │
-│  KEY INSIGHT: Forces propagate through connected elements!       │
-│  The network learns HOW forces flow through the structure.       │
-└─────────────────────────────────────────────────────────────────┘
-                              ↓
-┌─────────────────────────────────────────────────────────────────┐
-│                    FIELD PREDICTIONS                             │
-├─────────────────────────────────────────────────────────────────┤
-│  Displacement: [N_nodes, 6]  → Tx, Ty, Tz, Rx, Ry, Rz           │
-│  Stress:       [N_nodes, 6]  → σxx, σyy, σzz, τxy, τyz, τxz     │
-│  Von Mises:    [N_nodes, 1]  → Scalar stress measure            │
-└─────────────────────────────────────────────────────────────────┘
-```
-
-### Physics-Informed Loss Functions
-
-The network doesn't just minimize prediction error—it enforces physical laws:
-
-```
-L_total = λ_data × L_data           # Match FEA results
-        + λ_eq × L_equilibrium       # ∇·σ + f = 0 (force balance)
-        + λ_const × L_constitutive   # σ = C:ε (Hooke's law)
-        + λ_bc × L_boundary          # u = 0 at fixed nodes
-```
-
-**Why This Matters:**
-- **Faster convergence:** Network starts with physics intuition
-- **Better generalization:** Extrapolates correctly outside training range
-- **Physically plausible:** No "impossible" stress distributions
-- **Less data needed:** Physics provides strong inductive bias
-
-### What Makes This Different from Standard PINNs
-
-| Aspect | Academic PINNs | AtomizerField |
-|--------|----------------|---------------|
-| **Geometry** | Simple (rods, plates) | Complex industrial meshes |
-| **Data source** | Solve PDEs from scratch | Learn from existing FEA |
-| **Goal** | Replace physics solvers | Accelerate optimization |
-| **Mesh** | Regular grids | Arbitrary unstructured |
-| **Scalability** | ~100s of DOFs | ~50,000+ DOFs |
-
-AtomizerField is better described as a **"Data-Driven Surrogate Model for Structural Optimization"** or **"FEA-Informed Neural Network."**
-
----
-
-## Part 3: How to Test a Concrete Solution
-
-### Step 1: Generate Training Data (Critical Path)
-
-You need **50-500 FEA cases** with geometric/load variations.
-
-**Option A: Parametric Study in NX (Recommended)**
-
-```
-For your Simple Beam:
-1. Open beam_sim1 in NX
-2. Create design study with variations:
-   - Thickness: 1mm, 2mm, 3mm, 4mm, 5mm
-   - Width: 50mm, 75mm, 100mm
-   - Load: 1000N, 2000N, 3000N, 4000N
-   - Support position: 3 locations
-   
-   Total: 5 × 3 × 4 × 3 = 180 cases
-   
-3. Run all cases (automated with NX journal)
-4. Export BDF/OP2 for each case
-```
-
-**Option B: Design of Experiments**
-
-```python
-# Generate Latin Hypercube sampling
-import numpy as np
-from scipy.stats import qmc
-
-sampler = qmc.LatinHypercube(d=4)  # 4 design variables
-sample = sampler.random(n=100)     # 100 cases
-
-# Scale to your design space
-thickness = 1 + sample[:, 0] * 4    # 1-5 mm
-width = 50 + sample[:, 1] * 50      # 50-100 mm
-load = 1000 + sample[:, 2] * 3000   # 1000-4000 N
-# etc.
-```
-
-**Option C: Monte Carlo Sampling**
-
-Generate random combinations within bounds. Quick but less space-filling than LHS.
-
-### Step 2: Parse All Training Data
-
-```bash
-# Create directory structure
-mkdir training_data
-mkdir validation_data
-
-# Move 80% of cases to training, 20% to validation
-
-# Batch parse
-python batch_parser.py --input training_data/ --output parsed_training/
-python batch_parser.py --input validation_data/ --output parsed_validation/
-```
-
-### Step 3: Train the Model
-
-```bash
-# Initial training (MSE only)
-python train.py \
-    --data_dirs parsed_training/* \
-    --epochs 50 \
-    --batch_size 16 \
-    --loss mse \
-    --checkpoint_dir checkpoints/mse/
-
-# Physics-informed training (recommended)
-python train.py \
-    --data_dirs parsed_training/* \
-    --epochs 100 \
-    --batch_size 16 \
-    --loss physics \
-    --checkpoint_dir checkpoints/physics/
-
-# Monitor progress
-tensorboard --logdir runs/
-```
-
-**Expected Training Time:**
-- CPU: 6-24 hours (50-500 cases)
-- GPU: 1-4 hours (much faster)
-
-### Step 4: Validate the Trained Model
-
-```bash
-# Run full test suite
-python test_suite.py --full
-
-# Test on validation set
-python predict.py \
-    --model checkpoints/physics/best_model.pt \
-    --data parsed_validation/ \
-    --compare
-
-# Expected metrics:
-# - Displacement error: < 10%
-# - Stress error: < 15%
-# - Inference time: < 50ms
-```
-
-### Step 5: Quick Smoke Test (Do This First!)
-
-Before generating 500 cases, test with 10 cases:
-
-```bash
-# Generate 10 quick variations
-# Parse them
-python batch_parser.py --input quick_test/ --output parsed_quick/
-
-# Train for 20 epochs (5 minutes)
-python train.py \
-    --data_dirs parsed_quick/* \
-    --epochs 20 \
-    --batch_size 4
-
-# Check if loss decreases → Network is learning!
-```
-
----
-
-## Part 4: What Should Be Implemented Next
-
-### Immediate Priorities (This Week)
-
-| Task | Purpose | Effort |
-|------|---------|--------|
-| **1. Generate 10 test cases** | Validate learning capability | 2-4 hours |
-| **2. Run quick training** | Prove network learns | 30 min |
-| **3. Visualize predictions** | See if fields make sense | 1 hour |
-
-### Short-Term (Next 2 Weeks)
-
-| Task | Purpose | Effort |
-|------|---------|--------|
-| **4. Generate 100+ training cases** | Production-quality data | 1 week |
-| **5. Full training run** | Trained model | 4-8 hours |
-| **6. Physics validation** | Cantilever beam test | 2 hours |
-| **7. Accuracy benchmarks** | Quantify error rates | 4 hours |
-
-### Medium-Term (1-2 Months)
-
-| Task | Purpose | Effort |
-|------|---------|--------|
-| **8. Atomizer integration** | Connect to optimization loop | 1-2 weeks |
-| **9. Uncertainty deployment** | Know when to trust | 1 week |
-| **10. Online learning** | Improve during optimization | 1 week |
-| **11. Multi-project transfer** | Reuse across designs | 2 weeks |
-
-### Code That Needs Writing
-
-**1. Automated Training Data Generator** (~200 lines)
-```python
-# generate_training_data.py
-class TrainingDataGenerator:
-    """Generate parametric FEA studies for training"""
-    
-    def generate_parametric_study(self, base_model, variations):
-        # Create NX journal for parametric study
-        # Run all cases automatically
-        # Collect BDF/OP2 pairs
-        pass
-```
-
-**2. Transfer Learning Module** (~150 lines)
-```python
-# transfer_learning.py
-class TransferLearningManager:
-    """Adapt trained model to new project"""
-    
-    def fine_tune(self, base_model, new_data, freeze_layers=4):
-        # Freeze early layers (general physics)
-        # Train later layers (project-specific)
-        pass
-```
-
-**3. Real-Time Visualization** (~300 lines)
-```python
-# field_visualizer.py
-class RealTimeFieldVisualizer:
-    """Interactive 3D visualization of predicted fields"""
-    
-    def show_prediction(self, design, prediction):
-        # 3D mesh with displacement
-        # Color by stress
-        # Slider for design parameters
-        pass
-```
-
----
-
-## Part 5: Atomizer Integration Strategy
-
-### Current Atomizer Architecture
-
-```
-Atomizer (Main Platform)
-├── optimization_engine/
-│   ├── runner.py           # Manages optimization loop
-│   ├── multi_optimizer.py  # Optuna optimization
-│   └── hook_manager.py     # Plugin system
-├── nx_journals/
-│   └── update_and_solve.py # NX FEA automation
-└── dashboard/
-    └── React frontend      # Real-time monitoring
-```
-
-### Integration Points
-
-**1. Replace FEA Calls (Primary Integration)**
-
-In `runner.py`, replace:
-```python
-# Before
-def evaluate_design(self, parameters):
-    self.nx_solver.update_parameters(parameters)
-    self.nx_solver.run_fea()  # 30 minutes
-    results = self.nx_solver.extract_results()
-    return results
-```
-
-With:
-```python
-# After
-from atomizer_field import NeuralFieldOptimizer
-
-def evaluate_design(self, parameters):
-    # First: Neural prediction (50ms)
-    graph = self.build_graph(parameters)
-    prediction = self.neural_optimizer.predict(graph)
-    
-    # Check uncertainty
-    if prediction['uncertainty'] > 0.1:
-        # High uncertainty: run FEA for validation
-        self.nx_solver.run_fea()
-        fea_results = self.nx_solver.extract_results()
-        
-        # Update model online
-        self.neural_optimizer.update(graph, fea_results)
-        return fea_results
-    
-    return prediction  # Trust neural network
-```
-
-**2. Gradient-Based Optimization**
-
-Current Atomizer uses Optuna (TPE, GP). With AtomizerField:
-
-```python
-# Add gradient-based option
-from atomizer_field import NeuralFieldOptimizer
-
-optimizer = NeuralFieldOptimizer('model.pt')
-
-# Analytical gradients (instant!)
-gradients = optimizer.get_sensitivities(design_graph)
-
-# Gradient descent optimization
-for iteration in range(100):
-    gradients = optimizer.get_sensitivities(current_design)
-    current_design -= learning_rate * gradients  # Direct update!
-```
-
-**Benefits:**
-- 1,000,000× faster than finite differences
-- Can optimize 100+ parameters efficiently
-- Better local convergence
-
-**3. Dashboard Integration**
-
-Add neural prediction tab to React dashboard:
-- Real-time field visualization
-- Prediction vs FEA comparison
-- Uncertainty heatmap
-- Training progress monitoring
-
-### Integration Roadmap
-
-```
-Week 1-2: Basic Integration
-├── Add AtomizerField as dependency
-├── Create neural_evaluator.py in optimization_engine/
-├── Add --use-neural flag to runner
-└── Test on simple_beam_optimization study
-
-Week 3-4: Smart Switching
-├── Implement uncertainty-based FEA triggering
-├── Add online learning updates
-├── Compare optimization quality vs pure FEA
-└── Benchmark speedup
-
-Week 5-6: Full Production
-├── Dashboard integration
-├── Multi-project support
-├── Documentation and examples
-└── Performance profiling
-```
-
-### Expected Benefits After Integration
-
-| Metric | Current (FEA Only) | With AtomizerField |
-|--------|-------------------|-------------------|
-| **Time per evaluation** | 30-300 seconds | 5-50 ms |
-| **Evaluations per hour** | 12-120 | 72,000-720,000 |
-| **Optimization time (1000 trials)** | 8-80 hours | 5-50 seconds + validation FEA |
-| **Gradient computation** | Finite diff (slow) | Analytical (instant) |
-| **Field insights** | Only max values | Complete distributions |
-
-**Conservative Estimate:** 100-1000× speedup with hybrid approach (neural + selective FEA validation)
-
----
-
-## Part 6: Development Gap Analysis
-
-### Code Gaps
-
-| Component | Current State | What's Needed | Effort |
-|-----------|--------------|---------------|--------|
-| Training data generation | Manual | Automated NX journal | 1 week |
-| Real-time visualization | Basic | Interactive 3D | 1 week |
-| Atomizer bridge | Not started | Integration module | 1-2 weeks |
-| Transfer learning | Designed | Implementation | 3-5 days |
-| Multi-solution support | Not started | Extend parser | 3-5 days |
-
-### Testing Gaps
-
-| Test Type | Current | Needed |
-|-----------|---------|--------|
-| Smoke tests | ✅ Complete | - |
-| Physics validation | ⏳ Ready | Run after training |
-| Accuracy benchmarks | ⏳ Ready | Run after training |
-| Integration tests | Not started | After Atomizer merge |
-| Production stress tests | Not started | Before deployment |
-
-### Documentation Gaps
-
-| Document | Status |
-|----------|--------|
-| API reference | Partial (need docstrings) |
-| Training guide | ✅ Complete |
-| Integration guide | Needs writing |
-| User manual | Needs writing |
-| Video tutorials | Not started |
-
----
-
-## Part 7: Recommended Action Plan
-
-### This Week (Testing & Validation)
-
-```
-Day 1: Quick Validation
-├── Generate 10 Simple Beam variations in NX
-├── Parse all 10 cases
-└── Run 20-epoch training (30 min)
-    Goal: See loss decrease = network learns!
-
-Day 2-3: Expand Dataset
-├── Generate 50 variations with better coverage
-├── Include thickness, width, load, support variations
-└── Parse and organize train/val split (80/20)
-
-Day 4-5: Proper Training
-├── Train for 100 epochs with physics loss
-├── Monitor TensorBoard
-└── Validate on held-out cases
-    Goal: < 15% error on validation set
-```
-
-### Next 2 Weeks (Production Quality)
-
-```
-Week 1: Data & Training
-├── Generate 200+ training cases
-├── Train production model
-├── Run full test suite
-└── Document accuracy metrics
-
-Week 2: Integration Prep
-├── Create atomizer_field_bridge.py
-├── Add to Atomizer as submodule
-├── Test on existing optimization study
-└── Compare results vs pure FEA
-```
-
-### First Month (Full Integration)
-
-```
-Week 3-4:
-├── Full Atomizer integration
-├── Uncertainty-based FEA triggering
-├── Dashboard neural prediction tab
-├── Performance benchmarks
-
-Documentation:
-├── Integration guide
-├── Best practices
-├── Example workflows
-```
-
----
-
-## Conclusion
-
-### What You Have
-- ✅ Complete neural field learning system (~7,000 lines)
-- ✅ Physics-informed architecture
-- ✅ Validated pipeline (Simple Beam test passed)
-- ✅ Production-ready code structure
-- ✅ Comprehensive documentation
-
-### What You Need
-- ⏳ Training data (50-500 FEA cases)
-- ⏳ Trained model weights
-- ⏳ Atomizer integration code
-- ⏳ Production validation
-
-### The Key Insight
-
-**AtomizerField is not trying to replace FEA—it's learning FROM FEA to accelerate optimization.**
-
-The network encodes your engineering knowledge:
-- How forces propagate through structures
-- How geometry affects stress distribution
-- How boundary conditions constrain deformation
-
-Once trained, it can predict these patterns 1000× faster than computing them from scratch.
-
-### Next Concrete Step
-
-**Right now, today:**
-```bash
-# 1. Generate 10 Simple Beam variations in NX
-# 2. Parse them:
-python batch_parser.py --input ten_cases/ --output parsed_ten/
-
-# 3. Train for 20 epochs:
-python train.py --data_dirs parsed_ten/* --epochs 20
-
-# 4. Watch the loss decrease → Your network is learning physics!
-```
-
-This 2-hour test will prove the concept works. Then scale up.
-
----
-
-*Report generated: November 24, 2025*  
-*AtomizerField Version: 1.0*  
-*Status: Ready for Training Phase*

atomizer-field/COMPLETE_SUMMARY.md

@@ -1,567 +0,0 @@
-# AtomizerField - Complete Implementation Summary
-
-## ✅ What Has Been Built
-
-You now have a **complete, production-ready system** for neural field learning in structural optimization.
-
----
-
-## 📍 Location
-
-```
-c:\Users\antoi\Documents\Atomaste\Atomizer-Field\
-```
-
----
-
-## 📦 What's Inside (Complete File List)
-
-### Documentation (Read These!)
-```
-├── README.md                     # Phase 1 guide (parser)
-├── PHASE2_README.md              # Phase 2 guide (neural network)
-├── GETTING_STARTED.md            # Quick start tutorial
-├── SYSTEM_ARCHITECTURE.md        # System architecture (detailed!)
-├── COMPLETE_SUMMARY.md           # This file
-├── Context.md                    # Project vision
-└── Instructions.md               # Implementation spec
-```
-
-### Phase 1: Data Parser (✅ Implemented & Tested)
-```
-├── neural_field_parser.py        # Main parser: BDF/OP2 → Neural format
-├── validate_parsed_data.py       # Data validation
-├── batch_parser.py               # Batch processing
-└── metadata_template.json        # Design parameter template
-```
-
-### Phase 2: Neural Network (✅ Implemented & Tested)
-```
-├── neural_models/
-│   ├── __init__.py
-│   ├── field_predictor.py        # GNN (718K params) ✅ TESTED
-│   ├── physics_losses.py         # Loss functions ✅ TESTED
-│   └── data_loader.py            # Data pipeline ✅ TESTED
-│
-├── train.py                      # Training script
-└── predict.py                    # Inference script
-```
-
-### Configuration
-```
-└── requirements.txt              # All dependencies
-```
-
----
-
-## 🧪 Test Results
-
-### ✅ Phase 2 Neural Network Tests
-
-**1. GNN Model Test (field_predictor.py):**
-```
-Testing AtomizerField Model Creation...
-Model created: 718,221 parameters
-
-Test forward pass:
-  Displacement shape: torch.Size([100, 6])
-  Stress shape: torch.Size([100, 6])
-  Von Mises shape: torch.Size([100])
-
-Max values:
-  Max displacement: 3.249960
-  Max stress: 3.94
-
-Model test passed! ✓
-```
-
-**2. Loss Functions Test (physics_losses.py):**
-```
-Testing AtomizerField Loss Functions...
-
-Testing MSE loss...
-  Total loss: 3.885789 ✓
-
-Testing RELATIVE loss...
-  Total loss: 2.941448 ✓
-
-Testing PHYSICS loss...
-  Total loss: 3.850585 ✓
-  (All physics constraints working)
-
-Testing MAX loss...
-  Total loss: 20.127707 ✓
-
-Loss function tests passed! ✓
-```
-
-**Conclusion:** All neural network components working perfectly!
-
----
-
-## 🔍 How It Works - Visual Summary
-
-### The Big Picture
-
-```
-┌───────────────────────────────────────────────────────────┐
-│                    YOUR WORKFLOW                          │
-└───────────────────────────────────────────────────────────┘
-
-1️⃣ CREATE DESIGNS IN NX
-   ├─ Make 500 bracket variants
-   ├─ Different thicknesses, ribs, holes
-   └─ Run FEA on each → .bdf + .op2 files
-
-            ↓
-
-2️⃣ PARSE FEA DATA (Phase 1)
-   $ python batch_parser.py ./all_brackets
-
-   ├─ Converts 500 cases in ~2 hours
-   ├─ Output: neural_field_data.json + .h5
-   └─ Complete stress/displacement fields preserved
-
-            ↓
-
-3️⃣ TRAIN NEURAL NETWORK (Phase 2)
-   $ python train.py --train_dir brackets --epochs 150
-
-   ├─ Trains Graph Neural Network (GNN)
-   ├─ Learns physics of bracket behavior
-   ├─ Time: 8-12 hours (one-time!)
-   └─ Output: checkpoint_best.pt (3 MB)
-
-            ↓
-
-4️⃣ OPTIMIZE AT LIGHTNING SPEED
-   $ python predict.py --model checkpoint_best.pt --input new_design
-
-   ├─ Predicts in 15 milliseconds
-   ├─ Complete stress field (not just max!)
-   ├─ Test 10,000 designs in 2.5 minutes
-   └─ Find optimal design instantly!
-
-            ↓
-
-5️⃣ VERIFY & MANUFACTURE
-   ├─ Run full FEA on final design (verify accuracy)
-   └─ Manufacture optimal bracket
-```
-
----
-
-## 🎯 Key Innovation: Complete Fields
-
-### Old Way (Traditional Surrogate Models)
-```python
-# Only learns scalar values
-max_stress = neural_network(thickness, rib_height, hole_diameter)
-# Result: 450.2 MPa
-
-# Problems:
-❌ No spatial information
-❌ Can't see WHERE stress occurs
-❌ Can't guide design improvements
-❌ Black box optimization
-```
-
-### AtomizerField Way (Neural Field Learning)
-```python
-# Learns COMPLETE field at every point
-field_results = neural_network(mesh_graph)
-
-displacement = field_results['displacement']  # [15,432 nodes × 6 DOF]
-stress = field_results['stress']              # [15,432 nodes × 6 components]
-von_mises = field_results['von_mises']        # [15,432 nodes]
-
-# Now you know:
-✅ Max stress: 450.2 MPa
-✅ WHERE it occurs: Node 8,743 (near fillet)
-✅ Stress distribution across entire structure
-✅ Can intelligently add material where needed
-✅ Physics-guided optimization!
-```
-
----
-
-## 🧠 The Neural Network Architecture
-
-### What You Built
-
-```
-AtomizerFieldModel (718,221 parameters)
-
-INPUT:
-├─ Nodes: [x, y, z, BC_mask(6), loads(3)] → 12 features per node
-└─ Edges: [E, ν, ρ, G, α] → 5 features per edge (material)
-
-PROCESSING:
-├─ Node Encoder: 12 → 128 dimensions
-├─ Edge Encoder: 5 → 64 dimensions
-├─ Message Passing × 6 layers:
-│  ├─ Forces propagate through mesh
-│  ├─ Learns stiffness matrix behavior
-│  └─ Respects element connectivity
-│
-├─ Displacement Decoder: 128 → 6 (ux, uy, uz, θx, θy, θz)
-└─ Stress Predictor: displacement → stress tensor
-
-OUTPUT:
-├─ Displacement field at ALL nodes
-├─ Stress field at ALL elements
-└─ Von Mises stress everywhere
-```
-
-**Why This Works:**
-
-FEA solves: **K·u = f**
-- K = stiffness matrix (depends on mesh topology + materials)
-- u = displacement
-- f = forces
-
-Our GNN learns this relationship:
-- **Mesh topology** → Graph edges
-- **Materials** → Edge features
-- **BCs & loads** → Node features
-- **Message passing** → Mimics K·u = f solving!
-
-**Result:** Network learns physics, not just patterns!
-
----
-
-## 📊 Performance Benchmarks
-
-### Tested Performance
-
-| Component | Status | Performance |
-|-----------|--------|-------------|
-| GNN Forward Pass | ✅ Tested | 100 nodes in ~5ms |
-| Loss Functions | ✅ Tested | All 4 types working |
-| Data Pipeline | ✅ Implemented | Graph conversion ready |
-| Training Loop | ✅ Implemented | GPU-optimized |
-| Inference | ✅ Implemented | Batch prediction ready |
-
-### Expected Real-World Performance
-
-| Task | Traditional FEA | AtomizerField | Speedup |
-|------|----------------|---------------|---------|
-| 10k element model | 15 minutes | 5 ms | 180,000× |
-| 50k element model | 2 hours | 15 ms | 480,000× |
-| 100k element model | 8 hours | 35 ms | 823,000× |
-
-### Accuracy (Expected)
-
-| Metric | Target | Typical |
-|--------|--------|---------|
-| Displacement Error | < 5% | 2-3% |
-| Stress Error | < 10% | 5-8% |
-| Max Value Error | < 3% | 1-2% |
-
----
-
-## 🚀 How to Use (Step-by-Step)
-
-### Prerequisites
-
-1. **Python 3.8+** (you have Python 3.14)
-2. **NX Nastran** (you have it)
-3. **GPU recommended** for training (optional but faster)
-
-### Setup (One-Time)
-
-```bash
-# Navigate to project
-cd c:\Users\antoi\Documents\Atomaste\Atomizer-Field
-
-# Create virtual environment
-python -m venv atomizer_env
-
-# Activate
-atomizer_env\Scripts\activate
-
-# Install dependencies
-pip install -r requirements.txt
-```
-
-### Workflow
-
-#### Step 1: Generate FEA Data in NX
-
-```
-1. Create design in NX
-2. Mesh (CTETRA, CHEXA, CQUAD4, etc.)
-3. Apply materials (MAT1)
-4. Apply BCs (SPC)
-5. Apply loads (FORCE, PLOAD4)
-6. Run SOL 101 (Linear Static)
-7. Request: DISPLACEMENT=ALL, STRESS=ALL
-8. Get files: model.bdf, model.op2
-```
-
-#### Step 2: Parse FEA Results
-
-```bash
-# Organize files
-mkdir training_case_001
-mkdir training_case_001/input
-mkdir training_case_001/output
-cp your_model.bdf training_case_001/input/model.bdf
-cp your_model.op2 training_case_001/output/model.op2
-
-# Parse
-python neural_field_parser.py training_case_001
-
-# Validate
-python validate_parsed_data.py training_case_001
-
-# For many cases:
-python batch_parser.py ./all_your_cases
-```
-
-**Output:**
-- `neural_field_data.json` - Metadata (200 KB)
-- `neural_field_data.h5` - Fields (3 MB)
-
-#### Step 3: Train Neural Network
-
-```bash
-# Organize data
-mkdir training_data
-mkdir validation_data
-# Move 80% of parsed cases to training_data/
-# Move 20% of parsed cases to validation_data/
-
-# Train
-python train.py \
-    --train_dir ./training_data \
-    --val_dir ./validation_data \
-    --epochs 100 \
-    --batch_size 4 \
-    --lr 0.001 \
-    --loss_type physics
-
-# Monitor (in another terminal)
-tensorboard --logdir runs/tensorboard
-```
-
-**Training takes:** 2-24 hours depending on dataset size
-
-**Output:**
-- `runs/checkpoint_best.pt` - Best model
-- `runs/config.json` - Configuration
-- `runs/tensorboard/` - Training logs
-
-#### Step 4: Run Predictions
-
-```bash
-# Single prediction
-python predict.py \
-    --model runs/checkpoint_best.pt \
-    --input new_design_case \
-    --compare
-
-# Batch prediction
-python predict.py \
-    --model runs/checkpoint_best.pt \
-    --input ./test_designs \
-    --batch \
-    --output_dir ./results
-```
-
-**Each prediction:** 5-50 milliseconds!
-
----
-
-## 📚 Data Format Details
-
-### Parsed Data Structure
-
-**JSON (neural_field_data.json):**
-- Metadata (version, timestamp, analysis type)
-- Mesh statistics (nodes, elements, types)
-- Materials (E, ν, ρ, G, α)
-- Boundary conditions (SPCs, MPCs)
-- Loads (forces, pressures, gravity)
-- Results summary (max values, units)
-
-**HDF5 (neural_field_data.h5):**
-- `/mesh/node_coordinates` - [N × 3] coordinates
-- `/results/displacement` - [N × 6] complete field
-- `/results/stress/*` - Complete stress tensors
-- `/results/strain/*` - Complete strain tensors
-- `/results/reactions` - Reaction forces
-
-**Why Two Files?**
-- JSON: Human-readable, metadata, structure
-- HDF5: Efficient, compressed, large arrays
-- Combined: Best of both worlds!
-
----
-
-## 🎓 What Makes This Special
-
-### 1. Physics-Informed Learning
-
-```python
-# Standard neural network
-loss = prediction_error
-
-# AtomizerField
-loss = prediction_error
-     + equilibrium_violation      # ∇·σ + f = 0
-     + constitutive_law_error      # σ = C:ε
-     + boundary_condition_violation # u = 0 at fixed nodes
-
-# Result: Learns physics, needs less data!
-```
-
-### 2. Graph Neural Networks
-
-```
-Traditional NN:
-Input → Dense Layers → Output
-(Ignores mesh structure!)
-
-AtomizerField GNN:
-Mesh Graph → Message Passing → Field Prediction
-(Respects topology, learns force flow!)
-```
-
-### 3. Complete Field Prediction
-
-```
-Traditional:
-- Only max stress
-- No spatial info
-- Black box
-
-AtomizerField:
-- Complete stress distribution
-- Know WHERE concentrations are
-- Physics-guided design
-```
-
----
-
-## 🔧 Troubleshooting
-
-### Common Issues
-
-**1. "No module named torch"**
-```bash
-pip install torch torch-geometric tensorboard
-```
-
-**2. "Out of memory during training"**
-```bash
-# Reduce batch size
-python train.py --batch_size 2
-
-# Or use smaller model
-python train.py --hidden_dim 64 --num_layers 4
-```
-
-**3. "Poor predictions"**
-- Need more training data (aim for 500+ cases)
-- Increase model size: `--hidden_dim 256 --num_layers 8`
-- Use physics loss: `--loss_type physics`
-- Ensure test cases within training distribution
-
-**4. NumPy warnings (like you saw)**
-- This is a Windows/NumPy compatibility issue
-- Doesn't affect functionality
-- Can be ignored or use specific NumPy version
-- The neural network components work perfectly (as tested!)
-
----
-
-## 📈 Next Steps
-
-### Immediate
-1. ✅ System is ready to use
-2. Generate training dataset (50-500 FEA cases)
-3. Parse with `batch_parser.py`
-4. Train first model with `train.py`
-5. Test predictions with `predict.py`
-
-### Short-term
-- Generate comprehensive dataset
-- Train production model
-- Validate accuracy on test set
-- Use for optimization!
-
-### Long-term (Phase 3+)
-- Nonlinear analysis support
-- Modal analysis
-- Thermal coupling
-- Atomizer dashboard integration
-- Cloud deployment
-
----
-
-## 📊 System Capabilities
-
-### What It Can Do
-
-✅ **Parse NX Nastran** - BDF/OP2 to neural format
-✅ **Handle Mixed Elements** - Solid, shell, beam
-✅ **Preserve Complete Fields** - All nodes/elements
-✅ **Graph Neural Networks** - Mesh-aware learning
-✅ **Physics-Informed** - Equilibrium, constitutive laws
-✅ **Fast Training** - GPU-accelerated, checkpointing
-✅ **Lightning Inference** - Millisecond predictions
-✅ **Batch Processing** - Handle hundreds of cases
-✅ **Validation** - Comprehensive quality checks
-✅ **Logging** - TensorBoard visualization
-
-### What It Delivers
-
-🎯 **1000× speedup** over traditional FEA
-🎯 **Complete field predictions** (not just max values)
-🎯 **Physics understanding** (know WHERE stress occurs)
-🎯 **Rapid optimization** (test millions of designs)
-🎯 **Production-ready** (error handling, documentation)
-
----
-
-## 🎉 Summary
-
-You now have a **complete, revolutionary system** for structural optimization:
-
-1. **Phase 1 Parser** - Converts FEA to ML format (✅ Implemented)
-2. **Phase 2 Neural Network** - Learns complete physics fields (✅ Implemented & Tested)
-3. **Training Pipeline** - GPU-optimized with checkpointing (✅ Implemented)
-4. **Inference Engine** - Millisecond predictions (✅ Implemented)
-5. **Documentation** - Comprehensive guides (✅ Complete)
-
-**Total:**
-- ~3,000 lines of production code
-- 7 documentation files
-- 8 Python modules
-- Complete testing
-- Ready for real-world use
-
-**Key Files to Read:**
-1. `GETTING_STARTED.md` - Quick tutorial
-2. `SYSTEM_ARCHITECTURE.md` - Detailed architecture
-3. `README.md` - Phase 1 guide
-4. `PHASE2_README.md` - Phase 2 guide
-
-**Start Here:**
-```bash
-cd c:\Users\antoi\Documents\Atomaste\Atomizer-Field
-# Read GETTING_STARTED.md
-# Generate your first training dataset
-# Train your first model!
-```
-
----
-
-**You're ready to revolutionize structural optimization! 🚀**
-
-From hours of FEA to milliseconds of prediction.
-From black-box optimization to physics-guided design.
-From scalar outputs to complete field understanding.
-
-**AtomizerField - The future of engineering optimization is here.**

atomizer-field/Context.md

@@ -1,127 +0,0 @@
-Context Instructions for Claude Sonnet 3.5
-Project: AtomizerField - Neural Field Learning for Structural Optimization
-System Context
-You are helping develop AtomizerField, a revolutionary branch of the Atomizer optimization platform that uses neural networks to learn and predict complete FEA field results (stress, displacement, strain at every node/element) instead of just scalar values. This enables 1000x faster optimization with physics understanding.
-Core Objective
-Transform structural optimization from black-box number crunching to intelligent, field-aware design exploration by training neural networks on complete FEA data, not just maximum values.
-Technical Foundation
-Current Stack:
-
-FEA: NX Nastran (BDF input, OP2/F06 output)
-Python Libraries: pyNastran, PyTorch, NumPy, H5PY
-Parent Project: Atomizer (optimization platform with dashboard)
-Data Format: Custom schema v1.0 for future-proof field storage
-
-Key Innovation:
-Instead of: parameters → FEA → max_stress (scalar)
-We learn: parameters → Neural Network → complete stress field (45,000 values)
-Project Structure
-AtomizerField/
-├── data_pipeline/
-│   ├── parser/           # BDF/OP2 to neural field format
-│   ├── generator/        # Automated FEA case generation
-│   └── validator/        # Data quality checks
-├── neural_models/
-│   ├── field_predictor/  # Core neural network
-│   ├── physics_layers/   # Physics-informed constraints
-│   └── training/         # Training scripts
-├── integration/
-│   └── atomizer_bridge/  # Integration with main Atomizer
-└── data/
-    └── training_cases/   # FEA data repository
-Current Development Phase
-Phase 1 (Current): Data Pipeline Development
-
-Parsing NX Nastran files (BDF/OP2) into training data
-Creating standardized data format
-Building automated case generation
-
-Next Phases:
-
-Phase 2: Neural network architecture
-Phase 3: Training pipeline
-Phase 4: Integration with Atomizer
-Phase 5: Production deployment
-
-Key Technical Concepts to Understand
-
-Field Learning: We're teaching NNs to predict stress/displacement at EVERY point in a structure, not just max values
-Physics-Informed: The NN must respect equilibrium, compatibility, and constitutive laws
-Graph Neural Networks: Mesh topology matters - we use GNNs to understand how forces flow through elements
-Transfer Learning: Knowledge from one project speeds up optimization on similar structures
-
-Code Style & Principles
-
-Future-Proof Data: All data structures versioned, backwards compatible
-Modular Design: Each component (parser, trainer, predictor) independent
-Validation First: Every data point validated for physics consistency
-Progressive Enhancement: Start simple (max stress), expand to fields
-Documentation: Every function documented with clear physics meaning
-
-Specific Instructions for Implementation
-When implementing code for AtomizerField:
-
-Always preserve field dimensionality - Don't reduce to scalars unless explicitly needed
-Use pyNastran's existing methods - Don't reinvent BDF/OP2 parsing
-Store data efficiently - HDF5 for arrays, JSON for metadata
-Validate physics - Check equilibrium, energy balance
-Think in fields - Visualize operations as field transformations
-Enable incremental learning - New data should improve existing models
-
-Current Task Context
-The user has:
-
-Set up NX Nastran analyses with full field outputs
-Generated BDF (input) and OP2 (output) files
-Needs to parse these into neural network training data
-
-The parser must:
-
-Extract complete mesh (nodes, elements, connectivity)
-Capture all boundary conditions and loads
-Store complete field results (not just max values)
-Maintain relationships between parameters and results
-Be robust to different element types (solid, shell, beam)
-
-Expected Outputs
-When asked about AtomizerField, provide:
-
-Practical, runnable code - No pseudocode unless requested
-Clear data flow - Show how data moves from FEA to NN
-Physics explanations - Why certain approaches work/fail
-Incremental steps - Break complex tasks into testable chunks
-Validation methods - How to verify data/model correctness
-
-Common Challenges & Solutions
-
-Large Data: Use HDF5 chunking and compression
-Mixed Element Types: Handle separately, combine for training
-Coordinate Systems: Always transform to global before storage
-Units: Standardize early (SI units recommended)
-Missing Data: Op2 might not have all requested fields - handle gracefully
-
-Integration Notes
-AtomizerField will eventually merge into main Atomizer:
-
-Keep interfaces clean and documented
-Use consistent data formats with Atomizer
-Prepare for dashboard visualization needs
-Enable both standalone and integrated operation
-
-Key Questions to Ask
-When implementing features, consider:
-
-Will this work with 1 million element meshes?
-Can we incrementally update models with new data?
-Does this respect physical laws?
-Is the data format forward-compatible?
-Can non-experts understand and use this?
-
-Ultimate Goal
-Create a system where engineers can:
-
-Run normal FEA analyses
-Automatically build neural surrogates from results
-Explore millions of designs instantly
-Understand WHY designs work through field visualization
-Optimize with physical insight, not blind search

atomizer-field/ENHANCEMENTS_GUIDE.md

@@ -1,494 +0,0 @@
-# AtomizerField Enhancements Guide
-
-## 🎯 What's Been Added (Phase 2.1)
-
-Following the review, I've implemented critical enhancements to make AtomizerField production-ready for real optimization workflows.
-
----
-
-## ✨ New Features
-
-### 1. **Optimization Interface** (`optimization_interface.py`)
-
-Direct integration with Atomizer optimization platform.
-
-**Key Features:**
-- Drop-in FEA replacement (1000× faster)
-- Gradient computation for sensitivity analysis
-- Batch evaluation (test 1000 designs in seconds)
-- Automatic performance tracking
-
-**Usage:**
-```python
-from optimization_interface import NeuralFieldOptimizer
-
-# Create optimizer
-optimizer = NeuralFieldOptimizer('checkpoint_best.pt')
-
-# Evaluate design
-results = optimizer.evaluate(graph_data)
-print(f"Max stress: {results['max_stress']:.2f} MPa")
-print(f"Time: {results['inference_time_ms']:.1f} ms")
-
-# Get gradients for optimization
-gradients = optimizer.get_sensitivities(graph_data, objective='max_stress')
-
-# Update design using gradients (much faster than finite differences!)
-new_parameters = parameters - learning_rate * gradients['node_gradients']
-```
-
-**Benefits:**
-- **Gradient-based optimization** - Use analytical gradients instead of finite differences
-- **Field-aware optimization** - Know WHERE to add/remove material
-- **Performance tracking** - Monitor speedup vs traditional FEA
-
-### 2. **Uncertainty Quantification** (`neural_models/uncertainty.py`)
-
-Know when to trust predictions and when to run FEA!
-
-**Key Features:**
-- Ensemble-based uncertainty estimation
-- Confidence intervals for predictions
-- Automatic FEA recommendation
-- Online learning from new FEA results
-
-**Usage:**
-```python
-from neural_models.uncertainty import UncertainFieldPredictor
-
-# Create ensemble (5 models)
-ensemble = UncertainFieldPredictor(model_config, n_ensemble=5)
-
-# Get predictions with uncertainty
-predictions = ensemble(graph_data, return_uncertainty=True)
-
-# Check if FEA validation needed
-recommendation = ensemble.needs_fea_validation(predictions, threshold=0.1)
-
-if recommendation['recommend_fea']:
-    print("Run FEA - prediction uncertain")
-    run_full_fea()
-else:
-    print("Trust neural prediction - high confidence!")
-    use_neural_result()
-```
-
-**Benefits:**
-- **Risk management** - Know when predictions are reliable
-- **Adaptive workflow** - Use FEA only when needed
-- **Cost optimization** - Minimize expensive FEA runs
-
-### 3. **Configuration System** (`atomizer_field_config.yaml`)
-
-Long-term vision configuration for all features.
-
-**Key Sections:**
-- Model architecture (foundation models, adaptation layers)
-- Training (progressive, online learning, physics loss weights)
-- Data pipeline (normalization, augmentation, multi-resolution)
-- Optimization (gradients, uncertainty, FEA fallback)
-- Deployment (versioning, production settings)
-- Integration (Atomizer dashboard, API)
-
-**Usage:**
-```yaml
-# Enable foundation model transfer learning
-model:
-  foundation:
-    enabled: true
-    path: "models/physics_foundation_v1.pt"
-    freeze: true
-
-# Enable online learning during optimization
-training:
-  online:
-    enabled: true
-    update_frequency: 10
-```
-
-### 4. **Online Learning** (in `uncertainty.py`)
-
-Learn from FEA runs during optimization.
-
-**Workflow:**
-```python
-from neural_models.uncertainty import OnlineLearner
-
-# Create learner
-learner = OnlineLearner(model, learning_rate=0.0001)
-
-# During optimization:
-for design in optimization_loop:
-    # Fast neural prediction
-    result = model.predict(design)
-
-    # If high uncertainty, run FEA
-    if uncertainty > threshold:
-        fea_result = run_fea(design)
-
-        # Learn from it!
-        learner.add_fea_result(design, fea_result)
-
-        # Quick update (10 gradient steps)
-        if len(learner.replay_buffer) >= 10:
-            learner.quick_update(steps=10)
-
-    # Model gets better over time!
-```
-
-**Benefits:**
-- **Continuous improvement** - Model learns during optimization
-- **Less FEA needed** - Model adapts to current design space
-- **Virtuous cycle** - Better predictions → less FEA → faster optimization
-
----
-
-## 🚀 Complete Workflow Examples
-
-### Example 1: Basic Optimization
-
-```python
-# 1. Load trained model
-from optimization_interface import NeuralFieldOptimizer
-
-optimizer = NeuralFieldOptimizer('runs/checkpoint_best.pt')
-
-# 2. Evaluate 1000 designs
-results = []
-for design_params in design_space:
-    # Generate mesh
-    graph_data = create_mesh(design_params)
-
-    # Predict in milliseconds
-    pred = optimizer.evaluate(graph_data)
-
-    results.append({
-        'params': design_params,
-        'max_stress': pred['max_stress'],
-        'max_displacement': pred['max_displacement']
-    })
-
-# 3. Find best design
-best = min(results, key=lambda r: r['max_stress'])
-print(f"Optimal design: {best['params']}")
-print(f"Stress: {best['max_stress']:.2f} MPa")
-
-# 4. Validate with FEA
-fea_validation = run_fea(best['params'])
-```
-
-**Time:** 1000 designs in ~30 seconds (vs 3000 hours FEA!)
-
-### Example 2: Uncertainty-Guided Optimization
-
-```python
-from neural_models.uncertainty import UncertainFieldPredictor, OnlineLearner
-
-# 1. Create ensemble
-ensemble = UncertainFieldPredictor(model_config, n_ensemble=5)
-learner = OnlineLearner(ensemble.models[0])
-
-# 2. Optimization with smart FEA usage
-fea_count = 0
-
-for iteration in range(1000):
-    design = generate_candidate()
-
-    # Predict with uncertainty
-    pred = ensemble(design, return_uncertainty=True)
-
-    # Check if we need FEA
-    rec = ensemble.needs_fea_validation(pred, threshold=0.1)
-
-    if rec['recommend_fea']:
-        # High uncertainty - run FEA
-        fea_result = run_fea(design)
-        fea_count += 1
-
-        # Learn from it
-        learner.add_fea_result(design, fea_result)
-
-        # Update model every 10 FEA runs
-        if fea_count % 10 == 0:
-            learner.quick_update(steps=10)
-
-        # Use FEA result
-        result = fea_result
-    else:
-        # Low uncertainty - trust neural prediction
-        result = pred
-
-    # Continue optimization...
-
-print(f"Total FEA runs: {fea_count}/1000")
-print(f"FEA reduction: {(1 - fea_count/1000)*100:.1f}%")
-```
-
-**Result:** ~10-20 FEA runs instead of 1000 (98% reduction!)
-
-### Example 3: Gradient-Based Optimization
-
-```python
-from optimization_interface import NeuralFieldOptimizer
-import torch
-
-# 1. Initialize
-optimizer = NeuralFieldOptimizer('checkpoint_best.pt', enable_gradients=True)
-
-# 2. Starting design
-parameters = torch.tensor([2.5, 5.0, 15.0], requires_grad=True)  # thickness, radius, height
-
-# 3. Gradient-based optimization loop
-learning_rate = 0.1
-
-for step in range(100):
-    # Convert parameters to mesh
-    graph_data = parameters_to_mesh(parameters)
-
-    # Evaluate
-    result = optimizer.evaluate(graph_data)
-    stress = result['max_stress']
-
-    # Get sensitivities
-    grads = optimizer.get_sensitivities(graph_data, objective='max_stress')
-
-    # Update parameters (gradient descent)
-    with torch.no_grad():
-        parameters -= learning_rate * torch.tensor(grads['node_gradients'].mean(axis=0))
-
-    if step % 10 == 0:
-        print(f"Step {step}: Stress = {stress:.2f} MPa")
-
-print(f"Final design: {parameters.tolist()}")
-print(f"Final stress: {stress:.2f} MPa")
-```
-
-**Benefits:**
-- Uses analytical gradients (exact!)
-- Much faster than finite differences
-- Finds optimal designs quickly
-
----
-
-## 📊 Performance Improvements
-
-### With New Features:
-
-| Capability | Before | After |
-|-----------|--------|-------|
-| **Optimization** | Finite differences | Analytical gradients (10× faster) |
-| **Reliability** | No uncertainty info | Confidence intervals, FEA recommendations |
-| **Adaptivity** | Fixed model | Online learning during optimization |
-| **Integration** | Manual | Clean API for Atomizer |
-
-### Expected Workflow Performance:
-
-**Optimize 1000-design bracket study:**
-
-| Step | Traditional | With AtomizerField | Speedup |
-|------|-------------|-------------------|---------|
-| Generate designs | 1 day | 1 day | 1× |
-| Evaluate (FEA) | 3000 hours | 30 seconds (neural) | 360,000× |
-| + Validation (20 FEA) | - | 40 hours | - |
-| **Total** | **125 days** | **2 days** | **62× faster** |
-
----
-
-## 🔧 Implementation Priority
-
-### ✅ Phase 2.1 (Complete - Just Added)
-1. ✅ Optimization interface with gradients
-2. ✅ Uncertainty quantification with ensemble
-3. ✅ Online learning capability
-4. ✅ Configuration system
-5. ✅ Complete documentation
-
-### 📅 Phase 2.2 (Next Steps)
-1. Multi-resolution training (coarse → fine)
-2. Foundation model architecture
-3. Parameter encoding improvements
-4. Advanced data augmentation
-
-### 📅 Phase 3 (Future)
-1. Atomizer dashboard integration
-2. REST API deployment
-3. Real-time field visualization
-4. Cloud deployment
-
----
-
-## 📁 Updated File Structure
-
-```
-Atomizer-Field/
-│
-├── 🆕 optimization_interface.py    # NEW: Optimization API
-├── 🆕 atomizer_field_config.yaml   # NEW: Configuration system
-│
-├── neural_models/
-│   ├── field_predictor.py
-│   ├── physics_losses.py
-│   ├── data_loader.py
-│   └── 🆕 uncertainty.py           # NEW: Uncertainty & online learning
-│
-├── train.py
-├── predict.py
-├── neural_field_parser.py
-├── validate_parsed_data.py
-├── batch_parser.py
-│
-└── Documentation/
-    ├── README.md
-    ├── PHASE2_README.md
-    ├── GETTING_STARTED.md
-    ├── SYSTEM_ARCHITECTURE.md
-    ├── COMPLETE_SUMMARY.md
-    └── 🆕 ENHANCEMENTS_GUIDE.md     # NEW: This file
-```
-
----
-
-## 🎓 How to Use the Enhancements
-
-### Step 1: Basic Optimization (No Uncertainty)
-
-```bash
-# Use optimization interface for fast evaluation
-python -c "
-from optimization_interface import NeuralFieldOptimizer
-opt = NeuralFieldOptimizer('checkpoint_best.pt')
-# Evaluate designs...
-"
-```
-
-### Step 2: Add Uncertainty Quantification
-
-```bash
-# Train ensemble (5 models with different initializations)
-python train.py --ensemble 5 --epochs 100
-
-# Use ensemble for predictions with confidence
-python -c "
-from neural_models.uncertainty import UncertainFieldPredictor
-ensemble = UncertainFieldPredictor(config, n_ensemble=5)
-# Get predictions with uncertainty...
-"
-```
-
-### Step 3: Enable Online Learning
-
-```bash
-# During optimization, update model from FEA runs
-# See Example 2 above for complete code
-```
-
-### Step 4: Customize via Config
-
-```bash
-# Edit atomizer_field_config.yaml
-# Enable features you want:
-#   - Foundation models
-#   - Online learning
-#   - Multi-resolution
-#   - Etc.
-
-# Train with config
-python train.py --config atomizer_field_config.yaml
-```
-
----
-
-## 🎯 Key Benefits Summary
-
-### 1. **Faster Optimization**
-- Analytical gradients instead of finite differences
-- Batch evaluation (1000 designs/minute)
-- 10-100× faster than before
-
-### 2. **Smarter Workflow**
-- Know when to trust predictions (uncertainty)
-- Automatic FEA recommendation
-- Adaptive FEA usage (98% reduction)
-
-### 3. **Continuous Improvement**
-- Model learns during optimization
-- Less FEA needed over time
-- Better predictions on current design space
-
-### 4. **Production Ready**
-- Clean API for integration
-- Configuration management
-- Performance monitoring
-- Comprehensive documentation
-
----
-
-## 🚦 Getting Started with Enhancements
-
-### Quick Start:
-
-```python
-# 1. Use optimization interface (simplest)
-from optimization_interface import create_optimizer
-
-opt = create_optimizer('checkpoint_best.pt')
-result = opt.evaluate(graph_data)
-
-# 2. Add uncertainty (recommended)
-from neural_models.uncertainty import create_uncertain_predictor
-
-ensemble = create_uncertain_predictor(model_config, n_ensemble=5)
-pred = ensemble(graph_data, return_uncertainty=True)
-
-if pred['stress_rel_uncertainty'] > 0.1:
-    print("High uncertainty - recommend FEA")
-
-# 3. Enable online learning (advanced)
-from neural_models.uncertainty import OnlineLearner
-
-learner = OnlineLearner(model)
-# Learn from FEA during optimization...
-```
-
-### Full Integration:
-
-See examples above for complete workflows integrating:
-- Optimization interface
-- Uncertainty quantification
-- Online learning
-- Configuration management
-
----
-
-## 📚 Additional Resources
-
-**Documentation:**
-- [GETTING_STARTED.md](GETTING_STARTED.md) - Basic tutorial
-- [SYSTEM_ARCHITECTURE.md](SYSTEM_ARCHITECTURE.md) - System details
-- [PHASE2_README.md](PHASE2_README.md) - Neural network guide
-
-**Code Examples:**
-- `optimization_interface.py` - See `if __name__ == "__main__"` section
-- `uncertainty.py` - See usage examples at bottom
-
-**Configuration:**
-- `atomizer_field_config.yaml` - All configuration options
-
----
-
-## 🎉 Summary
-
-**Phase 2.1 adds four critical capabilities:**
-
-1. ✅ **Optimization Interface** - Easy integration with Atomizer
-2. ✅ **Uncertainty Quantification** - Know when to trust predictions
-3. ✅ **Online Learning** - Improve during optimization
-4. ✅ **Configuration System** - Manage all features
-
-**Result:** Production-ready neural field learning system that's:
-- Fast (1000× speedup)
-- Smart (uncertainty-aware)
-- Adaptive (learns during use)
-- Integrated (ready for Atomizer)
-
-**You're ready to revolutionize structural optimization!** 🚀

atomizer-field/ENVIRONMENT_SETUP.md

@@ -1,419 +0,0 @@
-# AtomizerField Environment Setup
-
-## ✅ Problem Solved!
-
-The NumPy MINGW-W64 segmentation fault issue has been resolved by creating a proper conda environment with compatible packages.
-
----
-
-## Solution Summary
-
-**Issue:** NumPy built with MINGW-W64 on Windows caused segmentation faults when importing
-
-**Solution:** Created conda environment `atomizer_field` with properly compiled NumPy from conda-forge
-
-**Result:** ✅ All tests passing! System ready for use.
-
----
-
-## Environment Details
-
-### Conda Environment: `atomizer_field`
-
-**Created with:**
-```bash
-conda create -n atomizer_field python=3.10 numpy scipy -y
-conda activate atomizer_field
-conda install pytorch torchvision torchaudio cpuonly -c pytorch -y
-pip install torch-geometric pyNastran h5py tensorboard
-```
-
-### Installed Packages:
-
-**Core Scientific:**
-- Python 3.10.19
-- NumPy 1.26.4 (conda-compiled, no MINGW-W64 issues!)
-- SciPy 1.15.3
-- Matplotlib 3.10.7
-
-**PyTorch Stack:**
-- PyTorch 2.5.1 (CPU)
-- TorchVision 0.20.1
-- TorchAudio 2.5.1
-- PyTorch Geometric 2.7.0
-
-**AtomizerField Dependencies:**
-- pyNastran 1.4.1
-- H5Py 3.15.1
-- TensorBoard 2.20.0
-
-**Total Environment Size:** ~2GB
-
----
-
-## Usage
-
-### Activate Environment
-
-```bash
-# Windows (PowerShell)
-conda activate atomizer_field
-
-# Windows (Command Prompt)
-activate atomizer_field
-
-# Linux/Mac
-conda activate atomizer_field
-```
-
-### Run Tests
-
-```bash
-# Activate environment
-conda activate atomizer_field
-
-# Quick smoke tests (30 seconds)
-python test_suite.py --quick
-
-# Physics validation (15 minutes)
-python test_suite.py --physics
-
-# Full test suite (1 hour)
-python test_suite.py --full
-
-# Test with Simple Beam
-python test_simple_beam.py
-```
-
-### Run AtomizerField
-
-```bash
-# Activate environment
-conda activate atomizer_field
-
-# Parse FEA data
-python neural_field_parser.py path/to/case
-
-# Train model
-python train.py --data_dirs case1 case2 case3 --epochs 100
-
-# Make predictions
-python predict.py --model best_model.pt --data test_case
-```
-
----
-
-## Test Results
-
-### First Successful Test Run
-
-```
-============================================================
-AtomizerField Test Suite v1.0
-Mode: QUICK
-============================================================
-
-PHASE 1: SMOKE TESTS (5 minutes)
-============================================================
-
-[TEST] Model Creation
-  Description: Verify GNN model can be instantiated
-    Creating GNN model...
-    Model created: 128,589 parameters
-  Status: [PASS]
-  Duration: 0.06s
-
-[TEST] Forward Pass
-  Description: Verify model can process dummy data
-    Testing forward pass...
-    Displacement shape: torch.Size([100, 6]) [OK]
-    Stress shape: torch.Size([100, 6]) [OK]
-    Von Mises shape: torch.Size([100]) [OK]
-  Status: [PASS]
-  Duration: 0.02s
-
-[TEST] Loss Computation
-  Description: Verify loss functions work
-    Testing loss functions...
-    MSE loss: 4.027361 [OK]
-    RELATIVE loss: 3.027167 [OK]
-    PHYSICS loss: 3.659333 [OK]
-    MAX loss: 13.615703 [OK]
-  Status: [PASS]
-  Duration: 0.00s
-
-============================================================
-TEST SUMMARY
-============================================================
-
-Total Tests: 3
-  + Passed: 3
-  - Failed: 0
-  Pass Rate: 100.0%
-
-[SUCCESS] ALL TESTS PASSED - SYSTEM READY!
-============================================================
-
-Total testing time: 0.0 minutes
-```
-
-**Status:** ✅ All smoke tests passing!
-
----
-
-## Environment Management
-
-### View Environment Info
-
-```bash
-# List all conda environments
-conda env list
-
-# View installed packages
-conda activate atomizer_field
-conda list
-```
-
-### Update Packages
-
-```bash
-conda activate atomizer_field
-
-# Update conda packages
-conda update numpy scipy pytorch
-
-# Update pip packages
-pip install --upgrade torch-geometric pyNastran h5py tensorboard
-```
-
-### Export Environment
-
-```bash
-# Export for reproducibility
-conda activate atomizer_field
-conda env export > environment.yml
-
-# Recreate from export
-conda env create -f environment.yml
-```
-
-### Remove Environment (if needed)
-
-```bash
-# Deactivate first
-conda deactivate
-
-# Remove environment
-conda env remove -n atomizer_field
-```
-
----
-
-## Troubleshooting
-
-### Issue: conda command not found
-
-**Solution:** Add conda to PATH or use Anaconda Prompt
-
-### Issue: Import errors
-
-**Solution:** Make sure environment is activated
-```bash
-conda activate atomizer_field
-```
-
-### Issue: CUDA/GPU not available
-
-**Note:** Current installation is CPU-only. For GPU support:
-```bash
-conda install pytorch torchvision torchaudio pytorch-cuda=11.8 -c pytorch -c nvidia
-```
-
-### Issue: Slow training
-
-**Solutions:**
-1. Use GPU (see above)
-2. Reduce batch size
-3. Reduce model size (hidden_dim)
-4. Use fewer training epochs
-
----
-
-## Performance Comparison
-
-### Before (pip-installed NumPy):
-```
-Error: Segmentation fault (core dumped)
-CRASHES ARE TO BE EXPECTED
-```
-
-### After (conda environment):
-```
-✅ All tests passing
-✅ Model creates successfully (128,589 parameters)
-✅ Forward pass working
-✅ All 4 loss functions operational
-✅ No crashes or errors
-```
-
----
-
-## Next Steps
-
-### 1. Run Full Test Suite
-
-```bash
-conda activate atomizer_field
-
-# Run all smoke tests
-python test_suite.py --quick
-
-# Run physics tests
-python test_suite.py --physics
-
-# Run complete validation
-python test_suite.py --full
-```
-
-### 2. Test with Simple Beam
-
-```bash
-conda activate atomizer_field
-python test_simple_beam.py
-```
-
-Expected output:
-- Files found ✓
-- Test case setup ✓
-- Modules imported ✓
-- Beam parsed ✓
-- Data validated ✓
-- Graph created ✓
-- Prediction made ✓
-
-### 3. Generate Training Data
-
-```bash
-# Parse multiple FEA cases
-conda activate atomizer_field
-python batch_parser.py --input Models/ --output training_data/
-```
-
-### 4. Train Model
-
-```bash
-conda activate atomizer_field
-
-python train.py \
-  --data_dirs training_data/* \
-  --epochs 100 \
-  --batch_size 16 \
-  --lr 0.001 \
-  --loss physics
-
-# Monitor with TensorBoard
-tensorboard --logdir runs/
-```
-
-### 5. Make Predictions
-
-```bash
-conda activate atomizer_field
-
-python predict.py \
-  --model checkpoints/best_model.pt \
-  --data test_case/ \
-  --output predictions/
-```
-
----
-
-## Environment Specifications
-
-### System Requirements
-
-**Minimum:**
-- CPU: 4 cores
-- RAM: 8GB
-- Disk: 5GB free space
-- OS: Windows 10/11, Linux, macOS
-
-**Recommended:**
-- CPU: 8+ cores
-- RAM: 16GB+
-- Disk: 20GB+ free space
-- GPU: NVIDIA with 8GB+ VRAM (optional)
-
-### Installation Time
-
-- Conda environment creation: ~5 minutes
-- Package downloads: ~10 minutes
-- Total setup time: ~15 minutes
-
-### Disk Usage
-
-```
-atomizer_field environment: ~2GB
-  - Python: ~200MB
-  - PyTorch: ~800MB
-  - NumPy/SciPy: ~400MB
-  - Other packages: ~600MB
-
-Training data (per case): ~1-10MB
-Model checkpoint: ~500KB-2MB
-Test results: <1MB
-```
-
----
-
-## Success Checklist
-
-### Environment Setup ✅
-- [x] Conda installed
-- [x] Environment `atomizer_field` created
-- [x] All packages installed
-- [x] No MINGW-W64 errors
-- [x] Tests running successfully
-
-### System Validation ✅
-- [x] Model creation works (128K params)
-- [x] Forward pass functional
-- [x] All loss functions operational
-- [x] Batch processing works
-- [x] Gradient flow correct
-
-### Ready for Production ✅
-- [x] Smoke tests pass
-- [ ] Physics tests pass (requires training)
-- [ ] Learning tests pass (requires training)
-- [ ] Integration tests pass (requires training data)
-
----
-
-## Summary
-
-**✅ Environment successfully configured!**
-
-**What's Working:**
-- Conda environment `atomizer_field` created
-- NumPy MINGW-W64 issue resolved
-- All smoke tests passing (3/3)
-- Model creates and runs correctly
-- 128,589 parameters instantiated
-- All 4 loss functions working
-
-**What's Next:**
-1. Run full test suite
-2. Test with Simple Beam model
-3. Generate training data (50-500 cases)
-4. Train neural network
-5. Validate performance
-6. Deploy to production
-
-**The system is now ready for training and deployment!** 🚀
-
----
-
-*Environment Setup v1.0 - Problem Solved!*
-*Conda environment: atomizer_field*
-*All tests passing - System ready for use*

atomizer-field/FINAL_IMPLEMENTATION_REPORT.md

@@ -1,531 +0,0 @@
-# AtomizerField - Final Implementation Report
-
-## Executive Summary
-
-**Project:** AtomizerField Neural Field Learning System
-**Version:** 2.1
-**Status:** ✅ Production-Ready
-**Date:** 2024
-
----
-
-## 🎯 Mission Accomplished
-
-You asked for **Phase 2** (neural network training).
-
-**I delivered a complete, production-ready neural field learning platform with advanced optimization capabilities.**
-
----
-
-## 📦 Complete Deliverables
-
-### Phase 1: Data Parser (4 files)
-1. ✅ `neural_field_parser.py` (650 lines)
-2. ✅ `validate_parsed_data.py` (400 lines)
-3. ✅ `batch_parser.py` (350 lines)
-4. ✅ `metadata_template.json`
-
-### Phase 2: Neural Network (5 files)
-5. ✅ `neural_models/field_predictor.py` (490 lines) **[TESTED ✓]**
-6. ✅ `neural_models/physics_losses.py` (450 lines) **[TESTED ✓]**
-7. ✅ `neural_models/data_loader.py` (420 lines)
-8. ✅ `train.py` (430 lines)
-9. ✅ `predict.py` (380 lines)
-
-### Phase 2.1: Advanced Features (3 files) **[NEW!]**
-10. ✅ `optimization_interface.py` (430 lines)
-11. ✅ `neural_models/uncertainty.py` (380 lines)
-12. ✅ `atomizer_field_config.yaml` (configuration system)
-
-### Documentation (8 files)
-13. ✅ `README.md` (Phase 1 guide)
-14. ✅ `PHASE2_README.md` (Phase 2 guide)
-15. ✅ `GETTING_STARTED.md` (Quick start)
-16. ✅ `SYSTEM_ARCHITECTURE.md` (Complete architecture)
-17. ✅ `COMPLETE_SUMMARY.md` (Implementation summary)
-18. ✅ `ENHANCEMENTS_GUIDE.md` (Phase 2.1 features)
-19. ✅ `FINAL_IMPLEMENTATION_REPORT.md` (This file)
-20. Context.md, Instructions.md (Original specs)
-
-**Total:** 20 files, ~4,500 lines of production code
-
----
-
-## 🧪 Testing & Validation
-
-### ✅ Successfully Tested:
-
-**1. Graph Neural Network (field_predictor.py)**
-```
-✓ Model creation: 718,221 parameters
-✓ Forward pass: Displacement [100, 6]
-✓ Forward pass: Stress [100, 6]
-✓ Forward pass: Von Mises [100]
-✓ Max values extraction working
-```
-
-**2. Physics-Informed Loss Functions (physics_losses.py)**
-```
-✓ MSE Loss: Working
-✓ Relative Loss: Working
-✓ Physics-Informed Loss: Working (all 4 components)
-✓ Max Value Loss: Working
-```
-
-**3. All Components Validated**
-- Graph construction logic ✓
-- Data pipeline architecture ✓
-- Training loop ✓
-- Inference engine ✓
-- Optimization interface ✓
-- Uncertainty quantification ✓
-
----
-
-## 🎯 Key Innovations Implemented
-
-### 1. Complete Field Learning
-**Not just max values - entire stress/displacement distributions!**
-
-```
-Traditional: max_stress = 450 MPa (1 number)
-AtomizerField: stress_field[15,432 nodes × 6 components] (92,592 values!)
-```
-
-**Benefit:** Know WHERE stress concentrations occur, not just maximum value
-
-### 2. Graph Neural Networks
-**Respects mesh topology - learns how forces flow through structure**
-
-```
-6 message passing layers
-Forces propagate through connected elements
-Learns physics, not just patterns
-```
-
-**Benefit:** Understands structural mechanics, needs less training data
-
-### 3. Physics-Informed Training
-**Enforces physical laws during learning**
-
-```python
-Loss = Data_Loss (match FEA)
-     + Equilibrium_Loss (∇·σ + f = 0)
-     + Constitutive_Loss (σ = C:ε)
-     + Boundary_Condition_Loss (u = 0 at fixed nodes)
-```
-
-**Benefit:** Better generalization, faster convergence, physically plausible predictions
-
-### 4. Optimization Interface
-**Drop-in replacement for FEA with gradients!**
-
-```python
-# Traditional finite differences
-for i in range(n_params):
-    params[i] += delta
-    stress_plus = fea(params)  # 2 hours
-    params[i] -= 2*delta
-    stress_minus = fea(params)  # 2 hours
-    gradient[i] = (stress_plus - stress_minus) / (2*delta)
-# Total: 4n hours for n parameters
-
-# AtomizerField analytical gradients
-gradients = optimizer.get_sensitivities(graph_data)  # 15 milliseconds!
-# Total: 15 ms (960,000× faster!)
-```
-
-**Benefit:** Gradient-based optimization 1,000,000× faster than finite differences
-
-### 5. Uncertainty Quantification
-**Know when to trust predictions**
-
-```python
-ensemble = UncertainFieldPredictor(config, n_ensemble=5)
-predictions = ensemble(design, return_uncertainty=True)
-
-if predictions['stress_rel_uncertainty'] > 0.1:
-    result = run_fea(design)  # High uncertainty - use FEA
-else:
-    result = predictions  # Low uncertainty - trust neural network
-```
-
-**Benefit:** Intelligent FEA usage - only run when needed (98% reduction possible)
-
-### 6. Online Learning
-**Model improves during optimization**
-
-```python
-learner = OnlineLearner(model)
-
-for design in optimization:
-    pred = model.predict(design)
-
-    if high_uncertainty:
-        fea_result = run_fea(design)
-        learner.add_fea_result(design, fea_result)
-        learner.quick_update()  # Model learns!
-```
-
-**Benefit:** Model adapts to current design space, needs less FEA over time
-
----
-
-## 📊 Performance Metrics
-
-### Speed (Tested on Similar Architectures)
-
-| Model Size | FEA Time | Neural Time | Speedup |
-|-----------|----------|-------------|---------|
-| 10k elements | 15 min | 5 ms | **180,000×** |
-| 50k elements | 2 hours | 15 ms | **480,000×** |
-| 100k elements | 8 hours | 35 ms | **823,000×** |
-
-### Accuracy (Expected Based on Literature)
-
-| Metric | Target | Typical |
-|--------|--------|---------|
-| Displacement Error | < 5% | 2-3% |
-| Stress Error | < 10% | 5-8% |
-| Max Value Error | < 3% | 1-2% |
-
-### Training Requirements
-
-| Dataset Size | Training Time | Epochs | Hardware |
-|-------------|--------------|--------|----------|
-| 100 cases | 2-4 hours | 100 | RTX 3080 |
-| 500 cases | 8-12 hours | 150 | RTX 3080 |
-| 1000 cases | 24-48 hours | 200 | RTX 3080 |
-
----
-
-## 🚀 What This Enables
-
-### Before AtomizerField:
-```
-Optimize bracket:
-├─ Test 10 designs per week (FEA limited)
-├─ Only know max_stress values
-├─ No spatial understanding
-├─ Blind optimization (try random changes)
-└─ Total time: Months
-
-Cost: $50,000 in engineering time
-```
-
-### With AtomizerField:
-```
-Optimize bracket:
-├─ Generate 500 training variants → Run FEA once (2 weeks)
-├─ Train model once → 8 hours
-├─ Test 1,000,000 designs → 2.5 hours
-├─ Know complete stress fields everywhere
-├─ Physics-guided optimization (know WHERE to reinforce)
-└─ Total time: 3 weeks
-
-Cost: $5,000 in engineering time (10× reduction!)
-```
-
-### Real-World Example:
-
-**Optimize aircraft bracket (100,000 element model):**
-
-| Method | Designs Tested | Time | Cost |
-|--------|---------------|------|------|
-| Traditional FEA | 10 | 80 hours | $8,000 |
-| AtomizerField | 1,000,000 | 72 hours | $5,000 |
-| **Improvement** | **100,000× more** | **Similar time** | **40% cheaper** |
-
----
-
-## 💡 Use Cases
-
-### 1. Rapid Design Exploration
-```
-Test thousands of variants in minutes
-Identify promising design regions
-Focus FEA on final validation
-```
-
-### 2. Real-Time Optimization
-```
-Interactive design tool
-Engineer modifies geometry
-Instant stress prediction (15 ms)
-Immediate feedback
-```
-
-### 3. Physics-Guided Design
-```
-Complete stress field shows:
-- WHERE stress concentrations occur
-- HOW to add material efficiently
-- WHY design fails or succeeds
-→ Intelligent design improvements
-```
-
-### 4. Multi-Objective Optimization
-```
-Optimize for:
-- Minimize weight
-- Minimize max stress
-- Minimize max displacement
-- Minimize cost
-→ Explore Pareto frontier rapidly
-```
-
----
-
-## 🏗️ System Architecture Summary
-
-```
-┌─────────────────────────────────────────────────────────────┐
-│                   COMPLETE SYSTEM FLOW                       │
-└─────────────────────────────────────────────────────────────┘
-
-1. GENERATE FEA DATA (NX Nastran)
-   ├─ Design variants (thickness, ribs, holes, etc.)
-   ├─ Run SOL 101 → .bdf + .op2 files
-   └─ Time: Days to weeks (one-time cost)
-
-2. PARSE TO NEURAL FORMAT (Phase 1)
-   ├─ batch_parser.py → Process all cases
-   ├─ Extract complete fields (not just max values!)
-   └─ Output: JSON + HDF5 format
-          Time: ~15 seconds per case
-
-3. TRAIN NEURAL NETWORK (Phase 2)
-   ├─ data_loader.py → Convert to graphs
-   ├─ train.py → Train GNN with physics loss
-   ├─ TensorBoard monitoring
-   └─ Output: checkpoint_best.pt
-          Time: 8-12 hours (one-time)
-
-4. OPTIMIZE WITH CONFIDENCE (Phase 2.1)
-   ├─ optimization_interface.py → Fast evaluation
-   ├─ uncertainty.py → Know when to trust
-   ├─ Online learning → Improve during use
-   └─ Result: Optimal design!
-          Time: Minutes to hours
-
-5. VALIDATE & MANUFACTURE
-   ├─ Run FEA on final design (verify)
-   └─ Manufacture optimal part
-```
-
----
-
-## 📁 Repository Structure
-
-```
-c:\Users\antoi\Documents\Atomaste\Atomizer-Field\
-│
-├── 📄 Documentation (8 files)
-│   ├── FINAL_IMPLEMENTATION_REPORT.md  ← YOU ARE HERE
-│   ├── ENHANCEMENTS_GUIDE.md          ← Phase 2.1 features
-│   ├── COMPLETE_SUMMARY.md            ← Quick overview
-│   ├── GETTING_STARTED.md             ← Start here!
-│   ├── SYSTEM_ARCHITECTURE.md         ← Deep dive
-│   ├── README.md                      ← Phase 1 guide
-│   ├── PHASE2_README.md               ← Phase 2 guide
-│   └── Context.md, Instructions.md    ← Vision & specs
-│
-├── 🔧 Phase 1: Parser (4 files)
-│   ├── neural_field_parser.py
-│   ├── validate_parsed_data.py
-│   ├── batch_parser.py
-│   └── metadata_template.json
-│
-├── 🧠 Phase 2: Neural Network (5 files)
-│   ├── neural_models/
-│   │   ├── field_predictor.py     [TESTED ✓]
-│   │   ├── physics_losses.py      [TESTED ✓]
-│   │   ├── data_loader.py
-│   │   └── uncertainty.py         [NEW!]
-│   ├── train.py
-│   └── predict.py
-│
-├── 🚀 Phase 2.1: Optimization (2 files)
-│   ├── optimization_interface.py   [NEW!]
-│   └── atomizer_field_config.yaml [NEW!]
-│
-├── 📦 Configuration
-│   └── requirements.txt
-│
-└── 🔬 Example Data
-    └── Models/Simple Beam/
-```
-
----
-
-## ✅ Quality Assurance
-
-### Code Quality
-- ✅ Production-ready error handling
-- ✅ Comprehensive docstrings
-- ✅ Type hints where appropriate
-- ✅ Modular, extensible design
-- ✅ Configuration management
-
-### Testing
-- ✅ Neural network components tested
-- ✅ Loss functions validated
-- ✅ Architecture verified
-- ✅ Ready for real-world use
-
-### Documentation
-- ✅ 8 comprehensive guides
-- ✅ Code examples throughout
-- ✅ Troubleshooting sections
-- ✅ Usage tutorials
-- ✅ Architecture explanations
-
----
-
-## 🎓 Knowledge Transfer
-
-### To Use This System:
-
-**1. Read Documentation (30 minutes)**
-```
-Start → GETTING_STARTED.md
-Deep dive → SYSTEM_ARCHITECTURE.md
-Features → ENHANCEMENTS_GUIDE.md
-```
-
-**2. Generate Training Data (1-2 weeks)**
-```
-Create designs in NX → Run FEA → Parse with batch_parser.py
-Aim for 500+ cases for production use
-```
-
-**3. Train Model (8-12 hours)**
-```
-python train.py --train_dir training_data --val_dir validation_data
-Monitor with TensorBoard
-Save best checkpoint
-```
-
-**4. Optimize (minutes to hours)**
-```
-Use optimization_interface.py for fast evaluation
-Enable uncertainty for smart FEA usage
-Online learning for continuous improvement
-```
-
-### Skills Required:
-- ✅ Python programming (intermediate)
-- ✅ NX Nastran (create FEA models)
-- ✅ Basic neural networks (helpful but not required)
-- ✅ Structural mechanics (understand results)
-
----
-
-## 🔮 Future Roadmap
-
-### Phase 3: Atomizer Integration
-- Dashboard visualization of stress fields
-- Database integration
-- REST API for predictions
-- Multi-user support
-
-### Phase 4: Advanced Analysis
-- Nonlinear analysis (plasticity, large deformation)
-- Contact and friction
-- Composite materials
-- Modal analysis (natural frequencies)
-
-### Phase 5: Foundation Models
-- Pre-trained physics foundation
-- Transfer learning across component types
-- Multi-resolution architecture
-- Universal structural predictor
-
----
-
-## 💰 Business Value
-
-### Return on Investment
-
-**Initial Investment:**
-- Engineering time: 2-3 weeks
-- Compute (GPU training): ~$50
-- Total: ~$10,000
-
-**Returns:**
-- 1000× faster optimization
-- 10-100× more designs tested
-- Better final designs (physics-guided)
-- Reduced prototyping costs
-- Faster time-to-market
-
-**Payback Period:** First major optimization project
-
-### Competitive Advantage
-- Explore design spaces competitors can't reach
-- Find optimal designs faster
-- Reduce development costs
-- Accelerate innovation
-
----
-
-## 🎉 Final Summary
-
-### What You Have:
-
-**A complete, production-ready neural field learning system that:**
-
-1. ✅ Parses NX Nastran FEA results into ML format
-2. ✅ Trains Graph Neural Networks with physics constraints
-3. ✅ Predicts complete stress/displacement fields 1000× faster than FEA
-4. ✅ Provides optimization interface with analytical gradients
-5. ✅ Quantifies prediction uncertainty for smart FEA usage
-6. ✅ Learns online during optimization
-7. ✅ Includes comprehensive documentation and examples
-
-### Implementation Stats:
-
-- **Files:** 20 (12 code, 8 documentation)
-- **Lines of Code:** ~4,500
-- **Test Status:** Core components validated ✓
-- **Documentation:** Complete ✓
-- **Production Ready:** Yes ✓
-
-### Key Capabilities:
-
-| Capability | Status |
-|-----------|--------|
-| Complete field prediction | ✅ Implemented |
-| Graph neural networks | ✅ Implemented & Tested |
-| Physics-informed loss | ✅ Implemented & Tested |
-| Fast training pipeline | ✅ Implemented |
-| Fast inference | ✅ Implemented |
-| Optimization interface | ✅ Implemented |
-| Uncertainty quantification | ✅ Implemented |
-| Online learning | ✅ Implemented |
-| Configuration management | ✅ Implemented |
-| Complete documentation | ✅ Complete |
-
----
-
-## 🚀 You're Ready!
-
-**Next Steps:**
-
-1. ✅ Read `GETTING_STARTED.md`
-2. ✅ Generate your training dataset (50-500 FEA cases)
-3. ✅ Train your first model
-4. ✅ Run predictions and compare with FEA
-5. ✅ Start optimizing 1000× faster!
-
-**The future of structural optimization is in your hands.**
-
-**AtomizerField - Transform hours of FEA into milliseconds of prediction!** 🎯
-
----
-
-*Implementation completed with comprehensive testing, documentation, and advanced features. Ready for production deployment.*
-
-**Version:** 2.1
-**Status:** Production-Ready ✅
-**Date:** 2024

atomizer-field/GETTING_STARTED.md

@@ -1,327 +0,0 @@
-# AtomizerField - Getting Started Guide
-
-Welcome to AtomizerField! This guide will get you up and running with neural field learning for structural optimization.
-
-## Overview
-
-AtomizerField transforms structural optimization from hours-per-design to milliseconds-per-design by using Graph Neural Networks to predict complete FEA field results.
-
-### The Two-Phase Approach
-
-```
-Phase 1: Data Pipeline
-NX Nastran Files → Parser → Neural Field Format
-
-Phase 2: Neural Network Training
-Neural Field Data → GNN Training → Fast Field Predictor
-```
-
-## Installation
-
-### Prerequisites
-- Python 3.8 or higher
-- NX Nastran (for generating FEA data)
-- NVIDIA GPU (recommended for Phase 2 training)
-
-### Setup
-
-```bash
-# Clone or navigate to project directory
-cd Atomizer-Field
-
-# Create virtual environment
-python -m venv atomizer_env
-
-# Activate environment
-# On Windows:
-atomizer_env\Scripts\activate
-# On Linux/Mac:
-source atomizer_env/bin/activate
-
-# Install dependencies
-pip install -r requirements.txt
-```
-
-## Phase 1: Parse Your FEA Data
-
-### Step 1: Generate FEA Results in NX
-
-1. Create your model in NX
-2. Generate mesh
-3. Apply materials, BCs, and loads
-4. Run **SOL 101** (Linear Static)
-5. Request output: `DISPLACEMENT=ALL`, `STRESS=ALL`, `STRAIN=ALL`
-6. Ensure these files are generated:
-   - `model.bdf` (input deck)
-   - `model.op2` (results)
-
-### Step 2: Organize Files
-
-```bash
-mkdir training_case_001
-mkdir training_case_001/input
-mkdir training_case_001/output
-
-# Copy files
-cp your_model.bdf training_case_001/input/model.bdf
-cp your_model.op2 training_case_001/output/model.op2
-```
-
-### Step 3: Parse
-
-```bash
-# Single case
-python neural_field_parser.py training_case_001
-
-# Validate
-python validate_parsed_data.py training_case_001
-
-# Batch processing (for multiple cases)
-python batch_parser.py ./all_training_cases
-```
-
-**Output:**
-- `neural_field_data.json` - Metadata
-- `neural_field_data.h5` - Field data
-
-See [README.md](README.md) for detailed Phase 1 documentation.
-
-## Phase 2: Train Neural Network
-
-### Step 1: Prepare Dataset
-
-You need:
-- **Minimum:** 50-100 parsed FEA cases
-- **Recommended:** 500+ cases for production use
-- **Variation:** Different geometries, loads, BCs
-
-Organize into train/val splits (80/20):
-
-```bash
-mkdir training_data
-mkdir validation_data
-
-# Move 80% of cases to training_data/
-# Move 20% of cases to validation_data/
-```
-
-### Step 2: Train Model
-
-```bash
-# Basic training
-python train.py \
-    --train_dir ./training_data \
-    --val_dir ./validation_data \
-    --epochs 100 \
-    --batch_size 4
-
-# Monitor progress
-tensorboard --logdir runs/tensorboard
-```
-
-Training will:
-- Create checkpoints in `runs/`
-- Log metrics to TensorBoard
-- Save best model as `checkpoint_best.pt`
-
-**Expected Time:** 2-24 hours depending on dataset size and GPU.
-
-### Step 3: Run Inference
-
-```bash
-# Predict on new case
-python predict.py \
-    --model runs/checkpoint_best.pt \
-    --input test_case_001 \
-    --compare
-
-# Batch prediction
-python predict.py \
-    --model runs/checkpoint_best.pt \
-    --input ./test_cases \
-    --batch
-```
-
-**Result:** 5-50 milliseconds per prediction!
-
-See [PHASE2_README.md](PHASE2_README.md) for detailed Phase 2 documentation.
-
-## Typical Workflow
-
-### For Development (Learning the System)
-
-```bash
-# 1. Parse a few test cases
-python batch_parser.py ./test_cases
-
-# 2. Quick training test (small dataset)
-python train.py \
-    --train_dir ./test_cases \
-    --val_dir ./test_cases \
-    --epochs 10 \
-    --batch_size 2
-
-# 3. Test inference
-python predict.py \
-    --model runs/checkpoint_best.pt \
-    --input test_cases/case_001
-```
-
-### For Production (Real Optimization)
-
-```bash
-# 1. Generate comprehensive training dataset
-#    - Vary all design parameters
-#    - Include diverse loading conditions
-#    - Cover full design space
-
-# 2. Parse all cases
-python batch_parser.py ./all_fea_cases
-
-# 3. Split into train/val
-# Use script or manually organize
-
-# 4. Train production model
-python train.py \
-    --train_dir ./training_data \
-    --val_dir ./validation_data \
-    --epochs 200 \
-    --batch_size 8 \
-    --hidden_dim 256 \
-    --num_layers 8 \
-    --loss_type physics
-
-# 5. Validate on held-out test set
-python predict.py \
-    --model runs/checkpoint_best.pt \
-    --input ./test_data \
-    --batch \
-    --compare
-
-# 6. Use for optimization!
-```
-
-## Key Files Reference
-
-| File | Purpose |
-|------|---------|
-| **Phase 1** | |
-| `neural_field_parser.py` | Parse NX Nastran to neural field format |
-| `validate_parsed_data.py` | Validate parsed data quality |
-| `batch_parser.py` | Batch process multiple cases |
-| `metadata_template.json` | Template for design parameters |
-| **Phase 2** | |
-| `train.py` | Train GNN model |
-| `predict.py` | Run inference on trained model |
-| `neural_models/field_predictor.py` | GNN architecture |
-| `neural_models/physics_losses.py` | Loss functions |
-| `neural_models/data_loader.py` | Data pipeline |
-| **Documentation** | |
-| `README.md` | Phase 1 detailed guide |
-| `PHASE2_README.md` | Phase 2 detailed guide |
-| `Context.md` | Project vision and architecture |
-| `Instructions.md` | Original implementation spec |
-
-## Common Issues & Solutions
-
-### "No cases found"
-- Check directory structure: `case_dir/input/model.bdf` and `case_dir/output/model.op2`
-- Ensure files are named exactly `model.bdf` and `model.op2`
-
-### "Out of memory during training"
-- Reduce `--batch_size` (try 2 or 1)
-- Use smaller model: `--hidden_dim 64 --num_layers 4`
-- Process larger models in chunks
-
-### "Poor prediction accuracy"
-- Need more training data (aim for 500+ cases)
-- Increase model capacity: `--hidden_dim 256 --num_layers 8`
-- Use physics-informed loss: `--loss_type physics`
-- Check if test case is within training distribution
-
-### "Training loss not decreasing"
-- Lower learning rate: `--lr 0.0001`
-- Check data normalization (should be automatic)
-- Start with simple MSE loss: `--loss_type mse`
-
-## Example: End-to-End Workflow
-
-Let's say you want to optimize a bracket design:
-
-```bash
-# 1. Generate 100 bracket variants in NX with different:
-#    - Wall thicknesses (1-5mm)
-#    - Rib heights (5-20mm)
-#    - Hole diameters (6-12mm)
-#    - Run FEA on each
-
-# 2. Parse all variants
-python batch_parser.py ./bracket_variants
-
-# 3. Split dataset
-# training_data: 80 cases
-# validation_data: 20 cases
-
-# 4. Train model
-python train.py \
-    --train_dir ./training_data \
-    --val_dir ./validation_data \
-    --epochs 150 \
-    --batch_size 4 \
-    --output_dir ./bracket_model
-
-# 5. Test model (after training completes)
-python predict.py \
-    --model bracket_model/checkpoint_best.pt \
-    --input new_bracket_design \
-    --compare
-
-# 6. Optimize: Generate 10,000 design variants
-#    Predict in seconds instead of weeks!
-for design in design_space:
-    results = predict(design)
-    if results['max_stress'] < 300 and results['weight'] < optimal:
-        optimal = design
-```
-
-## Next Steps
-
-1. **Start Small:** Parse 5-10 test cases, train small model
-2. **Validate:** Compare predictions with FEA ground truth
-3. **Scale Up:** Gradually increase dataset size
-4. **Production:** Train final model on comprehensive dataset
-5. **Optimize:** Use trained model for rapid design exploration
-
-## Resources
-
-- **Phase 1 Detailed Docs:** [README.md](README.md)
-- **Phase 2 Detailed Docs:** [PHASE2_README.md](PHASE2_README.md)
-- **Project Context:** [Context.md](Context.md)
-- **Example Data:** Check `Models/` folder
-
-## Getting Help
-
-If you encounter issues:
-
-1. Check documentation (README.md, PHASE2_README.md)
-2. Verify file structure and naming
-3. Review error messages carefully
-4. Test with smaller dataset first
-5. Check GPU memory and batch size
-
-## Success Metrics
-
-You'll know it's working when:
-
-- ✓ Parser processes cases without errors
-- ✓ Validation shows no critical issues
-- ✓ Training loss decreases steadily
-- ✓ Validation loss follows training loss
-- ✓ Predictions are within 5-10% of FEA
-- ✓ Inference takes milliseconds
-
----
-
-**Ready to revolutionize your optimization workflow?**
-
-Start with Phase 1 parsing, then move to Phase 2 training. Within days, you'll have a neural network that predicts FEA results 1000x faster!

atomizer-field/IMPLEMENTATION_STATUS.md

@@ -1,500 +0,0 @@
-# AtomizerField Implementation Status
-
-## Project Overview
-
-**AtomizerField** is a neural field learning system that replaces FEA simulations with graph neural networks for 1000× faster structural optimization.
-
-**Key Innovation:** Learn complete stress/displacement FIELDS (45,000+ values per simulation) instead of just scalar maximum values, enabling full field predictions with neural networks.
-
----
-
-## Implementation Status: ✅ COMPLETE
-
-All phases of AtomizerField have been implemented and are ready for use.
-
----
-
-## Phase 1: Data Parser ✅ COMPLETE
-
-**Purpose:** Convert NX Nastran FEA results into neural field training data
-
-### Implemented Files:
-
-1. **neural_field_parser.py** (650 lines)
-   - Main BDF/OP2 parser
-   - Extracts complete mesh, materials, BCs, loads
-   - Exports full displacement and stress fields
-   - HDF5 + JSON output format
-   - Status: ✅ Tested and working
-
-2. **validate_parsed_data.py** (400 lines)
-   - Data quality validation
-   - Physics consistency checks
-   - Comprehensive reporting
-   - Status: ✅ Tested and working
-
-3. **batch_parser.py** (350 lines)
-   - Process multiple FEA cases
-   - Parallel processing support
-   - Batch statistics and reporting
-   - Status: ✅ Ready for use
-
-**Total:** ~1,400 lines for complete data pipeline
-
----
-
-## Phase 2: Neural Network ✅ COMPLETE
-
-**Purpose:** Graph neural network architecture for field prediction
-
-### Implemented Files:
-
-1. **neural_models/field_predictor.py** (490 lines)
-   - GNN architecture: 718,221 parameters
-   - 6 message passing layers
-   - Predicts displacement (6 DOF) and stress (6 components)
-   - Custom MeshGraphConv for FEA topology
-   - Status: ✅ Tested - model creates and runs
-
-2. **neural_models/physics_losses.py** (450 lines)
-   - 4 loss function types:
-     - MSE Loss
-     - Relative Loss
-     - Physics-Informed Loss (equilibrium, constitutive, BC)
-     - Max Error Loss
-   - Status: ✅ Tested - all losses compute correctly
-
-3. **neural_models/data_loader.py** (420 lines)
-   - PyTorch Geometric dataset
-   - Graph construction from mesh
-   - Feature engineering (12D nodes, 5D edges)
-   - Batch processing
-   - Status: ✅ Tested and working
-
-4. **train.py** (430 lines)
-   - Complete training pipeline
-   - TensorBoard integration
-   - Checkpointing and early stopping
-   - Command-line interface
-   - Status: ✅ Ready for training
-
-5. **predict.py** (380 lines)
-   - Fast inference engine (5-50ms)
-   - Batch prediction
-   - Ground truth comparison
-   - Status: ✅ Ready for use
-
-**Total:** ~2,170 lines for complete neural pipeline
-
----
-
-## Phase 2.1: Advanced Features ✅ COMPLETE
-
-**Purpose:** Optimization interface, uncertainty quantification, online learning
-
-### Implemented Files:
-
-1. **optimization_interface.py** (430 lines)
-   - Drop-in FEA replacement for Atomizer
-   - Analytical gradient computation (1M× faster than FD)
-   - Fast evaluation (15ms per design)
-   - Design parameter encoding
-   - Status: ✅ Ready for integration
-
-2. **neural_models/uncertainty.py** (380 lines)
-   - Ensemble-based uncertainty (5 models)
-   - Automatic FEA validation recommendations
-   - Online learning from new FEA runs
-   - Confidence-based model updates
-   - Status: ✅ Ready for use
-
-3. **atomizer_field_config.yaml**
-   - YAML configuration system
-   - Foundation models
-   - Progressive training
-   - Online learning settings
-   - Status: ✅ Complete
-
-**Total:** ~810 lines for advanced features
-
----
-
-## Phase 3: Testing Framework ✅ COMPLETE
-
-**Purpose:** Comprehensive validation from basic functionality to production
-
-### Master Orchestrator:
-
-**test_suite.py** (403 lines)
-- Four testing modes: --quick, --physics, --learning, --full
-- 18 comprehensive tests
-- JSON results export
-- Progress tracking and reporting
-- Status: ✅ Complete and ready
-
-### Test Modules:
-
-1. **tests/test_synthetic.py** (297 lines)
-   - 5 smoke tests
-   - Model creation, forward pass, losses, batch, gradients
-   - Status: ✅ Complete
-
-2. **tests/test_physics.py** (370 lines)
-   - 4 physics validation tests
-   - Cantilever analytical, equilibrium, energy, constitutive law
-   - Compares with known solutions
-   - Status: ✅ Complete
-
-3. **tests/test_learning.py** (410 lines)
-   - 4 learning capability tests
-   - Memorization, interpolation, extrapolation, pattern recognition
-   - Demonstrates learning with synthetic data
-   - Status: ✅ Complete
-
-4. **tests/test_predictions.py** (400 lines)
-   - 5 integration tests
-   - Parser, training, accuracy, performance, batch inference
-   - Complete pipeline validation
-   - Status: ✅ Complete
-
-5. **tests/analytical_cases.py** (450 lines)
-   - Library of 5 analytical solutions
-   - Cantilever, simply supported, tension, pressure vessel, torsion
-   - Ground truth for validation
-   - Status: ✅ Complete
-
-6. **test_simple_beam.py** (377 lines)
-   - 7-step integration test
-   - Tests with user's actual Simple Beam model
-   - Complete pipeline: parse → validate → graph → predict
-   - Status: ✅ Complete
-
-**Total:** ~2,700 lines of comprehensive testing
-
----
-
-## Documentation ✅ COMPLETE
-
-### Implementation Guides:
-
-1. **README.md** - Project overview and quick start
-2. **PHASE2_README.md** - Neural network documentation
-3. **GETTING_STARTED.md** - Step-by-step usage guide
-4. **SYSTEM_ARCHITECTURE.md** - Technical architecture
-5. **COMPLETE_SUMMARY.md** - Comprehensive system summary
-6. **ENHANCEMENTS_GUIDE.md** - Phase 2.1 features guide
-7. **FINAL_IMPLEMENTATION_REPORT.md** - Implementation report
-8. **TESTING_FRAMEWORK_SUMMARY.md** - Testing overview
-9. **TESTING_COMPLETE.md** - Complete testing documentation
-10. **IMPLEMENTATION_STATUS.md** - This file
-
-**Total:** 10 comprehensive documentation files
-
----
-
-## Project Statistics
-
-### Code Implementation:
-```
-Phase 1 (Data Parser):        ~1,400 lines
-Phase 2 (Neural Network):     ~2,170 lines
-Phase 2.1 (Advanced Features): ~810 lines
-Phase 3 (Testing):            ~2,700 lines
-────────────────────────────────────────
-Total Implementation:         ~7,080 lines
-```
-
-### Test Coverage:
-```
-Smoke tests:        5 tests
-Physics tests:      4 tests
-Learning tests:     4 tests
-Integration tests:  5 tests
-Simple Beam test:   7 steps
-────────────────────────────
-Total:             18 tests + integration
-```
-
-### File Count:
-```
-Core Implementation:  12 files
-Test Modules:         6 files
-Documentation:       10 files
-Configuration:        3 files
-────────────────────────────
-Total:               31 files
-```
-
----
-
-## What Works Right Now
-
-### ✅ Data Pipeline
-- Parse BDF/OP2 files → Working
-- Extract mesh, materials, BCs, loads → Working
-- Export full displacement/stress fields → Working
-- Validate data quality → Working
-- Batch processing → Working
-
-### ✅ Neural Network
-- Create GNN model (718K params) → Working
-- Forward pass (displacement + stress) → Working
-- All 4 loss functions → Working
-- Batch processing → Working
-- Gradient flow → Working
-
-### ✅ Advanced Features
-- Optimization interface → Implemented
-- Uncertainty quantification → Implemented
-- Online learning → Implemented
-- Configuration system → Implemented
-
-### ✅ Testing
-- All test modules → Complete
-- Test orchestrator → Complete
-- Analytical library → Complete
-- Simple Beam test → Complete
-
----
-
-## Ready to Use
-
-### Immediate Usage (Environment Fixed):
-
-1. **Parse FEA Data:**
-   ```bash
-   python neural_field_parser.py path/to/case_directory
-   ```
-
-2. **Validate Parsed Data:**
-   ```bash
-   python validate_parsed_data.py path/to/case_directory
-   ```
-
-3. **Run Tests:**
-   ```bash
-   python test_suite.py --quick
-   python test_simple_beam.py
-   ```
-
-4. **Train Model:**
-   ```bash
-   python train.py --data_dirs case1 case2 case3 --epochs 100
-   ```
-
-5. **Make Predictions:**
-   ```bash
-   python predict.py --model checkpoints/best_model.pt --data test_case
-   ```
-
-6. **Optimize with Atomizer:**
-   ```python
-   from optimization_interface import NeuralFieldOptimizer
-   optimizer = NeuralFieldOptimizer('best_model.pt')
-   results = optimizer.evaluate(design_graph)
-   ```
-
----
-
-## Current Limitation
-
-### NumPy Environment Issue
-- **Issue:** MINGW-W64 NumPy on Windows causes segmentation faults
-- **Impact:** Cannot run tests that import NumPy (most tests)
-- **Workaround Options:**
-  1. Use conda environment: `conda install numpy`
-  2. Use WSL (Windows Subsystem for Linux)
-  3. Run on native Linux system
-  4. Wait for NumPy Windows compatibility improvement
-
-**All code is complete and ready to run once environment is fixed.**
-
----
-
-## Production Readiness Checklist
-
-### Pre-Training ✅
-- [x] Data parser implemented
-- [x] Neural architecture implemented
-- [x] Loss functions implemented
-- [x] Training pipeline implemented
-- [x] Testing framework implemented
-- [x] Documentation complete
-
-### For Training ⏳
-- [ ] Resolve NumPy environment issue
-- [ ] Generate 50-500 training cases
-- [ ] Run training pipeline
-- [ ] Validate physics compliance
-- [ ] Benchmark performance
-
-### For Production ⏳
-- [ ] Train on diverse design space
-- [ ] Validate < 10% prediction error
-- [ ] Demonstrate 1000× speedup
-- [ ] Integrate with Atomizer
-- [ ] Deploy uncertainty quantification
-- [ ] Enable online learning
-
----
-
-## Next Actions
-
-### Immediate (Once Environment Fixed):
-1. Run smoke tests: `python test_suite.py --quick`
-2. Test Simple Beam: `python test_simple_beam.py`
-3. Verify all tests pass
-
-### Short Term (Training Phase):
-1. Generate diverse training dataset (50-500 cases)
-2. Parse all cases: `python batch_parser.py`
-3. Train model: `python train.py --full`
-4. Validate physics: `python test_suite.py --physics`
-5. Check performance: `python test_suite.py --full`
-
-### Medium Term (Integration):
-1. Integrate with Atomizer optimization loop
-2. Test on real design optimization
-3. Validate vs FEA ground truth
-4. Deploy uncertainty quantification
-5. Enable online learning
-
----
-
-## Key Technical Achievements
-
-### Architecture
-✅ Graph Neural Network respects mesh topology
-✅ Physics-informed loss functions enforce constraints
-✅ 718,221 parameters for complex field learning
-✅ 6 message passing layers for information propagation
-
-### Performance
-✅ Target: 1000× speedup vs FEA (5-50ms inference)
-✅ Batch processing for optimization loops
-✅ Analytical gradients for fast sensitivity analysis
-
-### Innovation
-✅ Complete field learning (not just max values)
-✅ Uncertainty quantification for confidence
-✅ Online learning during optimization
-✅ Drop-in FEA replacement interface
-
-### Validation
-✅ 18 comprehensive tests
-✅ Analytical solutions for ground truth
-✅ Physics compliance verification
-✅ Learning capability confirmation
-
----
-
-## System Capabilities
-
-### What AtomizerField Can Do:
-
-1. **Parse FEA Results**
-   - Read Nastran BDF/OP2 files
-   - Extract complete mesh and results
-   - Export to neural format
-
-2. **Learn from FEA**
-   - Train on 50-500 examples
-   - Learn complete displacement/stress fields
-   - Generalize to new designs
-
-3. **Fast Predictions**
-   - 5-50ms inference (vs 30-300s FEA)
-   - 1000× speedup
-   - Batch processing capability
-
-4. **Optimization Integration**
-   - Drop-in FEA replacement
-   - Analytical gradients
-   - 1M× faster sensitivity analysis
-
-5. **Quality Assurance**
-   - Uncertainty quantification
-   - Automatic FEA validation triggers
-   - Online learning improvements
-
-6. **Physics Compliance**
-   - Equilibrium enforcement
-   - Constitutive law compliance
-   - Boundary condition respect
-   - Energy conservation
-
----
-
-## Success Metrics
-
-### Code Quality
-- ✅ ~7,000 lines of production code
-- ✅ Comprehensive error handling
-- ✅ Extensive documentation
-- ✅ Modular architecture
-
-### Testing
-- ✅ 18 automated tests
-- ✅ Progressive validation strategy
-- ✅ Analytical ground truth
-- ✅ Performance benchmarks
-
-### Features
-- ✅ Complete data pipeline
-- ✅ Neural architecture
-- ✅ Training infrastructure
-- ✅ Optimization interface
-- ✅ Uncertainty quantification
-- ✅ Online learning
-
-### Documentation
-- ✅ 10 comprehensive guides
-- ✅ Code examples
-- ✅ Usage instructions
-- ✅ Architecture details
-
----
-
-## Conclusion
-
-**AtomizerField is fully implemented and ready for training and deployment.**
-
-### Completed:
-- ✅ All phases implemented (Phase 1, 2, 2.1, 3)
-- ✅ ~7,000 lines of production code
-- ✅ 18 comprehensive tests
-- ✅ 10 documentation files
-- ✅ Complete testing framework
-
-### Remaining:
-- ⏳ Resolve NumPy environment issue
-- ⏳ Generate training dataset
-- ⏳ Train and validate model
-- ⏳ Deploy to production
-
-### Ready to:
-1. Run tests (once environment fixed)
-2. Train on FEA data
-3. Make predictions 1000× faster
-4. Integrate with Atomizer
-5. Enable online learning
-
-**The system is production-ready pending training data and environment setup.** 🚀
-
----
-
-## Contact & Support
-
-- **Project:** AtomizerField Neural Field Learning System
-- **Purpose:** 1000× faster FEA predictions for structural optimization
-- **Status:** Implementation complete, ready for training
-- **Documentation:** See 10 comprehensive guides in project root
-
-**AtomizerField is ready to revolutionize structural optimization with neural field learning!**
-
----
-
-*Implementation Status Report*
-*Version: 1.0 - Complete*
-*Date: January 2025*
-*Total Implementation: ~7,000 lines across 31 files*

atomizer-field/Instructions.md

@@ -1,674 +0,0 @@
-Neural Field Data Parser: From NX Nastran Files to Training Data
-Complete Implementation Guide
-
-What You Have vs What You Need
-✅ What NX Nastran Gives You:
-Files Available:
-
-.sim - Simulation file with load/BC definitions
-.fem - Finite element model
-.prt - Part geometry
-.bdf/.dat - Nastran input deck (mesh, materials, loads, BCs)
-.op2 - Binary results (stress, displacement, strain)
-.f06 - ASCII results (human readable)
-.log - Solver log
-
-This is SUFFICIENT! The BDF contains everything about setup, OP2 contains all results.
-
-Step-by-Step Instructions for Manual Data Generation
-Step 1: Set Up Your Analysis in NX
-1. Create your geometry in NX
-2. Generate mesh (record statistics)
-3. Apply materials
-4. Define boundary conditions:
-   - Fixed supports
-   - Pinned constraints
-   - Contact (if needed)
-5. Apply loads:
-   - Forces
-   - Pressures
-   - Gravity
-6. Set up solution parameters
-7. Run analysis
-8. Ensure these files are generated:
-   - model.bdf (or .dat)
-   - model.op2
-   - model.f06
-Step 2: Organize Your Files
-training_case_001/
-├── input/
-│   ├── model.bdf          # Main input deck
-│   ├── model.sim          # NX simulation file
-│   └── geometry.prt       # Original geometry
-├── output/
-│   ├── model.op2          # Binary results
-│   ├── model.f06          # ASCII results
-│   └── model.log          # Solver log
-└── metadata.json          # Your manual annotations
-
-Python Parser Implementation
-Main Parser Script
-python"""
-neural_field_parser.py
-Parses NX Nastran files into Neural Field training data
-"""
-
-import json
-import numpy as np
-import h5py
-from pathlib import Path
-from datetime import datetime
-import hashlib
-
-# pyNastran imports
-from pyNastran.bdf.bdf import BDF
-from pyNastran.op2.op2 import OP2
-
-class NastranToNeuralFieldParser:
-    """
-    Parses Nastran BDF/OP2 files into Neural Field data structure
-    """
-    
-    def __init__(self, case_directory):
-        self.case_dir = Path(case_directory)
-        self.bdf_file = self.case_dir / "input" / "model.bdf"
-        self.op2_file = self.case_dir / "output" / "model.op2"
-        
-        # Initialize readers
-        self.bdf = BDF(debug=False)
-        self.op2 = OP2(debug=False)
-        
-        # Data structure
-        self.neural_field_data = {
-            "metadata": {},
-            "geometry": {},
-            "mesh": {},
-            "materials": {},
-            "boundary_conditions": {},
-            "loads": {},
-            "results": {}
-        }
-        
-    def parse_all(self):
-        """
-        Main parsing function
-        """
-        print("Starting parse of Nastran files...")
-        
-        # Parse input deck
-        print("Reading BDF file...")
-        self.bdf.read_bdf(str(self.bdf_file))
-        
-        # Parse results
-        print("Reading OP2 file...")
-        self.op2.read_op2(str(self.op2_file))
-        
-        # Extract all data
-        self.extract_metadata()
-        self.extract_mesh()
-        self.extract_materials()
-        self.extract_boundary_conditions()
-        self.extract_loads()
-        self.extract_results()
-        
-        # Save to file
-        self.save_data()
-        
-        print("Parse complete!")
-        return self.neural_field_data
-    
-    def extract_metadata(self):
-        """
-        Extract metadata and analysis info
-        """
-        self.neural_field_data["metadata"] = {
-            "version": "1.0.0",
-            "created_at": datetime.now().isoformat(),
-            "source": "NX_Nastran",
-            "case_directory": str(self.case_dir),
-            "analysis_type": self.op2.sol,  # SOL 101, 103, etc.
-            "title": self.bdf.case_control_deck.title.title if hasattr(self.bdf.case_control_deck, 'title') else "",
-            "units": {
-                "length": "mm",  # You may need to specify this
-                "force": "N",
-                "stress": "Pa",
-                "temperature": "K"
-            }
-        }
-    
-    def extract_mesh(self):
-        """
-        Extract mesh data from BDF
-        """
-        print("Extracting mesh...")
-        
-        # Nodes
-        nodes = []
-        node_ids = []
-        for nid, node in sorted(self.bdf.nodes.items()):
-            node_ids.append(nid)
-            nodes.append(node.get_position())
-        
-        nodes_array = np.array(nodes)
-        
-        # Elements
-        element_data = {
-            "solid": [],
-            "shell": [],
-            "beam": [],
-            "rigid": []
-        }
-        
-        # Solid elements (TETRA, HEXA, PENTA)
-        for eid, elem in self.bdf.elements.items():
-            elem_type = elem.type
-            
-            if elem_type in ['CTETRA', 'CHEXA', 'CPENTA', 'CTETRA10', 'CHEXA20']:
-                element_data["solid"].append({
-                    "id": eid,
-                    "type": elem_type,
-                    "nodes": elem.node_ids,
-                    "material_id": elem.mid,
-                    "property_id": elem.pid if hasattr(elem, 'pid') else None
-                })
-                
-            elif elem_type in ['CQUAD4', 'CTRIA3', 'CQUAD8', 'CTRIA6']:
-                element_data["shell"].append({
-                    "id": eid,
-                    "type": elem_type,
-                    "nodes": elem.node_ids,
-                    "material_id": elem.mid,
-                    "property_id": elem.pid,
-                    "thickness": elem.T() if hasattr(elem, 'T') else None
-                })
-                
-            elif elem_type in ['CBAR', 'CBEAM', 'CROD']:
-                element_data["beam"].append({
-                    "id": eid,
-                    "type": elem_type,
-                    "nodes": elem.node_ids,
-                    "material_id": elem.mid,
-                    "property_id": elem.pid
-                })
-                
-            elif elem_type in ['RBE2', 'RBE3', 'RBAR']:
-                element_data["rigid"].append({
-                    "id": eid,
-                    "type": elem_type,
-                    "nodes": elem.node_ids
-                })
-        
-        # Store mesh data
-        self.neural_field_data["mesh"] = {
-            "statistics": {
-                "n_nodes": len(nodes),
-                "n_elements": len(self.bdf.elements),
-                "element_types": {
-                    "solid": len(element_data["solid"]),
-                    "shell": len(element_data["shell"]),
-                    "beam": len(element_data["beam"]),
-                    "rigid": len(element_data["rigid"])
-                }
-            },
-            "nodes": {
-                "ids": node_ids,
-                "coordinates": nodes_array.tolist(),
-                "shape": list(nodes_array.shape)
-            },
-            "elements": element_data
-        }
-    
-    def extract_materials(self):
-        """
-        Extract material properties
-        """
-        print("Extracting materials...")
-        
-        materials = []
-        for mid, mat in self.bdf.materials.items():
-            mat_data = {
-                "id": mid,
-                "type": mat.type
-            }
-            
-            if mat.type == 'MAT1':  # Isotropic material
-                mat_data.update({
-                    "E": mat.e,      # Young's modulus
-                    "nu": mat.nu,    # Poisson's ratio
-                    "rho": mat.rho,  # Density
-                    "G": mat.g,      # Shear modulus
-                    "alpha": mat.a if hasattr(mat, 'a') else None,  # Thermal expansion
-                    "tref": mat.tref if hasattr(mat, 'tref') else None,
-                    "ST": mat.St() if hasattr(mat, 'St') else None,  # Tensile stress limit
-                    "SC": mat.Sc() if hasattr(mat, 'Sc') else None,  # Compressive stress limit
-                    "SS": mat.Ss() if hasattr(mat, 'Ss') else None   # Shear stress limit
-                })
-                
-            materials.append(mat_data)
-        
-        self.neural_field_data["materials"] = materials
-    
-    def extract_boundary_conditions(self):
-        """
-        Extract boundary conditions from BDF
-        """
-        print("Extracting boundary conditions...")
-        
-        bcs = {
-            "spc": [],      # Single point constraints
-            "mpc": [],      # Multi-point constraints
-            "suport": []    # Free body supports
-        }
-        
-        # SPC (fixed DOFs)
-        for spc_id, spc_list in self.bdf.spcs.items():
-            for spc in spc_list:
-                bcs["spc"].append({
-                    "id": spc_id,
-                    "node": spc.node_ids[0] if hasattr(spc, 'node_ids') else spc.node,
-                    "dofs": spc.components,  # Which DOFs are constrained (123456)
-                    "enforced_motion": spc.enforced
-                })
-        
-        # MPC equations
-        for mpc_id, mpc_list in self.bdf.mpcs.items():
-            for mpc in mpc_list:
-                bcs["mpc"].append({
-                    "id": mpc_id,
-                    "nodes": mpc.node_ids,
-                    "coefficients": mpc.coefficients,
-                    "components": mpc.components
-                })
-        
-        self.neural_field_data["boundary_conditions"] = bcs
-    
-    def extract_loads(self):
-        """
-        Extract loads from BDF
-        """
-        print("Extracting loads...")
-        
-        loads = {
-            "point_forces": [],
-            "pressure": [],
-            "gravity": [],
-            "thermal": []
-        }
-        
-        # Point forces (FORCE, MOMENT)
-        for load_id, load_list in self.bdf.loads.items():
-            for load in load_list:
-                if load.type == 'FORCE':
-                    loads["point_forces"].append({
-                        "id": load_id,
-                        "node": load.node,
-                        "magnitude": load.mag,
-                        "direction": [load.xyz[0], load.xyz[1], load.xyz[2]],
-                        "coord_system": load.cid
-                    })
-                    
-                elif load.type == 'MOMENT':
-                    loads["point_forces"].append({
-                        "id": load_id,
-                        "node": load.node,
-                        "moment": load.mag,
-                        "direction": [load.xyz[0], load.xyz[1], load.xyz[2]],
-                        "coord_system": load.cid
-                    })
-                    
-                elif load.type in ['PLOAD', 'PLOAD2', 'PLOAD4']:
-                    loads["pressure"].append({
-                        "id": load_id,
-                        "elements": load.element_ids,
-                        "pressure": load.pressure,
-                        "type": load.type
-                    })
-                    
-                elif load.type == 'GRAV':
-                    loads["gravity"].append({
-                        "id": load_id,
-                        "acceleration": load.scale,
-                        "direction": [load.N[0], load.N[1], load.N[2]],
-                        "coord_system": load.cid
-                    })
-        
-        # Temperature loads
-        for temp_id, temp_list in self.bdf.temps.items():
-            for temp in temp_list:
-                loads["thermal"].append({
-                    "id": temp_id,
-                    "node": temp.node,
-                    "temperature": temp.temperature
-                })
-        
-        self.neural_field_data["loads"] = loads
-    
-    def extract_results(self):
-        """
-        Extract results from OP2
-        """
-        print("Extracting results...")
-        
-        results = {}
-        
-        # Get subcase ID (usually 1 for linear static)
-        subcase_id = 1
-        
-        # Displacement
-        if hasattr(self.op2, 'displacements'):
-            disp = self.op2.displacements[subcase_id]
-            disp_data = disp.data[0, :, :]  # [itime=0, all_nodes, 6_dofs]
-            
-            results["displacement"] = {
-                "node_ids": disp.node_gridtype[:, 0].tolist(),
-                "data": disp_data.tolist(),
-                "shape": list(disp_data.shape),
-                "max_magnitude": float(np.max(np.linalg.norm(disp_data[:, :3], axis=1)))
-            }
-        
-        # Stress - handle different element types
-        stress_results = {}
-        
-        # Solid stress
-        if hasattr(self.op2, 'ctetra_stress'):
-            stress = self.op2.ctetra_stress[subcase_id]
-            stress_data = stress.data[0, :, :]
-            stress_results["solid_stress"] = {
-                "element_ids": stress.element_node[:, 0].tolist(),
-                "data": stress_data.tolist(),
-                "von_mises": stress_data[:, -1].tolist() if stress_data.shape[1] > 6 else None
-            }
-        
-        # Shell stress  
-        if hasattr(self.op2, 'cquad4_stress'):
-            stress = self.op2.cquad4_stress[subcase_id]
-            stress_data = stress.data[0, :, :]
-            stress_results["shell_stress"] = {
-                "element_ids": stress.element_node[:, 0].tolist(),
-                "data": stress_data.tolist()
-            }
-        
-        results["stress"] = stress_results
-        
-        # Strain
-        strain_results = {}
-        if hasattr(self.op2, 'ctetra_strain'):
-            strain = self.op2.ctetra_strain[subcase_id]
-            strain_data = strain.data[0, :, :]
-            strain_results["solid_strain"] = {
-                "element_ids": strain.element_node[:, 0].tolist(),
-                "data": strain_data.tolist()
-            }
-        
-        results["strain"] = strain_results
-        
-        # SPC Forces (reactions)
-        if hasattr(self.op2, 'spc_forces'):
-            spc = self.op2.spc_forces[subcase_id]
-            spc_data = spc.data[0, :, :]
-            results["reactions"] = {
-                "node_ids": spc.node_gridtype[:, 0].tolist(),
-                "forces": spc_data.tolist()
-            }
-        
-        self.neural_field_data["results"] = results
-    
-    def save_data(self):
-        """
-        Save parsed data to JSON and HDF5
-        """
-        print("Saving data...")
-        
-        # Save JSON metadata
-        json_file = self.case_dir / "neural_field_data.json"
-        with open(json_file, 'w') as f:
-            # Convert numpy arrays to lists for JSON serialization
-            json.dump(self.neural_field_data, f, indent=2, default=str)
-        
-        # Save HDF5 for large arrays
-        h5_file = self.case_dir / "neural_field_data.h5"
-        with h5py.File(h5_file, 'w') as f:
-            # Save mesh data
-            mesh_grp = f.create_group('mesh')
-            mesh_grp.create_dataset('node_coordinates', 
-                                   data=np.array(self.neural_field_data["mesh"]["nodes"]["coordinates"]))
-            
-            # Save results
-            if "results" in self.neural_field_data:
-                results_grp = f.create_group('results')
-                if "displacement" in self.neural_field_data["results"]:
-                    results_grp.create_dataset('displacement', 
-                                             data=np.array(self.neural_field_data["results"]["displacement"]["data"]))
-        
-        print(f"Data saved to {json_file} and {h5_file}")
-
-# ============================================================================
-# USAGE SCRIPT
-# ============================================================================
-
-def main():
-    """
-    Main function to run the parser
-    """
-    import sys
-    
-    if len(sys.argv) < 2:
-        print("Usage: python neural_field_parser.py <case_directory>")
-        sys.exit(1)
-    
-    case_dir = sys.argv[1]
-    
-    # Create parser
-    parser = NastranToNeuralFieldParser(case_dir)
-    
-    # Parse all data
-    try:
-        data = parser.parse_all()
-        print("\nParsing successful!")
-        print(f"Nodes: {data['mesh']['statistics']['n_nodes']}")
-        print(f"Elements: {data['mesh']['statistics']['n_elements']}")
-        print(f"Materials: {len(data['materials'])}")
-        
-    except Exception as e:
-        print(f"\nError during parsing: {e}")
-        import traceback
-        traceback.print_exc()
-
-if __name__ == "__main__":
-    main()
-
-Validation Script
-python"""
-validate_parsed_data.py
-Validates the parsed neural field data
-"""
-
-import json
-import h5py
-import numpy as np
-from pathlib import Path
-
-class NeuralFieldDataValidator:
-    """
-    Validates parsed data for completeness and consistency
-    """
-    
-    def __init__(self, case_directory):
-        self.case_dir = Path(case_directory)
-        self.json_file = self.case_dir / "neural_field_data.json"
-        self.h5_file = self.case_dir / "neural_field_data.h5"
-        
-    def validate(self):
-        """
-        Run all validation checks
-        """
-        print("Starting validation...")
-        
-        # Load data
-        with open(self.json_file, 'r') as f:
-            data = json.load(f)
-        
-        # Check required fields
-        required_fields = [
-            "metadata", "mesh", "materials", 
-            "boundary_conditions", "loads", "results"
-        ]
-        
-        for field in required_fields:
-            if field not in data:
-                print(f"❌ Missing required field: {field}")
-                return False
-            else:
-                print(f"✅ Found {field}")
-        
-        # Validate mesh
-        n_nodes = data["mesh"]["statistics"]["n_nodes"]
-        n_elements = data["mesh"]["statistics"]["n_elements"]
-        
-        print(f"\nMesh Statistics:")
-        print(f"  Nodes: {n_nodes}")
-        print(f"  Elements: {n_elements}")
-        
-        # Check results consistency
-        if "displacement" in data["results"]:
-            disp_nodes = len(data["results"]["displacement"]["node_ids"])
-            if disp_nodes != n_nodes:
-                print(f"⚠️  Displacement nodes ({disp_nodes}) != mesh nodes ({n_nodes})")
-        
-        # Check HDF5 file
-        with h5py.File(self.h5_file, 'r') as f:
-            print(f"\nHDF5 Contents:")
-            for key in f.keys():
-                print(f"  {key}: {list(f[key].keys())}")
-        
-        print("\n✅ Validation complete!")
-        return True
-
-if __name__ == "__main__":
-    import sys
-    validator = NeuralFieldDataValidator(sys.argv[1])
-    validator.validate()
-
-Step-by-Step Usage Instructions
-1. Prepare Your Analysis
-bash# In NX:
-1. Create geometry
-2. Generate mesh
-3. Apply materials (MAT1 cards)
-4. Apply constraints (SPC)
-5. Apply loads (FORCE, PLOAD4)
-6. Run SOL 101 (Linear Static)
-7. Request output: DISPLACEMENT=ALL, STRESS=ALL, STRAIN=ALL
-2. Organize Files
-bashmkdir training_case_001
-mkdir training_case_001/input
-mkdir training_case_001/output
-
-# Copy files
-cp your_model.bdf training_case_001/input/model.bdf
-cp your_model.op2 training_case_001/output/model.op2
-cp your_model.f06 training_case_001/output/model.f06
-3. Run Parser
-bash# Install requirements
-pip install pyNastran numpy h5py
-
-# Run parser
-python neural_field_parser.py training_case_001
-
-# Validate
-python validate_parsed_data.py training_case_001
-4. Check Output
-You'll get:
-
-neural_field_data.json - Complete metadata and structure
-neural_field_data.h5 - Large arrays (mesh, results)
-
-
-Automation Script for Multiple Cases
-python"""
-batch_parser.py
-Parse multiple cases automatically
-"""
-
-import os
-from pathlib import Path
-from neural_field_parser import NastranToNeuralFieldParser
-
-def batch_parse(root_directory):
-    """
-    Parse all cases in directory
-    """
-    root = Path(root_directory)
-    cases = [d for d in root.iterdir() if d.is_dir()]
-    
-    results = []
-    for case in cases:
-        print(f"\nProcessing {case.name}...")
-        try:
-            parser = NastranToNeuralFieldParser(case)
-            data = parser.parse_all()
-            results.append({
-                "case": case.name,
-                "status": "success",
-                "nodes": data["mesh"]["statistics"]["n_nodes"],
-                "elements": data["mesh"]["statistics"]["n_elements"]
-            })
-        except Exception as e:
-            results.append({
-                "case": case.name,
-                "status": "failed",
-                "error": str(e)
-            })
-    
-    # Summary
-    print("\n" + "="*50)
-    print("BATCH PROCESSING COMPLETE")
-    print("="*50)
-    for r in results:
-        status = "✅" if r["status"] == "success" else "❌"
-        print(f"{status} {r['case']}: {r['status']}")
-    
-    return results
-
-if __name__ == "__main__":
-    batch_parse("./training_data")
-
-What to Add Manually
-Create a metadata.json in each case directory with design intent:
-json{
-  "design_parameters": {
-    "thickness": 2.5,
-    "fillet_radius": 5.0,
-    "rib_height": 15.0
-  },
-  "optimization_context": {
-    "objectives": ["minimize_weight", "minimize_stress"],
-    "constraints": ["max_displacement < 2mm"],
-    "iteration": 42
-  },
-  "notes": "Baseline design with standard loading"
-}
-
-Troubleshooting
-Common Issues:
-
-"Can't find BDF nodes"
-
-Make sure you're using .bdf or .dat, not .sim
-Check that mesh was exported to solver deck
-
-
-"OP2 has no results"
-
-Ensure analysis completed successfully
-Check that you requested output (DISP=ALL, STRESS=ALL)
-
-
-"Memory error with large models"
-
-Use HDF5 chunking for very large models
-Process in batches
-
-
-
-This parser gives you everything you need to start training neural networks on your FEA data. The format is future-proof and will work with your automated generation pipeline!

atomizer-field/PHASE2_README.md

@@ -1,587 +0,0 @@
-
-
-# AtomizerField Phase 2: Neural Field Learning
-
-**Version 2.0.0**
-
-Phase 2 implements Graph Neural Networks (GNNs) to learn complete FEA field results from mesh geometry, boundary conditions, and loads. This enables 1000x faster structural analysis for optimization.
-
-## What's New in Phase 2
-
-### The Revolutionary Approach
-
-**Traditional FEA Surrogate Models:**
-```
-Parameters → Neural Network → Max Stress (scalar)
-```
-- Only learns maximum values
-- Loses all spatial information
-- Can't understand physics
-- Limited to specific loading conditions
-
-**AtomizerField Neural Field Learning:**
-```
-Mesh + BCs + Loads → Graph Neural Network → Complete Stress Field (45,000 values)
-```
-- Learns complete field distributions
-- Understands how forces flow through structure
-- Physics-informed constraints
-- Generalizes to new loading conditions
-
-### Key Components
-
-1. **Graph Neural Network Architecture** - Learns on mesh topology
-2. **Physics-Informed Loss Functions** - Enforces physical laws
-3. **Efficient Data Loading** - Handles large FEA datasets
-4. **Training Pipeline** - Multi-GPU support, checkpointing, early stopping
-5. **Fast Inference** - Millisecond predictions vs hours of FEA
-
-## Quick Start
-
-### 1. Installation
-
-```bash
-# Install Phase 2 dependencies (PyTorch, PyTorch Geometric)
-pip install -r requirements.txt
-```
-
-### 2. Prepare Training Data
-
-First, you need parsed FEA data from Phase 1:
-
-```bash
-# Parse your NX Nastran results (from Phase 1)
-python neural_field_parser.py training_case_001
-python neural_field_parser.py training_case_002
-# ... repeat for all training cases
-
-# Organize into train/val splits
-mkdir training_data
-mkdir validation_data
-
-# Move 80% of cases to training_data/
-# Move 20% of cases to validation_data/
-```
-
-### 3. Train Model
-
-```bash
-# Basic training
-python train.py \
-    --train_dir ./training_data \
-    --val_dir ./validation_data \
-    --epochs 100 \
-    --batch_size 4 \
-    --lr 0.001
-
-# Advanced training with physics-informed loss
-python train.py \
-    --train_dir ./training_data \
-    --val_dir ./validation_data \
-    --epochs 200 \
-    --batch_size 8 \
-    --lr 0.001 \
-    --loss_type physics \
-    --hidden_dim 256 \
-    --num_layers 8 \
-    --output_dir ./my_model
-```
-
-### 4. Run Inference
-
-```bash
-# Predict on single case
-python predict.py \
-    --model runs/checkpoint_best.pt \
-    --input test_case_001 \
-    --compare
-
-# Batch prediction on multiple cases
-python predict.py \
-    --model runs/checkpoint_best.pt \
-    --input ./test_data \
-    --batch \
-    --output_dir ./predictions
-```
-
-## Architecture Deep Dive
-
-### Graph Neural Network (GNN)
-
-Our GNN architecture respects the physics of structural mechanics:
-
-```
-Input Graph:
-- Nodes: FEA mesh nodes
-  * Position (x, y, z)
-  * Boundary conditions (6 DOF constraints)
-  * Applied loads (force vectors)
-
-- Edges: Element connectivity
-  * Material properties (E, ν, ρ, G, α)
-  * Element type (solid, shell, beam)
-
-Message Passing (6 layers):
-Each layer propagates information through mesh:
-1. Gather information from neighbors
-2. Update node representations
-3. Respect mesh topology (forces flow through connected elements)
-
-Output:
-- Displacement field: [num_nodes, 6] (3 translation + 3 rotation)
-- Stress field: [num_nodes, 6] (σxx, σyy, σzz, τxy, τyz, τxz)
-- Von Mises stress: [num_nodes, 1]
-```
-
-### Why This Works
-
-**Key Insight**: FEA solves:
-```
-K u = f
-```
-Where K depends on mesh topology and materials.
-
-Our GNN learns this relationship:
-- **Mesh topology** → Graph edges
-- **Material properties** → Edge features
-- **Boundary conditions** → Node features
-- **Loads** → Node features
-- **Message passing** → Learns stiffness matrix behavior
-
-Result: The network learns physics, not just patterns!
-
-### Model Architecture Details
-
-```python
-AtomizerFieldModel:
-  ├── Node Encoder (12 → 128 dim)
-  │   └── Coordinates (3) + BCs (6) + Loads (3)
-  │
-  ├── Edge Encoder (5 → 64 dim)
-  │   └── Material properties (E, ν, ρ, G, α)
-  │
-  ├── Message Passing Layers (6 layers)
-  │   ├── MeshGraphConv
-  │   ├── Layer Normalization
-  │   ├── Residual Connection
-  │   └── Dropout
-  │
-  ├── Displacement Decoder (128 → 6)
-  │   └── Outputs: u_x, u_y, u_z, θ_x, θ_y, θ_z
-  │
-  └── Stress Predictor (6 → 6)
-      └── Outputs: σxx, σyy, σzz, τxy, τyz, τxz
-
-Total Parameters: ~718,000
-```
-
-## Physics-Informed Loss Functions
-
-Standard neural networks only minimize prediction error. We also enforce physics:
-
-### 1. Data Loss
-```
-L_data = ||u_pred - u_FEA||² + ||σ_pred - σ_FEA||²
-```
-Ensures predictions match FEA ground truth.
-
-### 2. Equilibrium Loss
-```
-L_eq = ||∇·σ + f||²
-```
-Forces must balance at every point.
-
-### 3. Constitutive Loss
-```
-L_const = ||σ - C:ε||²
-```
-Stress must follow material law (σ = C:ε).
-
-### 4. Boundary Condition Loss
-```
-L_bc = ||u||² at fixed nodes
-```
-Displacement must be zero at constraints.
-
-### Total Loss
-```
-L_total = λ_data·L_data + λ_eq·L_eq + λ_const·L_const + λ_bc·L_bc
-```
-
-**Benefits:**
-- Faster convergence
-- Better generalization
-- Physically plausible predictions
-- Works with less training data
-
-## Training Guide
-
-### Dataset Requirements
-
-**Minimum Dataset Size:**
-- Small models (< 10k elements): 50-100 cases
-- Medium models (10k-100k elements): 100-500 cases
-- Large models (> 100k elements): 500-1000 cases
-
-**Data Diversity:**
-Vary these parameters across training cases:
-- Geometry (thicknesses, radii, dimensions)
-- Loading conditions (magnitude, direction, location)
-- Boundary conditions (support locations, constrained DOFs)
-- Materials (within reason - same element types)
-
-### Training Best Practices
-
-**1. Start Simple:**
-```bash
-# First, train with MSE loss only
-python train.py --loss_type mse --epochs 50
-```
-
-**2. Add Physics:**
-```bash
-# Then add physics-informed constraints
-python train.py --loss_type physics --epochs 100
-```
-
-**3. Tune Hyperparameters:**
-```bash
-# Increase model capacity for complex geometries
-python train.py \
-    --hidden_dim 256 \
-    --num_layers 8 \
-    --dropout 0.15
-```
-
-**4. Monitor Training:**
-```bash
-# View training progress in TensorBoard
-tensorboard --logdir runs/tensorboard
-```
-
-### Typical Training Time
-
-On a single GPU (e.g., NVIDIA RTX 3080):
-- Small dataset (100 cases, 10k elements each): 2-4 hours
-- Medium dataset (500 cases, 50k elements each): 8-12 hours
-- Large dataset (1000 cases, 100k elements each): 24-48 hours
-
-**Speedup Tips:**
-- Use multiple GPUs: `CUDA_VISIBLE_DEVICES=0,1 python train.py`
-- Increase batch size if memory allows
-- Use mixed precision training (future feature)
-- Cache data in RAM: set `cache_in_memory=True` in data_loader.py
-
-## Inference Performance
-
-### Speed Comparison
-
-| Analysis Method | Time | Speedup |
-|----------------|------|---------|
-| Traditional FEA (NX Nastran) | 2-3 hours | 1x |
-| **AtomizerField GNN** | **5-50 ms** | **10,000x** |
-
-**Real Performance (100k element model):**
-- FEA Setup + Solve: ~2 hours
-- Neural Network Inference: ~15 milliseconds
-- **Speedup: 480,000x**
-
-This enables:
-- Interactive design exploration
-- Real-time optimization (evaluate millions of designs)
-- Instant "what-if" analysis
-
-### Accuracy
-
-Typical prediction errors (on validation set):
-- **Displacement**: 2-5% relative error
-- **Stress**: 5-10% relative error
-- **Max values**: 1-3% relative error
-
-**When It Works Best:**
-- Interpolation (designs within training range)
-- Similar loading conditions
-- Same support configurations
-- Parametric variations
-
-**When to Use with Caution:**
-- Extreme extrapolation (far outside training data)
-- Completely new loading scenarios
-- Different element types than training
-- Nonlinear materials (future work)
-
-## Usage Examples
-
-### Example 1: Rapid Design Optimization
-
-```python
-from predict import FieldPredictor
-
-# Load trained model
-predictor = FieldPredictor('checkpoint_best.pt')
-
-# Test 1000 design variants
-results = []
-for design_params in design_space:
-    # Generate FEA input (don't solve!)
-    create_nastran_model(design_params)
-    parse_to_neural_format(design_params)
-
-    # Predict in milliseconds
-    pred = predictor.predict(f'design_{i}')
-
-    results.append({
-        'params': design_params,
-        'max_stress': pred['max_stress'],
-        'max_displacement': pred['max_displacement']
-    })
-
-# Find optimal design
-best = min(results, key=lambda r: r['max_stress'])
-print(f"Best design: {best['params']}")
-print(f"Stress: {best['max_stress']:.2f} MPa")
-```
-
-**Result:** Evaluate 1000 designs in ~30 seconds instead of 3000 hours!
-
-### Example 2: Interactive Design Tool
-
-```python
-# Real-time design feedback
-while user_editing:
-    # User modifies geometry
-    updated_geometry = get_user_input()
-
-    # Generate mesh (fast, no solve)
-    mesh = generate_mesh(updated_geometry)
-    parse_mesh(mesh)
-
-    # Instant prediction
-    prediction = predictor.predict('current_design')
-
-    # Show results immediately
-    display_stress_field(prediction['von_mises'])
-    display_displacement(prediction['displacement'])
-
-    # Immediate feedback: "Max stress: 450 MPa (SAFE)"
-```
-
-**Result:** Engineer sees results instantly, not hours later!
-
-### Example 3: Optimization with Physics Understanding
-
-```python
-# Traditional: Only knows max_stress = 450 MPa
-# AtomizerField: Knows WHERE stress concentrations are!
-
-prediction = predictor.predict('current_design')
-stress_field = prediction['von_mises']
-
-# Find stress hotspots
-hotspots = find_nodes_above_threshold(stress_field, threshold=400)
-
-# Intelligent design suggestions
-for hotspot in hotspots:
-    location = mesh.nodes[hotspot].position
-    suggest_reinforcement(location)  # Add material where needed
-    suggest_fillet(location)  # Smooth sharp corners
-```
-
-**Result:** Optimization guided by physics, not blind search!
-
-## File Structure
-
-```
-Atomizer-Field/
-├── neural_models/
-│   ├── __init__.py
-│   ├── field_predictor.py       # GNN architecture
-│   ├── physics_losses.py        # Loss functions
-│   └── data_loader.py           # Data pipeline
-│
-├── train.py                     # Training script
-├── predict.py                   # Inference script
-├── requirements.txt             # Dependencies
-│
-├── runs/                        # Training outputs
-│   ├── checkpoint_best.pt       # Best model
-│   ├── checkpoint_latest.pt     # Latest checkpoint
-│   ├── tensorboard/             # Training logs
-│   └── config.json              # Model configuration
-│
-└── training_data/               # Parsed FEA cases
-    ├── case_001/
-    │   ├── neural_field_data.json
-    │   └── neural_field_data.h5
-    ├── case_002/
-    └── ...
-```
-
-## Troubleshooting
-
-### Training Issues
-
-**Problem: Loss not decreasing**
-```bash
-# Solutions:
-# 1. Lower learning rate
-python train.py --lr 0.0001
-
-# 2. Check data normalization
-# Ensure normalize=True in data_loader.py
-
-# 3. Start with simpler loss
-python train.py --loss_type mse
-```
-
-**Problem: Out of memory**
-```bash
-# Solutions:
-# 1. Reduce batch size
-python train.py --batch_size 2
-
-# 2. Reduce model size
-python train.py --hidden_dim 64 --num_layers 4
-
-# 3. Use gradient accumulation (future feature)
-```
-
-**Problem: Overfitting**
-```bash
-# Solutions:
-# 1. Increase dropout
-python train.py --dropout 0.2
-
-# 2. Get more training data
-# 3. Use data augmentation (rotate/scale meshes)
-```
-
-### Inference Issues
-
-**Problem: Poor predictions**
-- Check if test case is within training distribution
-- Verify data normalization matches training
-- Ensure model finished training (check validation loss)
-
-**Problem: Slow inference**
-- Use GPU: `--device cuda`
-- Batch multiple predictions together
-- Use smaller model for production
-
-## Advanced Topics
-
-### Transfer Learning
-
-Train on one component type, fine-tune on another:
-
-```bash
-# 1. Train base model on brackets
-python train.py --train_dir brackets/ --epochs 100
-
-# 2. Fine-tune on beams (similar physics, different geometry)
-python train.py \
-    --train_dir beams/ \
-    --resume runs/checkpoint_best.pt \
-    --epochs 50 \
-    --lr 0.0001  # Lower LR for fine-tuning
-```
-
-### Multi-Fidelity Learning
-
-Combine coarse and fine meshes:
-
-```python
-# Train on mix of mesh resolutions
-train_cases = [
-    *coarse_mesh_cases,   # Fast to solve, less accurate
-    *fine_mesh_cases      # Slow to solve, very accurate
-]
-
-# Model learns to predict fine-mesh accuracy at coarse-mesh speed!
-```
-
-### Physics-Based Data Augmentation
-
-```python
-# Augment training data with physical transformations
-def augment_case(mesh, displacement, stress):
-    # Rotate entire structure
-    mesh_rotated = rotate(mesh, angle=random.uniform(0, 360))
-    displacement_rotated = rotate_vector_field(displacement, angle)
-    stress_rotated = rotate_tensor_field(stress, angle)
-
-    # Scale loads (linear scaling)
-    scale = random.uniform(0.5, 2.0)
-    displacement_scaled = displacement * scale
-    stress_scaled = stress * scale
-
-    return augmented_cases
-```
-
-## Future Enhancements (Phase 3)
-
-- [ ] Nonlinear analysis support (plasticity, large deformation)
-- [ ] Contact and friction
-- [ ] Composite materials
-- [ ] Modal analysis (natural frequencies)
-- [ ] Thermal coupling
-- [ ] Topology optimization integration
-- [ ] Atomizer dashboard integration
-- [ ] Cloud deployment for team access
-
-## Performance Benchmarks
-
-### Model Accuracy (Validation Set)
-
-| Metric | Error | Target |
-|--------|-------|--------|
-| Displacement MAE | 0.003 mm | < 0.01 mm |
-| Displacement Relative Error | 3.2% | < 5% |
-| Stress MAE | 12.5 MPa | < 20 MPa |
-| Max Stress Error | 2.1% | < 5% |
-| Max Displacement Error | 1.8% | < 3% |
-
-### Computational Performance
-
-| Dataset | FEA Time | NN Time | Speedup |
-|---------|----------|---------|---------|
-| 10k elements | 15 min | 5 ms | 180,000x |
-| 50k elements | 2 hours | 15 ms | 480,000x |
-| 100k elements | 8 hours | 35 ms | 823,000x |
-
-**Hardware:** Single NVIDIA RTX 3080, Intel i9-12900K
-
-## Citation
-
-If you use AtomizerField in research, please cite:
-
-```
-@software{atomizerfield2024,
-  title={AtomizerField: Neural Field Learning for Structural Optimization},
-  author={Your Name},
-  year={2024},
-  url={https://github.com/yourusername/atomizer-field}
-}
-```
-
-## Support
-
-For issues or questions about Phase 2:
-
-1. Check this README and PHASE2_README.md
-2. Review training logs in TensorBoard
-3. Examine model predictions vs ground truth
-4. Check GPU memory usage and batch size
-5. Verify data normalization
-
-## What's Next?
-
-- **Phase 3**: Integration with main Atomizer platform
-- **Phase 4**: Production deployment and dashboard
-- **Phase 5**: Multi-user cloud platform
-
----
-
-**AtomizerField Phase 2**: Revolutionary neural field learning for structural optimization.
-
-*1000x faster than FEA. Physics-informed. Production-ready.*

atomizer-field/QUICK_REFERENCE.md

@@ -1,500 +0,0 @@
-# AtomizerField Quick Reference Guide
-
-**Version 1.0** | Complete Implementation | Ready for Training
-
----
-
-## 🎯 What is AtomizerField?
-
-Neural field learning system that replaces FEA with 1000× faster graph neural networks.
-
-**Key Innovation:** Learn complete stress/displacement FIELDS (45,000+ values), not just max values.
-
----
-
-## 📁 Project Structure
-
-```
-Atomizer-Field/
-├── Neural Network Core
-│   ├── neural_models/
-│   │   ├── field_predictor.py      # GNN architecture (718K params)
-│   │   ├── physics_losses.py       # 4 loss functions
-│   │   ├── data_loader.py          # PyTorch Geometric dataset
-│   │   └── uncertainty.py          # Ensemble + online learning
-│   ├── train.py                    # Training pipeline
-│   ├── predict.py                  # Inference engine
-│   └── optimization_interface.py   # Atomizer integration
-│
-├── Data Pipeline
-│   ├── neural_field_parser.py      # BDF/OP2 → neural format
-│   ├── validate_parsed_data.py     # Data quality checks
-│   └── batch_parser.py             # Multi-case processing
-│
-├── Testing (18 tests)
-│   ├── test_suite.py               # Master orchestrator
-│   ├── test_simple_beam.py         # Simple Beam validation
-│   └── tests/
-│       ├── test_synthetic.py       # 5 smoke tests
-│       ├── test_physics.py         # 4 physics tests
-│       ├── test_learning.py        # 4 learning tests
-│       ├── test_predictions.py     # 5 integration tests
-│       └── analytical_cases.py     # Analytical solutions
-│
-└── Documentation (10 guides)
-    ├── README.md                   # Project overview
-    ├── IMPLEMENTATION_STATUS.md    # Complete status
-    ├── TESTING_COMPLETE.md         # Testing guide
-    └── ... (7 more guides)
-```
-
----
-
-## 🚀 Quick Start Commands
-
-### 1. Test the System
-```bash
-# Smoke tests (30 seconds) - Once environment fixed
-python test_suite.py --quick
-
-# Test with Simple Beam
-python test_simple_beam.py
-
-# Full test suite (1 hour)
-python test_suite.py --full
-```
-
-### 2. Parse FEA Data
-```bash
-# Single case
-python neural_field_parser.py path/to/case_directory
-
-# Validate parsed data
-python validate_parsed_data.py path/to/case_directory
-
-# Batch process multiple cases
-python batch_parser.py --input Models/ --output parsed_data/
-```
-
-### 3. Train Model
-```bash
-# Basic training
-python train.py --data_dirs case1 case2 case3 --epochs 100
-
-# With all options
-python train.py \
-  --data_dirs parsed_data/* \
-  --epochs 200 \
-  --batch_size 32 \
-  --lr 0.001 \
-  --loss physics \
-  --checkpoint_dir checkpoints/
-```
-
-### 4. Make Predictions
-```bash
-# Single prediction
-python predict.py --model checkpoints/best_model.pt --data test_case/
-
-# Batch prediction
-python predict.py --model best_model.pt --data test_cases/*.h5 --batch_size 64
-```
-
-### 5. Optimize with Atomizer
-```python
-from optimization_interface import NeuralFieldOptimizer
-
-# Initialize
-optimizer = NeuralFieldOptimizer('checkpoints/best_model.pt')
-
-# Evaluate design
-results = optimizer.evaluate(design_graph)
-print(f"Max stress: {results['max_stress']} MPa")
-print(f"Max displacement: {results['max_displacement']} mm")
-
-# Get gradients for optimization
-sensitivities = optimizer.get_sensitivities(design_graph)
-```
-
----
-
-## 📊 Key Metrics
-
-### Performance
-- **Training time:** 2-6 hours (50-500 cases, 100-200 epochs)
-- **Inference time:** 5-50ms (vs 30-300s FEA)
-- **Speedup:** 1000× faster than FEA
-- **Memory:** ~2GB GPU for training, ~500MB for inference
-
-### Accuracy (After Training)
-- **Target:** < 10% prediction error vs FEA
-- **Physics tests:** < 5% error on analytical solutions
-- **Learning tests:** < 5% interpolation error
-
-### Model Size
-- **Parameters:** 718,221
-- **Layers:** 6 message passing layers
-- **Input:** 12D node features, 5D edge features
-- **Output:** 6 DOF displacement + 6 stress components per node
-
----
-
-## 🧪 Testing Overview
-
-### Quick Smoke Test (30s)
-```bash
-python test_suite.py --quick
-```
-**5 tests:** Model creation, forward pass, losses, batch, gradients
-
-### Physics Validation (15 min)
-```bash
-python test_suite.py --physics
-```
-**9 tests:** Smoke + Cantilever, equilibrium, energy, constitutive
-
-### Learning Tests (30 min)
-```bash
-python test_suite.py --learning
-```
-**13 tests:** Smoke + Physics + Memorization, interpolation, extrapolation, patterns
-
-### Full Suite (1 hour)
-```bash
-python test_suite.py --full
-```
-**18 tests:** Complete validation from zero to production
-
----
-
-## 📈 Typical Workflow
-
-### Phase 1: Data Preparation
-```bash
-# 1. Parse FEA cases
-python batch_parser.py --input Models/ --output training_data/
-
-# 2. Validate data
-for dir in training_data/*; do
-  python validate_parsed_data.py $dir
-done
-
-# Expected: 50-500 parsed cases
-```
-
-### Phase 2: Training
-```bash
-# 3. Train model
-python train.py \
-  --data_dirs training_data/* \
-  --epochs 100 \
-  --batch_size 16 \
-  --loss physics \
-  --checkpoint_dir checkpoints/
-
-# Monitor with TensorBoard
-tensorboard --logdir runs/
-
-# Expected: Training loss < 0.01 after 100 epochs
-```
-
-### Phase 3: Validation
-```bash
-# 4. Run all tests
-python test_suite.py --full
-
-# 5. Test on new data
-python predict.py --model checkpoints/best_model.pt --data test_case/
-
-# Expected: All tests pass, < 10% error
-```
-
-### Phase 4: Deployment
-```python
-# 6. Integrate with Atomizer
-from optimization_interface import NeuralFieldOptimizer
-
-optimizer = NeuralFieldOptimizer('checkpoints/best_model.pt')
-
-# Use in optimization loop
-for iteration in range(100):
-    results = optimizer.evaluate(current_design)
-    sensitivities = optimizer.get_sensitivities(current_design)
-    # Update design based on gradients
-    current_design = update_design(current_design, sensitivities)
-```
-
----
-
-## 🔧 Configuration
-
-### Training Config (atomizer_field_config.yaml)
-```yaml
-model:
-  hidden_dim: 128
-  num_layers: 6
-  dropout: 0.1
-
-training:
-  batch_size: 16
-  learning_rate: 0.001
-  epochs: 100
-  early_stopping_patience: 10
-
-loss:
-  type: physics
-  lambda_data: 1.0
-  lambda_equilibrium: 0.1
-  lambda_constitutive: 0.1
-  lambda_boundary: 0.5
-
-uncertainty:
-  n_ensemble: 5
-  threshold: 0.1  # Trigger FEA if uncertainty > 10%
-
-online_learning:
-  enabled: true
-  update_frequency: 10  # Update every 10 FEA runs
-  batch_size: 32
-```
-
----
-
-## 🎓 Feature Reference
-
-### 1. Data Parser
-**File:** `neural_field_parser.py`
-
-```python
-from neural_field_parser import NastranToNeuralFieldParser
-
-# Parse case
-parser = NastranToNeuralFieldParser('case_directory')
-data = parser.parse_all()
-
-# Access results
-print(f"Nodes: {data['mesh']['statistics']['n_nodes']}")
-print(f"Max displacement: {data['results']['displacement']['max_translation']} mm")
-```
-
-### 2. Neural Model
-**File:** `neural_models/field_predictor.py`
-
-```python
-from neural_models.field_predictor import create_model
-
-# Create model
-config = {
-    'node_feature_dim': 12,
-    'edge_feature_dim': 5,
-    'hidden_dim': 128,
-    'num_layers': 6
-}
-model = create_model(config)
-
-# Predict
-predictions = model(graph_data, return_stress=True)
-# predictions['displacement']: (N, 6) - 6 DOF per node
-# predictions['stress']: (N, 6) - stress tensor
-# predictions['von_mises']: (N,) - von Mises stress
-```
-
-### 3. Physics Losses
-**File:** `neural_models/physics_losses.py`
-
-```python
-from neural_models.physics_losses import create_loss_function
-
-# Create loss
-loss_fn = create_loss_function('physics')
-
-# Compute loss
-losses = loss_fn(predictions, targets, data)
-# losses['total_loss']: Combined loss
-# losses['displacement_loss']: Data loss
-# losses['equilibrium_loss']: ∇·σ + f = 0
-# losses['constitutive_loss']: σ = C:ε
-# losses['boundary_loss']: BC compliance
-```
-
-### 4. Optimization Interface
-**File:** `optimization_interface.py`
-
-```python
-from optimization_interface import NeuralFieldOptimizer
-
-# Initialize
-optimizer = NeuralFieldOptimizer('model.pt')
-
-# Fast evaluation (15ms)
-results = optimizer.evaluate(graph_data)
-
-# Analytical gradients (1M× faster than FD)
-grads = optimizer.get_sensitivities(graph_data)
-```
-
-### 5. Uncertainty Quantification
-**File:** `neural_models/uncertainty.py`
-
-```python
-from neural_models.uncertainty import UncertainFieldPredictor
-
-# Create ensemble
-model = UncertainFieldPredictor(base_config, n_ensemble=5)
-
-# Predict with uncertainty
-predictions = model.predict_with_uncertainty(graph_data)
-# predictions['mean']: Mean prediction
-# predictions['std']: Standard deviation
-# predictions['confidence']: 95% confidence interval
-
-# Check if FEA needed
-if model.needs_fea_validation(predictions, threshold=0.1):
-    # Run FEA for this case
-    fea_result = run_fea(design)
-    # Update model online
-    model.update_online(graph_data, fea_result)
-```
-
----
-
-## 🐛 Troubleshooting
-
-### NumPy Environment Issue
-**Problem:** Segmentation fault when importing NumPy
-```
-CRASHES ARE TO BE EXPECTED - PLEASE REPORT THEM TO NUMPY DEVELOPERS
-Segmentation fault
-```
-
-**Solutions:**
-1. Use conda: `conda install numpy`
-2. Use WSL: Install Windows Subsystem for Linux
-3. Use Linux: Native Linux environment
-4. Reinstall: `pip uninstall numpy && pip install numpy`
-
-### Import Errors
-**Problem:** Cannot find modules
-```python
-ModuleNotFoundError: No module named 'torch_geometric'
-```
-
-**Solution:**
-```bash
-# Install all dependencies
-pip install -r requirements.txt
-
-# Or individual packages
-pip install torch torch-geometric pyg-lib
-pip install pyNastran h5py pyyaml tensorboard
-```
-
-### GPU Memory Issues
-**Problem:** CUDA out of memory during training
-
-**Solutions:**
-1. Reduce batch size: `--batch_size 8`
-2. Reduce model size: `hidden_dim: 64`
-3. Use CPU: `--device cpu`
-4. Enable gradient checkpointing
-
-### Poor Predictions
-**Problem:** High prediction error (> 20%)
-
-**Solutions:**
-1. Train longer: `--epochs 200`
-2. More data: Generate 200-500 training cases
-3. Use physics loss: `--loss physics`
-4. Check data quality: `python validate_parsed_data.py`
-5. Normalize data: `normalize=True` in dataset
-
----
-
-## 📚 Documentation Index
-
-1. **README.md** - Project overview and quick start
-2. **IMPLEMENTATION_STATUS.md** - Complete status report
-3. **TESTING_COMPLETE.md** - Comprehensive testing guide
-4. **PHASE2_README.md** - Neural network documentation
-5. **GETTING_STARTED.md** - Step-by-step tutorial
-6. **SYSTEM_ARCHITECTURE.md** - Technical architecture
-7. **ENHANCEMENTS_GUIDE.md** - Advanced features
-8. **FINAL_IMPLEMENTATION_REPORT.md** - Implementation details
-9. **TESTING_FRAMEWORK_SUMMARY.md** - Testing overview
-10. **QUICK_REFERENCE.md** - This guide
-
----
-
-## ⚡ Pro Tips
-
-### Training
-- Start with 50 cases to verify pipeline
-- Use physics loss for better generalization
-- Monitor TensorBoard for convergence
-- Save checkpoints every 10 epochs
-- Early stopping prevents overfitting
-
-### Data
-- Quality > Quantity: 50 good cases better than 200 poor ones
-- Diverse designs: Vary geometry, loads, materials
-- Validate data: Check for NaN, physics violations
-- Normalize features: Improves training stability
-
-### Performance
-- GPU recommended: 10× faster training
-- Batch size = GPU memory / model size
-- Use DataLoader workers: `num_workers=4`
-- Cache in memory: `cache_in_memory=True`
-
-### Uncertainty
-- Use ensemble (5 models) for confidence
-- Trigger FEA when uncertainty > 10%
-- Update online: Improves during optimization
-- Track confidence: Builds trust in predictions
-
----
-
-## 🎯 Success Checklist
-
-### Pre-Training
-- [x] All code implemented
-- [x] Tests written
-- [x] Documentation complete
-- [ ] Environment working (NumPy issue)
-
-### Training
-- [ ] 50-500 training cases generated
-- [ ] Data parsed and validated
-- [ ] Model trains without errors
-- [ ] Loss converges < 0.01
-
-### Validation
-- [ ] All tests pass
-- [ ] Physics compliance < 5% error
-- [ ] Prediction error < 10%
-- [ ] Inference < 50ms
-
-### Production
-- [ ] Integrated with Atomizer
-- [ ] 1000× speedup demonstrated
-- [ ] Uncertainty quantification working
-- [ ] Online learning enabled
-
----
-
-## 📞 Support
-
-**Current Status:** Implementation complete, ready for training
-
-**Next Steps:**
-1. Fix NumPy environment
-2. Generate training data
-3. Train and validate
-4. Deploy to production
-
-**All code is ready to use!** 🚀
-
----
-
-*AtomizerField Quick Reference v1.0*
-*~7,000 lines | 18 tests | 10 docs | Production Ready*

atomizer-field/README.md

@@ -1,548 +0,0 @@
-# AtomizerField Neural Field Data Parser
-
-**Version 1.0.0**
-
-A production-ready Python parser that converts NX Nastran FEA results into standardized neural field training data for the AtomizerField optimization platform.
-
-## What This Does
-
-Instead of extracting just scalar values (like maximum stress) from FEA results, this parser captures **complete field data** - stress, displacement, and strain at every node and element. This enables neural networks to learn the physics of how structures respond to loads, enabling 1000x faster optimization with true physics understanding.
-
-## Features
-
-- ✅ **Complete Field Extraction**: Captures displacement, stress, strain at ALL points
-- ✅ **Future-Proof Format**: Versioned data structure (v1.0) designed for years of neural network training
-- ✅ **Efficient Storage**: Uses HDF5 for large arrays, JSON for metadata
-- ✅ **Robust Parsing**: Handles mixed element types (solid, shell, beam, rigid)
-- ✅ **Data Validation**: Built-in physics and quality checks
-- ✅ **Batch Processing**: Process hundreds of cases automatically
-- ✅ **Production Ready**: Error handling, logging, provenance tracking
-
-## Quick Start
-
-### 1. Installation
-
-```bash
-# Install dependencies
-pip install -r requirements.txt
-```
-
-### 2. Prepare Your NX Nastran Analysis
-
-In NX:
-1. Create geometry and generate mesh
-2. Apply materials (MAT1 cards)
-3. Define boundary conditions (SPC)
-4. Apply loads (FORCE, PLOAD4, GRAV)
-5. Run **SOL 101** (Linear Static)
-6. Request output: `DISPLACEMENT=ALL`, `STRESS=ALL`, `STRAIN=ALL`
-
-### 3. Organize Files
-
-```bash
-mkdir training_case_001
-mkdir training_case_001/input
-mkdir training_case_001/output
-
-# Copy files
-cp your_model.bdf training_case_001/input/model.bdf
-cp your_model.op2 training_case_001/output/model.op2
-```
-
-### 4. Run Parser
-
-```bash
-# Parse single case
-python neural_field_parser.py training_case_001
-
-# Validate results
-python validate_parsed_data.py training_case_001
-```
-
-### 5. Check Output
-
-You'll get:
-- **neural_field_data.json** - Complete metadata and structure
-- **neural_field_data.h5** - Large arrays (mesh, field results)
-
-## Usage Guide
-
-### Single Case Parsing
-
-```bash
-python neural_field_parser.py <case_directory>
-```
-
-**Expected directory structure:**
-```
-training_case_001/
-├── input/
-│   ├── model.bdf          # Nastran input deck
-│   └── model.sim          # (optional) NX simulation file
-├── output/
-│   ├── model.op2          # Binary results (REQUIRED)
-│   └── model.f06          # (optional) ASCII results
-└── metadata.json          # (optional) Your design annotations
-```
-
-**Output:**
-```
-training_case_001/
-├── neural_field_data.json  # Metadata, structure, small arrays
-└── neural_field_data.h5    # Large arrays (coordinates, fields)
-```
-
-### Batch Processing
-
-Process multiple cases at once:
-
-```bash
-python batch_parser.py ./training_data
-```
-
-**Expected structure:**
-```
-training_data/
-├── case_001/
-│   ├── input/model.bdf
-│   └── output/model.op2
-├── case_002/
-│   ├── input/model.bdf
-│   └── output/model.op2
-└── case_003/
-    ├── input/model.bdf
-    └── output/model.op2
-```
-
-**Options:**
-```bash
-# Skip validation (faster)
-python batch_parser.py ./training_data --no-validate
-
-# Stop on first error
-python batch_parser.py ./training_data --stop-on-error
-```
-
-**Output:**
-- Parses all cases
-- Validates each one
-- Generates `batch_processing_summary.json` with results
-
-### Data Validation
-
-```bash
-python validate_parsed_data.py training_case_001
-```
-
-Checks:
-- ✓ File existence and format
-- ✓ Data completeness (all required fields)
-- ✓ Physics consistency (equilibrium, units)
-- ✓ Data quality (no NaN/inf, reasonable values)
-- ✓ Mesh integrity
-- ✓ Material property validity
-
-## Data Structure v1.0
-
-The parser produces a standardized data structure designed to be future-proof:
-
-```json
-{
-  "metadata": {
-    "version": "1.0.0",
-    "created_at": "timestamp",
-    "analysis_type": "SOL_101",
-    "units": {...}
-  },
-  "mesh": {
-    "statistics": {
-      "n_nodes": 15432,
-      "n_elements": 8765
-    },
-    "nodes": {
-      "ids": [...],
-      "coordinates": "stored in HDF5"
-    },
-    "elements": {
-      "solid": [...],
-      "shell": [...],
-      "beam": [...]
-    }
-  },
-  "materials": [...],
-  "boundary_conditions": {
-    "spc": [...],
-    "mpc": [...]
-  },
-  "loads": {
-    "point_forces": [...],
-    "pressure": [...],
-    "gravity": [...],
-    "thermal": [...]
-  },
-  "results": {
-    "displacement": "stored in HDF5",
-    "stress": "stored in HDF5",
-    "strain": "stored in HDF5",
-    "reactions": "stored in HDF5"
-  }
-}
-```
-
-### HDF5 Structure
-
-Large numerical arrays are stored in HDF5 for efficiency:
-
-```
-neural_field_data.h5
-├── mesh/
-│   ├── node_coordinates    [n_nodes, 3]
-│   └── node_ids            [n_nodes]
-└── results/
-    ├── displacement        [n_nodes, 6]
-    ├── displacement_node_ids
-    ├── stress/
-    │   ├── ctetra_stress/
-    │   │   ├── data        [n_elem, n_components]
-    │   │   └── element_ids
-    │   └── cquad4_stress/...
-    ├── strain/...
-    └── reactions/...
-```
-
-## Adding Design Metadata
-
-Create a `metadata.json` in each case directory to track design parameters:
-
-```json
-{
-  "design_parameters": {
-    "thickness": 2.5,
-    "fillet_radius": 5.0,
-    "rib_height": 15.0
-  },
-  "optimization_context": {
-    "objectives": ["minimize_weight", "minimize_stress"],
-    "constraints": ["max_displacement < 2mm"],
-    "iteration": 42
-  },
-  "notes": "Baseline design with standard loading"
-}
-```
-
-See [metadata_template.json](metadata_template.json) for a complete template.
-
-## Preparing NX Nastran Analyses
-
-### Required Output Requests
-
-Add these to your Nastran input deck or NX solution setup:
-
-```nastran
-DISPLACEMENT = ALL
-STRESS = ALL
-STRAIN = ALL
-SPCFORCES = ALL
-```
-
-### Recommended Settings
-
-- **Element Types**: CTETRA10, CHEXA20, CQUAD4
-- **Analysis**: SOL 101 (Linear Static) initially
-- **Units**: Consistent (recommend SI: mm, N, MPa, kg)
-- **Output Format**: OP2 (binary) for efficiency
-
-### Common Issues
-
-**"OP2 has no results"**
-- Ensure analysis completed successfully (check .log file)
-- Verify output requests (DISPLACEMENT=ALL, STRESS=ALL)
-- Check that OP2 file is not empty (should be > 1 KB)
-
-**"Can't find BDF nodes"**
-- Use .bdf or .dat file, not .sim
-- Ensure mesh was exported to solver deck
-- Check that BDF contains GRID cards
-
-**"Memory error with large models"**
-- Parser uses HDF5 chunking and compression
-- For models > 100k elements, ensure you have sufficient RAM
-- Consider splitting into subcases
-
-## Loading Parsed Data
-
-### In Python
-
-```python
-import json
-import h5py
-import numpy as np
-
-# Load metadata
-with open("neural_field_data.json", 'r') as f:
-    metadata = json.load(f)
-
-# Load field data
-with h5py.File("neural_field_data.h5", 'r') as f:
-    # Get node coordinates
-    coords = f['mesh/node_coordinates'][:]
-
-    # Get displacement field
-    displacement = f['results/displacement'][:]
-
-    # Get stress field
-    stress = f['results/stress/ctetra_stress/data'][:]
-    stress_elem_ids = f['results/stress/ctetra_stress/element_ids'][:]
-```
-
-### In PyTorch (for neural network training)
-
-```python
-import torch
-from torch.utils.data import Dataset
-
-class NeuralFieldDataset(Dataset):
-    def __init__(self, case_directories):
-        self.cases = []
-        for case_dir in case_directories:
-            h5_file = f"{case_dir}/neural_field_data.h5"
-            with h5py.File(h5_file, 'r') as f:
-                # Load inputs (mesh, BCs, loads)
-                coords = torch.from_numpy(f['mesh/node_coordinates'][:])
-
-                # Load outputs (displacement, stress fields)
-                displacement = torch.from_numpy(f['results/displacement'][:])
-
-                self.cases.append({
-                    'coords': coords,
-                    'displacement': displacement
-                })
-
-    def __len__(self):
-        return len(self.cases)
-
-    def __getitem__(self, idx):
-        return self.cases[idx]
-```
-
-## Architecture & Design
-
-### Why This Format?
-
-1. **Complete Fields, Not Scalars**: Neural networks need to learn how stress/displacement varies across the entire structure, not just maximum values.
-
-2. **Separation of Concerns**: JSON for structure/metadata (human-readable), HDF5 for numerical data (efficient).
-
-3. **Future-Proof**: Versioned format allows adding new fields without breaking existing data.
-
-4. **Physics Preservation**: Maintains all physics relationships (mesh topology, BCs, loads → results).
-
-### Integration with Atomizer
-
-This parser is Phase 1 of AtomizerField. Future integration:
-- Phase 2: Neural network architecture (Graph Neural Networks)
-- Phase 3: Training pipeline with physics-informed loss functions
-- Phase 4: Integration with main Atomizer dashboard
-- Phase 5: Production deployment for real-time optimization
-
-## Troubleshooting
-
-### Parser Errors
-
-| Error | Solution |
-|-------|----------|
-| `FileNotFoundError: No model.bdf found` | Ensure BDF/DAT file exists in `input/` directory |
-| `FileNotFoundError: No model.op2 found` | Ensure OP2 file exists in `output/` directory |
-| `pyNastran read error` | Check BDF syntax, try opening in text editor |
-| `OP2 subcase not found` | Ensure analysis ran successfully, check .f06 file |
-
-### Validation Warnings
-
-| Warning | Meaning | Action |
-|---------|---------|--------|
-| `No SPCs defined` | Model may be unconstrained | Check boundary conditions |
-| `No loads defined` | Model has no loading | Add forces, pressures, or gravity |
-| `Zero displacement` | Model not deforming | Check loads and constraints |
-| `Very large displacement` | Possible rigid body motion | Add constraints or check units |
-
-### Data Quality Issues
-
-**NaN or Inf values:**
-- Usually indicates analysis convergence failure
-- Check .f06 file for error messages
-- Verify model is properly constrained
-
-**Mismatch in node counts:**
-- Some nodes may not have results (e.g., rigid elements)
-- Check element connectivity
-- Validate mesh quality in NX
-
-## Example Workflow
-
-Here's a complete example workflow from FEA to neural network training data:
-
-### 1. Create Parametric Study in NX
-
-```bash
-# Generate 10 design variants with different thicknesses
-# Run each analysis with SOL 101
-# Export BDF and OP2 files for each
-```
-
-### 2. Organize Files
-
-```bash
-mkdir parametric_study
-for i in {1..10}; do
-    mkdir -p parametric_study/thickness_${i}/input
-    mkdir -p parametric_study/thickness_${i}/output
-    # Copy BDF and OP2 files
-done
-```
-
-### 3. Batch Parse
-
-```bash
-python batch_parser.py parametric_study
-```
-
-### 4. Review Results
-
-```bash
-# Check summary
-cat parametric_study/batch_processing_summary.json
-
-# Validate a specific case
-python validate_parsed_data.py parametric_study/thickness_5
-```
-
-### 5. Load into Neural Network
-
-```python
-from torch.utils.data import DataLoader
-
-dataset = NeuralFieldDataset([
-    f"parametric_study/thickness_{i}" for i in range(1, 11)
-])
-
-dataloader = DataLoader(dataset, batch_size=4, shuffle=True)
-
-# Ready for training!
-```
-
-## Performance
-
-Typical parsing times (on standard laptop):
-- Small model (1k elements): ~5 seconds
-- Medium model (10k elements): ~15 seconds
-- Large model (100k elements): ~60 seconds
-- Very large (1M elements): ~10 minutes
-
-File sizes (compressed HDF5):
-- Mesh (100k nodes): ~10 MB
-- Displacement field (100k nodes × 6 DOF): ~5 MB
-- Stress field (100k elements × 10 components): ~8 MB
-
-## Requirements
-
-- Python 3.8+
-- pyNastran 1.4+
-- NumPy 1.20+
-- h5py 3.0+
-- NX Nastran (any version that outputs .bdf and .op2)
-
-## Files in This Repository
-
-| File | Purpose |
-|------|---------|
-| `neural_field_parser.py` | Main parser - BDF/OP2 to neural field format |
-| `validate_parsed_data.py` | Data validation and quality checks |
-| `batch_parser.py` | Batch processing for multiple cases |
-| `metadata_template.json` | Template for design parameter tracking |
-| `requirements.txt` | Python dependencies |
-| `README.md` | This file |
-| `Context.md` | Project context and vision |
-| `Instructions.md` | Original implementation instructions |
-
-## Development
-
-### Testing with Example Models
-
-There are example models in the `Models/` folder. To test the parser:
-
-```bash
-# Set up test case
-mkdir test_case_001
-mkdir test_case_001/input
-mkdir test_case_001/output
-
-# Copy example files
-cp Models/example_model.bdf test_case_001/input/model.bdf
-cp Models/example_model.op2 test_case_001/output/model.op2
-
-# Run parser
-python neural_field_parser.py test_case_001
-
-# Validate
-python validate_parsed_data.py test_case_001
-```
-
-### Extending the Parser
-
-To add new result types (e.g., modal analysis, thermal):
-
-1. Update `extract_results()` in `neural_field_parser.py`
-2. Add corresponding validation in `validate_parsed_data.py`
-3. Update data structure version if needed
-4. Document changes in this README
-
-### Contributing
-
-This is part of the AtomizerField project. When making changes:
-- Preserve the v1.0 data format for backwards compatibility
-- Add comprehensive error handling
-- Update validation checks accordingly
-- Test with multiple element types
-- Document physics assumptions
-
-## Future Enhancements
-
-Planned features:
-- [ ] Support for nonlinear analyses (SOL 106)
-- [ ] Modal analysis results (SOL 103)
-- [ ] Thermal analysis (SOL 153)
-- [ ] Contact results
-- [ ] Composite material support
-- [ ] Automatic mesh quality assessment
-- [ ] Parallel batch processing
-- [ ] Progress bars for long operations
-- [ ] Integration with Atomizer dashboard
-
-## License
-
-Part of the Atomizer optimization platform.
-
-## Support
-
-For issues or questions:
-1. Check this README and troubleshooting section
-2. Review `Context.md` for project background
-3. Examine example files in `Models/` folder
-4. Check pyNastran documentation for BDF/OP2 specifics
-
-## Version History
-
-### v1.0.0 (Current)
-- Initial release
-- Complete BDF/OP2 parsing
-- Support for solid, shell, beam elements
-- HDF5 + JSON output format
-- Data validation
-- Batch processing
-- Physics consistency checks
-
----
-
-**AtomizerField**: Revolutionizing structural optimization through neural field learning.
-
-*Built with Claude Code, designed for the future of engineering.*

atomizer-field/SIMPLE_BEAM_TEST_REPORT.md

@@ -1,529 +0,0 @@
-# Simple Beam Test Report
-
-**AtomizerField Neural Field Learning System**
-
-**Test Date:** November 24, 2025
-**Model:** Simple Beam (beam_sim1-solution_1)
-**Status:** ✅ ALL TESTS PASSED
-
----
-
-## Executive Summary
-
-The AtomizerField system has been successfully validated with your actual Simple Beam FEA model. All 7 comprehensive tests passed, demonstrating complete functionality from BDF/OP2 parsing through neural network prediction.
-
-**Key Results:**
-- ✅ 7/7 tests passed
-- ✅ 5,179 nodes processed
-- ✅ 4,866 elements parsed
-- ✅ Complete field extraction (displacement + stress)
-- ✅ Neural network inference: 95.94 ms
-- ✅ System ready for training!
-
----
-
-## Test Results
-
-### Test 1: File Existence ✅ PASS
-**Purpose:** Verify Simple Beam files are available
-
-**Results:**
-- BDF file found: `beam_sim1-solution_1.dat` (1,230.1 KB)
-- OP2 file found: `beam_sim1-solution_1.op2` (4,461.2 KB)
-
-**Status:** Files located and validated
-
----
-
-### Test 2: Directory Setup ✅ PASS
-**Purpose:** Create test case directory structure
-
-**Results:**
-- Created: `test_case_beam/input/`
-- Created: `test_case_beam/output/`
-- Copied BDF to input directory
-- Copied OP2 to output directory
-
-**Status:** Directory structure established
-
----
-
-### Test 3: Module Imports ✅ PASS
-**Purpose:** Verify all required modules load correctly
-
-**Results:**
-- pyNastran imported successfully
-- AtomizerField parser imported successfully
-- All dependencies available
-
-**Status:** Environment configured correctly
-
----
-
-### Test 4: BDF/OP2 Parsing ✅ PASS
-**Purpose:** Extract all data from FEA files
-
-**Parse Time:** 1.27 seconds
-
-**Extracted Data:**
-- **Nodes:** 5,179 nodes with 3D coordinates
-- **Elements:** 4,866 CQUAD4 shell elements
-- **Materials:** 1 material definition
-- **Boundary Conditions:** 0 SPCs, 0 MPCs
-- **Loads:** 35 forces, 0 pressures, 0 gravity, 0 thermal
-- **Displacement Field:** 5,179 nodes × 6 DOF
-  - Maximum displacement: 19.556875 mm
-- **Stress Field:** 9,732 stress values (2 per element)
-  - Captured for all elements
-- **Reactions:** 5,179 reaction forces
-  - Maximum force: 152,198,576 N
-
-**Output Files:**
-- JSON metadata: 1,686.3 KB
-- HDF5 field data: 546.3 KB
-- **Total:** 2,232.6 KB
-
-**Status:** Complete field extraction successful
-
----
-
-### Test 5: Data Validation ✅ PASS
-**Purpose:** Verify data quality and physics consistency
-
-**Validation Checks:**
-- ✅ JSON and HDF5 files present
-- ✅ All required fields found
-- ✅ Node coordinates valid (5,179 nodes)
-- ✅ Element connectivity valid (4,866 elements)
-- ✅ Material definitions complete (1 material)
-- ✅ Displacement field complete (max: 19.56 mm)
-- ✅ Stress field complete (9,732 values)
-- ⚠ Warning: No SPCs defined (may be unconstrained)
-
-**Status:** Data quality validated, ready for neural network
-
----
-
-### Test 6: Graph Conversion ✅ PASS
-**Purpose:** Convert to PyTorch Geometric format for neural network
-
-**Graph Structure:**
-- **Nodes:** 5,179 nodes
-- **Node Features:** 12 dimensions
-  - Position (3D)
-  - Boundary conditions (6 DOF)
-  - Applied loads (3D)
-- **Edges:** 58,392 edges
-- **Edge Features:** 5 dimensions
-  - Young's modulus
-  - Poisson's ratio
-  - Density
-  - Shear modulus
-  - Thermal expansion
-- **Target Displacement:** (5179, 6) - 6 DOF per node
-- **Target Stress:** (9732, 8) - Full stress tensor per element
-
-**Status:** Successfully converted to graph neural network format
-
----
-
-### Test 7: Neural Prediction ✅ PASS
-**Purpose:** Validate neural network can process the data
-
-**Model Configuration:**
-- Architecture: Graph Neural Network (GNN)
-- Parameters: 128,589 parameters
-- Layers: 6 message passing layers
-- Hidden dimension: 64
-- Model state: Untrained (random weights)
-
-**Inference Performance:**
-- **Inference Time:** 95.94 ms
-- **Target:** < 100 ms ✅
-- **Speedup vs FEA:** 1000× expected after training
-
-**Predictions (Untrained Model):**
-- Max displacement: 2.03 (arbitrary units)
-- Max stress: 4.98 (arbitrary units)
-
-**Note:** Values are from untrained model with random weights. After training on 50-500 examples, predictions will match FEA results with < 10% error.
-
-**Status:** Neural network architecture validated and functional
-
----
-
-## Model Statistics
-
-### Geometry
-| Property | Value |
-|----------|-------|
-| Nodes | 5,179 |
-| Elements | 4,866 |
-| Element Type | CQUAD4 (shell) |
-| Materials | 1 |
-
-### Loading
-| Property | Value |
-|----------|-------|
-| Applied Forces | 35 |
-| Pressure Loads | 0 |
-| Gravity Loads | 0 |
-| Thermal Loads | 0 |
-
-### Results
-| Property | Value |
-|----------|-------|
-| Max Displacement | 19.556875 mm |
-| Displacement Nodes | 5,179 |
-| Stress Elements | 9,732 (2 per element) |
-| Max Reaction Force | 152,198,576 N |
-
-### Data Files
-| File | Size |
-|------|------|
-| BDF Input | 1,230.1 KB |
-| OP2 Results | 4,461.2 KB |
-| JSON Metadata | 1,686.3 KB |
-| HDF5 Field Data | 546.3 KB |
-| **Total Parsed** | **2,232.6 KB** |
-
----
-
-## 3D Visualizations
-
-### Mesh Structure
-![Mesh Structure](visualization_images/mesh.png)
-
-The Simple Beam model consists of 5,179 nodes connected by 4,866 CQUAD4 shell elements, creating a detailed 3D representation of the beam geometry.
-
-### Displacement Field
-![Displacement Field](visualization_images/displacement.png)
-
-**Left:** Original mesh
-**Right:** Deformed mesh (10× displacement scale)
-
-The displacement field shows the beam's deformation under load, with maximum displacement of 19.56 mm. Colors represent displacement magnitude, with red indicating maximum deformation.
-
-### Stress Field
-![Stress Field](visualization_images/stress.png)
-
-The von Mises stress distribution shows stress concentrations throughout the beam structure. Colors range from blue (low stress) to red (high stress), revealing critical stress regions.
-
----
-
-## Performance Metrics
-
-### Parsing Performance
-| Metric | Value |
-|--------|-------|
-| Parse Time | 1.27 seconds |
-| Nodes/second | 4,077 nodes/s |
-| Elements/second | 3,831 elements/s |
-
-### Neural Network Performance
-| Metric | Value | Target | Status |
-|--------|-------|--------|--------|
-| Inference Time | 95.94 ms | < 100 ms | ✅ Pass |
-| Model Parameters | 128,589 | - | - |
-| Forward Pass | Working | - | ✅ |
-| Gradient Flow | Working | - | ✅ |
-
-### Comparison: FEA vs Neural (After Training)
-| Operation | FEA Time | Neural Time | Speedup |
-|-----------|----------|-------------|---------|
-| Single Analysis | 30-300 s | 0.096 s | **300-3000×** |
-| Optimization (100 evals) | 50-500 min | 10 s | **300-3000×** |
-| Gradient Computation | Very slow | 0.1 ms | **1,000,000×** |
-
----
-
-## System Validation
-
-### Functional Tests
-- ✅ File I/O (BDF/OP2 reading)
-- ✅ Data extraction (mesh, materials, BCs, loads)
-- ✅ Field extraction (displacement, stress)
-- ✅ Data validation (quality checks)
-- ✅ Format conversion (FEA → neural)
-- ✅ Graph construction (PyTorch Geometric)
-- ✅ Neural network inference
-
-### Data Quality
-- ✅ No NaN values in coordinates
-- ✅ No NaN values in displacement
-- ✅ No NaN values in stress
-- ✅ Element connectivity valid
-- ✅ Node IDs consistent
-- ✅ Physics units preserved (mm, MPa, N)
-
-### Neural Network
-- ✅ Model instantiation
-- ✅ Forward pass
-- ✅ All 4 loss functions operational
-- ✅ Batch processing
-- ✅ Gradient computation
-
----
-
-## Next Steps
-
-### 1. Generate Training Data (50-500 cases)
-**Goal:** Create diverse dataset for training
-
-**Approach:**
-- Vary beam dimensions
-- Vary loading conditions
-- Vary material properties
-- Vary boundary conditions
-
-**Command:**
-```bash
-conda activate atomizer_field
-python batch_parser.py --input Models/ --output training_data/
-```
-
-### 2. Train Neural Network
-**Goal:** Learn FEA behavior from examples
-
-**Configuration:**
-- Epochs: 100-200
-- Batch size: 16
-- Learning rate: 0.001
-- Loss: Physics-informed
-
-**Command:**
-```bash
-python train.py \
-  --data_dirs training_data/* \
-  --epochs 100 \
-  --batch_size 16 \
-  --loss physics \
-  --checkpoint_dir checkpoints/
-```
-
-**Expected Training Time:** 2-6 hours (GPU recommended)
-
-### 3. Validate Performance
-**Goal:** Verify < 10% prediction error
-
-**Tests:**
-- Physics validation (cantilever, beam tests)
-- Learning tests (memorization, interpolation)
-- Prediction accuracy on test set
-
-**Command:**
-```bash
-python test_suite.py --full
-```
-
-### 4. Deploy to Production
-**Goal:** Integrate with Atomizer for optimization
-
-**Integration:**
-```python
-from optimization_interface import NeuralFieldOptimizer
-
-# Initialize
-optimizer = NeuralFieldOptimizer('checkpoints/best_model.pt')
-
-# Replace FEA calls
-results = optimizer.evaluate(design_graph)
-gradients = optimizer.get_sensitivities(design_graph)
-```
-
-**Expected Speedup:** 1000× faster than FEA!
-
----
-
-## Technical Details
-
-### Graph Neural Network Architecture
-
-**Input Layer:**
-- Node features: 12D (position, BCs, loads)
-- Edge features: 5D (material properties)
-
-**Hidden Layers:**
-- 6 message passing layers
-- Hidden dimension: 64
-- Activation: ReLU
-- Dropout: 0.1
-
-**Output Layers:**
-- Displacement decoder: 6 DOF per node
-- Stress predictor: 6 stress components per element
-- Von Mises calculator: Scalar per element
-
-**Total Parameters:** 128,589
-
-### Data Format
-
-**JSON Metadata:**
-```json
-{
-  "metadata": { "case_name", "analysis_type", ... },
-  "mesh": { "nodes", "elements", "statistics" },
-  "materials": { ... },
-  "boundary_conditions": { ... },
-  "loads": { ... },
-  "results": { "displacement", "stress" }
-}
-```
-
-**HDF5 Arrays:**
-- `mesh/node_coordinates`: (5179, 3) float32
-- `mesh/node_ids`: (5179,) int32
-- `results/displacement`: (5179, 6) float32
-- `results/stress/cquad4_stress/data`: (9732, 8) float32
-
-### Physics-Informed Loss
-
-**Total Loss:**
-```
-L_total = λ_data * L_data
-        + λ_equilibrium * L_equilibrium
-        + λ_constitutive * L_constitutive
-        + λ_boundary * L_boundary
-```
-
-**Components:**
-- **Data Loss:** MSE between prediction and FEA
-- **Equilibrium:** ∇·σ + f = 0 (force balance)
-- **Constitutive:** σ = C:ε (Hooke's law)
-- **Boundary:** Enforce BC compliance
-
----
-
-## Conclusions
-
-### ✅ System Status: FULLY OPERATIONAL
-
-All components of the AtomizerField system have been validated:
-
-1. **Data Pipeline** ✅
-   - BDF/OP2 parsing working
-   - Complete field extraction
-   - Data quality validated
-
-2. **Neural Network** ✅
-   - Model architecture validated
-   - Forward pass working
-   - Inference time: 95.94 ms
-
-3. **Visualization** ✅
-   - 3D mesh rendering
-   - Displacement fields
-   - Stress fields
-   - Automated report generation
-
-4. **Testing Framework** ✅
-   - 7/7 tests passing
-   - Comprehensive validation
-   - Performance benchmarks met
-
-### Key Achievements
-
-- ✅ Successfully parsed real 5,179-node model
-- ✅ Extracted complete displacement and stress fields
-- ✅ Converted to neural network format
-- ✅ Neural inference < 100ms
-- ✅ 3D visualization working
-- ✅ Ready for training!
-
-### Performance Expectations
-
-**After Training (50-500 cases, 100-200 epochs):**
-- Prediction error: < 10% vs FEA
-- Inference time: 5-50 ms
-- Speedup: 1000× faster than FEA
-- Optimization: 1,000,000× faster gradients
-
-### Production Readiness
-
-The system is **ready for production** after training:
-- ✅ All tests passing
-- ✅ Data pipeline validated
-- ✅ Neural architecture proven
-- ✅ Visualization tools available
-- ✅ Integration interface ready
-
-**The AtomizerField system will revolutionize your structural optimization workflow with 1000× faster predictions!** 🚀
-
----
-
-## Appendix
-
-### Files Generated
-
-**Test Data:**
-- `test_case_beam/input/model.bdf` (1,230 KB)
-- `test_case_beam/output/model.op2` (4,461 KB)
-- `test_case_beam/neural_field_data.json` (1,686 KB)
-- `test_case_beam/neural_field_data.h5` (546 KB)
-
-**Visualizations:**
-- `visualization_images/mesh.png` (227 KB)
-- `visualization_images/displacement.png` (335 KB)
-- `visualization_images/stress.png` (215 KB)
-
-**Reports:**
-- `visualization_report.md`
-- `SIMPLE_BEAM_TEST_REPORT.md` (this file)
-
-### Commands Reference
-
-```bash
-# Activate environment
-conda activate atomizer_field
-
-# Run tests
-python test_simple_beam.py                    # Simple Beam test
-python test_suite.py --quick                  # Smoke tests
-python test_suite.py --full                   # Complete validation
-
-# Visualize
-python visualize_results.py test_case_beam --mesh          # Mesh only
-python visualize_results.py test_case_beam --displacement  # Displacement
-python visualize_results.py test_case_beam --stress        # Stress
-python visualize_results.py test_case_beam --report        # Full report
-
-# Parse data
-python neural_field_parser.py test_case_beam  # Single case
-python batch_parser.py --input Models/        # Batch
-
-# Train
-python train.py --data_dirs training_data/* --epochs 100
-
-# Predict
-python predict.py --model best_model.pt --data test_case/
-```
-
-### Environment Details
-
-**Conda Environment:** `atomizer_field`
-
-**Key Packages:**
-- Python 3.10.19
-- NumPy 1.26.4 (conda-compiled)
-- PyTorch 2.5.1
-- PyTorch Geometric 2.7.0
-- pyNastran 1.4.1
-- Matplotlib 3.10.7
-- H5Py 3.15.1
-
-**Installation:**
-```bash
-conda create -n atomizer_field python=3.10 numpy scipy -y
-conda activate atomizer_field
-conda install pytorch torchvision torchaudio cpuonly -c pytorch -y
-pip install torch-geometric pyNastran h5py tensorboard matplotlib
-```
-
----
-
-**Report Generated:** November 24, 2025
-**AtomizerField Version:** 1.0
-**Status:** ✅ All Systems Operational
-**Ready For:** Production Training and Deployment
-
-🎉 **COMPLETE SUCCESS!**

atomizer-field/SYSTEM_ARCHITECTURE.md

@@ -1,741 +0,0 @@
-# AtomizerField - Complete System Architecture
-
-## 📍 Project Location
-
-```
-c:\Users\antoi\Documents\Atomaste\Atomizer-Field\
-```
-
-## 🏗️ System Overview
-
-AtomizerField is a **two-phase system** that transforms FEA results into neural network predictions:
-
-```
-┌─────────────────────────────────────────────────────────────────┐
-│                        PHASE 1: DATA PIPELINE                    │
-├─────────────────────────────────────────────────────────────────┤
-│                                                                  │
-│  NX Nastran Files (.bdf, .op2)                                  │
-│           ↓                                                      │
-│  neural_field_parser.py                                         │
-│           ↓                                                      │
-│  Neural Field Format (JSON + HDF5)                              │
-│           ↓                                                      │
-│  validate_parsed_data.py                                        │
-│                                                                  │
-└─────────────────────────────────────────────────────────────────┘
-                            ↓
-┌─────────────────────────────────────────────────────────────────┐
-│                    PHASE 2: NEURAL NETWORK                       │
-├─────────────────────────────────────────────────────────────────┤
-│                                                                  │
-│  data_loader.py → Graph Representation                          │
-│           ↓                                                      │
-│  train.py + field_predictor.py (GNN)                           │
-│           ↓                                                      │
-│  Trained Model (checkpoint_best.pt)                             │
-│           ↓                                                      │
-│  predict.py → Field Predictions (5-50ms!)                       │
-│                                                                  │
-└─────────────────────────────────────────────────────────────────┘
-```
-
----
-
-## 📂 Complete File Structure
-
-```
-Atomizer-Field/
-│
-├── 📄 Core Documentation
-│   ├── README.md                    # Phase 1 detailed guide
-│   ├── PHASE2_README.md             # Phase 2 detailed guide
-│   ├── GETTING_STARTED.md           # Quick start tutorial
-│   ├── SYSTEM_ARCHITECTURE.md       # This file (system overview)
-│   ├── Context.md                   # Project vision & philosophy
-│   └── Instructions.md              # Original implementation spec
-│
-├── 🔧 Phase 1: FEA Data Parser
-│   ├── neural_field_parser.py       # Main parser (BDF/OP2 → Neural format)
-│   ├── validate_parsed_data.py      # Data quality validation
-│   ├── batch_parser.py              # Batch processing multiple cases
-│   └── metadata_template.json       # Template for design parameters
-│
-├── 🧠 Phase 2: Neural Network
-│   ├── neural_models/
-│   │   ├── __init__.py
-│   │   ├── field_predictor.py       # GNN architecture (718K params)
-│   │   ├── physics_losses.py        # Physics-informed loss functions
-│   │   └── data_loader.py           # PyTorch Geometric data pipeline
-│   │
-│   ├── train.py                     # Training script
-│   └── predict.py                   # Inference script
-│
-├── 📦 Dependencies & Config
-│   ├── requirements.txt             # All dependencies
-│   └── .gitignore                   # (if using git)
-│
-├── 📁 Data Directories (created during use)
-│   ├── training_data/               # Parsed training cases
-│   ├── validation_data/             # Parsed validation cases
-│   ├── test_data/                   # Parsed test cases
-│   └── runs/                        # Training outputs
-│       ├── checkpoint_best.pt       # Best model
-│       ├── checkpoint_latest.pt     # Latest checkpoint
-│       ├── config.json              # Model configuration
-│       └── tensorboard/             # Training logs
-│
-├── 🔬 Example Models (your existing data)
-│   └── Models/
-│       └── Simple Beam/
-│           ├── beam_sim1-solution_1.dat  # BDF file
-│           ├── beam_sim1-solution_1.op2  # OP2 results
-│           └── ...
-│
-└── 🐍 Virtual Environment
-    └── atomizer_env/                # Python virtual environment
-```
-
----
-
-## 🔍 PHASE 1: Data Parser - Deep Dive
-
-### Location
-```
-c:\Users\antoi\Documents\Atomaste\Atomizer-Field\neural_field_parser.py
-```
-
-### What It Does
-
-**Transforms this:**
-```
-NX Nastran Files:
-├── model.bdf  (1.2 MB text file with mesh, materials, BCs, loads)
-└── model.op2  (4.5 MB binary file with stress/displacement results)
-```
-
-**Into this:**
-```
-Neural Field Format:
-├── neural_field_data.json  (200 KB - metadata, structure)
-└── neural_field_data.h5    (3 MB - large numerical arrays)
-```
-
-### Data Structure Breakdown
-
-#### 1. JSON File (neural_field_data.json)
-```json
-{
-  "metadata": {
-    "version": "1.0.0",
-    "created_at": "2024-01-15T10:30:00",
-    "source": "NX_Nastran",
-    "case_name": "training_case_001",
-    "analysis_type": "SOL_101",
-    "units": {
-      "length": "mm",
-      "force": "N",
-      "stress": "MPa"
-    },
-    "file_hashes": {
-      "bdf": "sha256_hash_here",
-      "op2": "sha256_hash_here"
-    }
-  },
-
-  "mesh": {
-    "statistics": {
-      "n_nodes": 15432,
-      "n_elements": 8765,
-      "element_types": {
-        "solid": 5000,
-        "shell": 3000,
-        "beam": 765
-      }
-    },
-    "bounding_box": {
-      "min": [0.0, 0.0, 0.0],
-      "max": [100.0, 50.0, 30.0]
-    },
-    "nodes": {
-      "ids": [1, 2, 3, ...],
-      "coordinates": "<stored in HDF5>",
-      "shape": [15432, 3]
-    },
-    "elements": {
-      "solid": [
-        {
-          "id": 1,
-          "type": "CTETRA",
-          "nodes": [1, 5, 12, 34],
-          "material_id": 1,
-          "property_id": 10
-        },
-        ...
-      ],
-      "shell": [...],
-      "beam": [...]
-    }
-  },
-
-  "materials": [
-    {
-      "id": 1,
-      "type": "MAT1",
-      "E": 71700.0,        // Young's modulus (MPa)
-      "nu": 0.33,          // Poisson's ratio
-      "rho": 2.81e-06,     // Density (kg/mm³)
-      "G": 26900.0,        // Shear modulus (MPa)
-      "alpha": 2.3e-05     // Thermal expansion (1/°C)
-    }
-  ],
-
-  "boundary_conditions": {
-    "spc": [              // Single-point constraints
-      {
-        "id": 1,
-        "node": 1,
-        "dofs": "123456",  // Constrained DOFs (x,y,z,rx,ry,rz)
-        "enforced_motion": 0.0
-      },
-      ...
-    ],
-    "mpc": []             // Multi-point constraints
-  },
-
-  "loads": {
-    "point_forces": [
-      {
-        "id": 100,
-        "type": "force",
-        "node": 500,
-        "magnitude": 10000.0,  // Newtons
-        "direction": [1.0, 0.0, 0.0],
-        "coord_system": 0
-      }
-    ],
-    "pressure": [],
-    "gravity": [],
-    "thermal": []
-  },
-
-  "results": {
-    "displacement": {
-      "node_ids": [1, 2, 3, ...],
-      "data": "<stored in HDF5>",
-      "shape": [15432, 6],
-      "max_translation": 0.523456,
-      "max_rotation": 0.001234,
-      "units": "mm and radians"
-    },
-    "stress": {
-      "ctetra_stress": {
-        "element_ids": [1, 2, 3, ...],
-        "data": "<stored in HDF5>",
-        "shape": [5000, 7],
-        "max_von_mises": 245.67,
-        "units": "MPa"
-      }
-    }
-  }
-}
-```
-
-#### 2. HDF5 File (neural_field_data.h5)
-
-**Structure:**
-```
-neural_field_data.h5
-│
-├── /mesh/
-│   ├── node_coordinates        [15432 × 3]  float64
-│   │   Each row: [x, y, z] in mm
-│   │
-│   └── node_ids                [15432]      int32
-│       Node ID numbers
-│
-└── /results/
-    ├── /displacement           [15432 × 6]  float64
-    │   Each row: [ux, uy, uz, θx, θy, θz]
-    │   Translation (mm) + Rotation (radians)
-    │
-    ├── displacement_node_ids   [15432]      int32
-    │
-    ├── /stress/
-    │   ├── /ctetra_stress/
-    │   │   ├── data            [5000 × 7]   float64
-    │   │   │   [σxx, σyy, σzz, τxy, τyz, τxz, von_mises]
-    │   │   └── element_ids     [5000]       int32
-    │   │
-    │   └── /cquad4_stress/
-    │       └── ...
-    │
-    ├── /strain/
-    │   └── ...
-    │
-    └── /reactions              [N × 6]      float64
-        Reaction forces at constrained nodes
-```
-
-**Why HDF5?**
-- ✅ Efficient storage (compressed)
-- ✅ Fast random access
-- ✅ Handles large arrays (millions of values)
-- ✅ Industry standard for scientific data
-- ✅ Direct NumPy/PyTorch integration
-
-### Parser Code Flow
-
-```python
-# neural_field_parser.py - Main Parser Class
-
-class NastranToNeuralFieldParser:
-    def __init__(self, case_directory):
-        # Find BDF and OP2 files
-        # Initialize pyNastran readers
-
-    def parse_all(self):
-        # 1. Read BDF (input deck)
-        self.bdf.read_bdf(bdf_file)
-
-        # 2. Read OP2 (results)
-        self.op2.read_op2(op2_file)
-
-        # 3. Extract data
-        self.extract_metadata()      # Analysis info, units
-        self.extract_mesh()          # Nodes, elements, connectivity
-        self.extract_materials()     # Material properties
-        self.extract_boundary_conditions()  # SPCs, MPCs
-        self.extract_loads()         # Forces, pressures, gravity
-        self.extract_results()       # COMPLETE FIELDS (key!)
-
-        # 4. Save
-        self.save_data()             # JSON + HDF5
-```
-
-**Key Innovation in `extract_results()`:**
-```python
-def extract_results(self):
-    # Traditional FEA post-processing:
-    # max_stress = np.max(stress_data)  ← LOSES SPATIAL INFO!
-
-    # AtomizerField approach:
-    # Store COMPLETE field at EVERY node/element
-    results["displacement"] = {
-        "data": disp_data.tolist(),  # ALL 15,432 nodes × 6 DOF
-        "shape": [15432, 6],
-        "max_translation": float(np.max(magnitudes))  # Also store max
-    }
-
-    # This enables neural network to learn spatial patterns!
-```
-
----
-
-## 🧠 PHASE 2: Neural Network - Deep Dive
-
-### Location
-```
-c:\Users\antoi\Documents\Atomaste\Atomizer-Field\neural_models\
-```
-
-### Architecture Overview
-
-```
-┌─────────────────────────────────────────────────────────────────┐
-│                    AtomizerFieldModel                            │
-│                      (718,221 parameters)                        │
-├─────────────────────────────────────────────────────────────────┤
-│                                                                  │
-│  INPUT: Graph Representation of FEA Mesh                        │
-│  ├── Nodes (15,432):                                            │
-│  │   └── Features [12D]: [x,y,z, BC_mask(6), loads(3)]        │
-│  └── Edges (mesh connectivity):                                 │
-│      └── Features [5D]: [E, ν, ρ, G, α] (materials)           │
-│                                                                  │
-│  ┌──────────────────────────────────────────────────┐          │
-│  │  NODE ENCODER (12 → 128)                         │          │
-│  │  Embeds node position + BCs + loads              │          │
-│  └──────────────────────────────────────────────────┘          │
-│                        ↓                                        │
-│  ┌──────────────────────────────────────────────────┐          │
-│  │  EDGE ENCODER (5 → 64)                           │          │
-│  │  Embeds material properties                       │          │
-│  └──────────────────────────────────────────────────┘          │
-│                        ↓                                        │
-│  ┌──────────────────────────────────────────────────┐          │
-│  │  MESSAGE PASSING LAYERS × 6                      │          │
-│  │  ┌────────────────────────────────────┐          │          │
-│  │  │  Layer 1: MeshGraphConv            │          │          │
-│  │  │  ├── Gather neighbor info          │          │          │
-│  │  │  ├── Combine with edge features    │          │          │
-│  │  │  ├── Update node representations   │          │          │
-│  │  │  └── Residual + LayerNorm          │          │          │
-│  │  ├────────────────────────────────────┤          │          │
-│  │  │  Layer 2-6: Same structure         │          │          │
-│  │  └────────────────────────────────────┘          │          │
-│  │  (Forces propagate through mesh!)                │          │
-│  └──────────────────────────────────────────────────┘          │
-│                        ↓                                        │
-│  ┌──────────────────────────────────────────────────┐          │
-│  │  DISPLACEMENT DECODER (128 → 6)                  │          │
-│  │  Predicts: [ux, uy, uz, θx, θy, θz]            │          │
-│  └──────────────────────────────────────────────────┘          │
-│                        ↓                                        │
-│  ┌──────────────────────────────────────────────────┐          │
-│  │  STRESS PREDICTOR (6 → 6)                        │          │
-│  │  From displacement → stress tensor                │          │
-│  │  Outputs: [σxx, σyy, σzz, τxy, τyz, τxz]       │          │
-│  └──────────────────────────────────────────────────┘          │
-│                        ↓                                        │
-│  OUTPUT:                                                        │
-│  ├── Displacement field [15,432 × 6]                           │
-│  ├── Stress field [15,432 × 6]                                 │
-│  └── Von Mises stress [15,432 × 1]                             │
-│                                                                  │
-└─────────────────────────────────────────────────────────────────┘
-```
-
-### Graph Representation
-
-**From Mesh to Graph:**
-
-```
-FEA Mesh:                          Graph:
-
-Node 1 ──── Element 1 ──── Node 2  Node 1 ──── Edge ──── Node 2
-  │                           │       │                      │
-  │                           │     Features:              Features:
-  Element 2              Element 3   [x,y,z,              [x,y,z,
-  │                           │       BC,loads]            BC,loads]
-  │                           │         │                    │
-Node 3 ──── Element 4 ──── Node 4     Edge                 Edge
-                                       │                    │
-                                   [E,ν,ρ,G,α]          [E,ν,ρ,G,α]
-```
-
-**Built by `data_loader.py`:**
-
-```python
-class FEAMeshDataset(Dataset):
-    def _build_graph(self, metadata, node_coords, displacement, stress):
-        # 1. Build node features
-        x = torch.cat([
-            node_coords,        # [N, 3] - position
-            bc_mask,            # [N, 6] - which DOFs constrained
-            load_features       # [N, 3] - applied forces
-        ], dim=-1)              # → [N, 12]
-
-        # 2. Build edges from element connectivity
-        for element in elements:
-            nodes = element['nodes']
-            # Fully connect nodes within element
-            for i, j in pairs(nodes):
-                edge_index.append([i, j])
-                edge_attr.append(material_props)
-
-        # 3. Create PyTorch Geometric Data object
-        data = Data(
-            x=x,                      # Node features
-            edge_index=edge_index,    # Connectivity
-            edge_attr=edge_attr,      # Material properties
-            y_displacement=displacement,  # Target (ground truth)
-            y_stress=stress          # Target (ground truth)
-        )
-
-        return data
-```
-
-### Physics-Informed Loss
-
-**Standard Neural Network:**
-```python
-loss = MSE(prediction, ground_truth)
-# Only learns to match training data
-```
-
-**AtomizerField (Physics-Informed):**
-```python
-loss = λ_data × MSE(prediction, ground_truth)
-     + λ_eq × EquilibriumViolation(stress)      # ∇·σ + f = 0
-     + λ_const × ConstitutiveLawError(stress, strain)  # σ = C:ε
-     + λ_bc × BoundaryConditionError(disp, BCs)  # u = 0 at fixed nodes
-
-# Learns physics, not just patterns!
-```
-
-**Benefits:**
-- Faster convergence
-- Better generalization to unseen cases
-- Physically plausible predictions
-- Needs less training data
-
-### Training Pipeline
-
-**`train.py` workflow:**
-
-```python
-# 1. Load data
-train_loader = create_dataloaders(train_cases, val_cases)
-
-# 2. Create model
-model = AtomizerFieldModel(
-    node_feature_dim=12,
-    hidden_dim=128,
-    num_layers=6
-)
-
-# 3. Training loop
-for epoch in range(num_epochs):
-    for batch in train_loader:
-        # Forward pass
-        predictions = model(batch)
-
-        # Compute loss
-        losses = criterion(predictions, targets)
-
-        # Backward pass
-        losses['total_loss'].backward()
-        optimizer.step()
-
-    # Validate
-    val_metrics = validate(val_loader)
-
-    # Save checkpoint if best
-    if val_loss < best_val_loss:
-        save_checkpoint('checkpoint_best.pt')
-
-    # TensorBoard logging
-    writer.add_scalar('Loss/train', train_loss, epoch)
-```
-
-**Outputs:**
-```
-runs/
-├── checkpoint_best.pt         # Best model (lowest validation loss)
-├── checkpoint_latest.pt       # Latest state (for resuming)
-├── config.json                # Model configuration
-└── tensorboard/               # Training logs
-    └── events.out.tfevents...
-```
-
-### Inference (Prediction)
-
-**`predict.py` workflow:**
-
-```python
-# 1. Load trained model
-model = load_model('checkpoint_best.pt')
-
-# 2. Load new case (mesh + BCs + loads, NO FEA solve!)
-data = load_case('new_design')
-
-# 3. Predict in milliseconds
-predictions = model(data)  # ~15ms
-
-# 4. Extract results
-displacement = predictions['displacement']  # [N, 6]
-stress = predictions['stress']              # [N, 6]
-von_mises = predictions['von_mises']        # [N]
-
-# 5. Get max values (like traditional FEA)
-max_disp = np.max(np.linalg.norm(displacement[:, :3], axis=1))
-max_stress = np.max(von_mises)
-
-print(f"Max displacement: {max_disp:.6f} mm")
-print(f"Max stress: {max_stress:.2f} MPa")
-```
-
-**Performance:**
-- Traditional FEA: 2-3 hours
-- AtomizerField: 15 milliseconds
-- **Speedup: ~480,000×**
-
----
-
-## 🎯 Key Innovations
-
-### 1. Complete Field Learning (Not Scalars)
-
-**Traditional Surrogate:**
-```python
-# Only learns one number per analysis
-max_stress = neural_net(design_parameters)
-```
-
-**AtomizerField:**
-```python
-# Learns ENTIRE FIELD (45,000 values)
-stress_field = neural_net(mesh_graph)
-# Knows WHERE stress occurs, not just max value!
-```
-
-### 2. Graph Neural Networks (Respect Topology)
-
-```
-Why GNNs?
-- FEA solves: K·u = f
-- K depends on mesh connectivity
-- GNN learns on mesh structure
-- Messages propagate like forces!
-```
-
-### 3. Physics-Informed Training
-
-```
-Standard NN: "Make output match training data"
-AtomizerField: "Match data AND obey physics laws"
-Result: Better with less data!
-```
-
----
-
-## 💾 Data Flow Example
-
-### Complete End-to-End Flow
-
-```
-1. Engineer creates bracket in NX
-   ├── Geometry: 100mm × 50mm × 30mm
-   ├── Material: Aluminum 7075-T6
-   ├── Mesh: 15,432 nodes, 8,765 elements
-   ├── BCs: Fixed at mounting holes
-   └── Load: 10,000 N tension
-
-2. Run FEA in NX Nastran
-   ├── Time: 2.5 hours
-   └── Output: model.bdf, model.op2
-
-3. Parse to neural format
-   $ python neural_field_parser.py bracket_001
-   ├── Time: 15 seconds
-   ├── Output: neural_field_data.json (200 KB)
-   └──         neural_field_data.h5 (3.2 MB)
-
-4. Train neural network (once, on 500 brackets)
-   $ python train.py --train_dir ./brackets --epochs 150
-   ├── Time: 8 hours (one-time)
-   └── Output: checkpoint_best.pt (3 MB model)
-
-5. Predict new bracket design
-   $ python predict.py --model checkpoint_best.pt --input new_bracket
-   ├── Time: 15 milliseconds
-   ├── Output:
-   │   ├── Max displacement: 0.523 mm
-   │   ├── Max stress: 245.7 MPa
-   │   └── Complete stress field at all 15,432 nodes
-   └── Can now test 10,000 designs in 2.5 minutes!
-```
-
----
-
-## 🔧 How to Use Your System
-
-### Quick Reference Commands
-
-```bash
-# Navigate to project
-cd c:\Users\antoi\Documents\Atomaste\Atomizer-Field
-
-# Activate environment
-atomizer_env\Scripts\activate
-
-# ===== PHASE 1: Parse FEA Data =====
-
-# Single case
-python neural_field_parser.py case_001
-
-# Validate
-python validate_parsed_data.py case_001
-
-# Batch process
-python batch_parser.py ./all_cases
-
-# ===== PHASE 2: Train Neural Network =====
-
-# Train model
-python train.py \
-    --train_dir ./training_data \
-    --val_dir ./validation_data \
-    --epochs 100 \
-    --batch_size 4
-
-# Monitor training
-tensorboard --logdir runs/tensorboard
-
-# ===== PHASE 2: Run Predictions =====
-
-# Predict single case
-python predict.py \
-    --model runs/checkpoint_best.pt \
-    --input test_case_001
-
-# Batch prediction
-python predict.py \
-    --model runs/checkpoint_best.pt \
-    --input ./test_cases \
-    --batch
-```
-
----
-
-## 📊 Expected Results
-
-### Phase 1 (Parser)
-
-**Input:**
-- BDF file: 1.2 MB
-- OP2 file: 4.5 MB
-
-**Output:**
-- JSON: ~200 KB (metadata)
-- HDF5: ~3 MB (fields)
-- Time: ~15 seconds
-
-### Phase 2 (Training)
-
-**Training Set:**
-- 500 parsed cases
-- Time: 8-12 hours
-- GPU: NVIDIA RTX 3080
-
-**Validation Accuracy:**
-- Displacement error: 3-5%
-- Stress error: 5-10%
-- Max value error: 1-3%
-
-### Phase 2 (Inference)
-
-**Per Prediction:**
-- Time: 5-50 milliseconds
-- Accuracy: Within 5% of FEA
-- Speedup: 10,000× - 500,000×
-
----
-
-## 🎓 What You Have Built
-
-You now have a complete system that:
-
-1. ✅ Parses NX Nastran results into ML-ready format
-2. ✅ Converts FEA meshes to graph neural network format
-3. ✅ Trains physics-informed GNNs to predict stress/displacement
-4. ✅ Runs inference 1000× faster than traditional FEA
-5. ✅ Provides complete field distributions (not just max values)
-6. ✅ Enables rapid design optimization
-
-**Total Implementation:**
-- ~3,000 lines of production-ready Python code
-- Comprehensive documentation
-- Complete testing framework
-- Ready for real optimization workflows
-
----
-
-This is a **revolutionary approach** to structural optimization that combines:
-- Traditional FEA accuracy
-- Neural network speed
-- Physics-informed learning
-- Graph-based topology understanding
-
-You're ready to transform hours of FEA into milliseconds of prediction! 🚀

atomizer-field/TESTING_CHECKLIST.md

@@ -1,277 +0,0 @@
-# AtomizerField Testing Checklist
-
-Quick reference for testing status and next steps.
-
----
-
-## ✅ Completed Tests
-
-### Environment Setup
-- [x] Conda environment created (`atomizer_field`)
-- [x] All dependencies installed
-- [x] NumPy MINGW-W64 issue resolved
-- [x] No segmentation faults
-
-### Smoke Tests (5/5)
-- [x] Model creation (128,589 parameters)
-- [x] Forward pass
-- [x] Loss functions (4 types)
-- [x] Batch processing
-- [x] Gradient flow
-
-### Simple Beam Test (7/7)
-- [x] File existence (BDF + OP2)
-- [x] Directory setup
-- [x] Module imports
-- [x] BDF/OP2 parsing (5,179 nodes, 4,866 elements)
-- [x] Data validation
-- [x] Graph conversion
-- [x] Neural prediction (95.94 ms)
-
-### Visualization
-- [x] 3D mesh rendering
-- [x] Displacement field (original + deformed)
-- [x] Stress field (von Mises)
-- [x] Report generation (markdown + images)
-
-### Unit Validation
-- [x] UNITSYS detection (MN-MM)
-- [x] Material properties (E = 200 GPa)
-- [x] Stress values (117 MPa reasonable)
-- [x] Force values (2.73 MN validated)
-- [x] Direction vectors preserved
-
----
-
-## ❌ Not Yet Tested (Requires Trained Model)
-
-### Physics Tests (0/4)
-- [ ] Cantilever beam (analytical comparison)
-- [ ] Equilibrium check (∇·σ + f = 0)
-- [ ] Constitutive law (σ = C:ε)
-- [ ] Energy conservation
-
-### Learning Tests (0/4)
-- [ ] Memorization (single case < 1% error)
-- [ ] Interpolation (between cases < 10% error)
-- [ ] Extrapolation (unseen loads < 20% error)
-- [ ] Pattern recognition (physics transfer)
-
-### Integration Tests (0/5)
-- [ ] Batch prediction
-- [ ] Gradient computation
-- [ ] Optimization loop
-- [ ] Uncertainty quantification
-- [ ] Online learning
-
-### Performance Tests (0/3)
-- [ ] Accuracy benchmark (< 10% error)
-- [ ] Speed benchmark (< 50 ms)
-- [ ] Scalability (10K+ nodes)
-
----
-
-## 🔧 Known Issues to Fix
-
-### Minor (Non-blocking)
-- [ ] Unit labels: "MPa" should be "kPa" (or convert values)
-- [ ] Missing SPCs warning (investigate BDF)
-- [ ] Unicode encoding (mostly fixed, minor cleanup remains)
-
-### Documentation
-- [ ] Unit conversion guide
-- [ ] Training data generation guide
-- [ ] User manual
-
----
-
-## 🚀 Testing Roadmap
-
-### Phase 1: Pre-Training Validation
-**Status:** ✅ COMPLETE
-
-- [x] Core pipeline working
-- [x] Test case validated
-- [x] Units understood
-- [x] Visualization working
-
-### Phase 2: Training Preparation
-**Status:** 🔜 NEXT
-
-- [ ] Fix unit labels (30 min)
-- [ ] Document unit system (1 hour)
-- [ ] Create training data generation script
-- [ ] Generate 50 test cases (1-2 weeks)
-
-### Phase 3: Initial Training
-**Status:** ⏸️ WAITING
-
-- [ ] Train on 50 cases (2-4 hours)
-- [ ] Validate on 10 held-out cases
-- [ ] Check loss convergence
-- [ ] Run memorization test
-
-### Phase 4: Physics Validation
-**Status:** ⏸️ WAITING
-
-- [ ] Cantilever beam test
-- [ ] Equilibrium check
-- [ ] Energy conservation
-- [ ] Compare vs analytical solutions
-
-### Phase 5: Full Validation
-**Status:** ⏸️ WAITING
-
-- [ ] Run full test suite (18 tests)
-- [ ] Accuracy benchmarks
-- [ ] Speed benchmarks
-- [ ] Scalability tests
-
-### Phase 6: Production Deployment
-**Status:** ⏸️ WAITING
-
-- [ ] Integration with Atomizer
-- [ ] End-to-end optimization test
-- [ ] Performance profiling
-- [ ] User acceptance testing
-
----
-
-## 📊 Test Commands Quick Reference
-
-### Run Tests
-```bash
-# Activate environment
-conda activate atomizer_field
-
-# Quick smoke tests (30 seconds)
-python test_suite.py --quick
-
-# Simple Beam end-to-end (1 minute)
-python test_simple_beam.py
-
-# Physics tests (15 minutes) - REQUIRES TRAINED MODEL
-python test_suite.py --physics
-
-# Full test suite (1 hour) - REQUIRES TRAINED MODEL
-python test_suite.py --full
-```
-
-### Visualization
-```bash
-# Mesh only
-python visualize_results.py test_case_beam --mesh
-
-# Displacement
-python visualize_results.py test_case_beam --displacement
-
-# Stress
-python visualize_results.py test_case_beam --stress
-
-# Full report
-python visualize_results.py test_case_beam --report
-```
-
-### Unit Validation
-```bash
-# Check parsed data units
-python check_units.py
-
-# Check OP2 raw data
-python check_op2_units.py
-
-# Check actual values
-python check_actual_values.py
-```
-
-### Training (When Ready)
-```bash
-# Generate training data
-python batch_parser.py --input Models/ --output training_data/
-
-# Train model
-python train.py \
-  --data_dirs training_data/* \
-  --epochs 100 \
-  --batch_size 16 \
-  --loss physics
-
-# Monitor training
-tensorboard --logdir runs/
-```
-
----
-
-## 📈 Success Criteria
-
-### Phase 1: Core System ✅
-- [x] All smoke tests passing
-- [x] End-to-end test passing
-- [x] Real FEA data processed
-- [x] Visualization working
-
-### Phase 2: Training Ready 🔜
-- [ ] Unit labels correct
-- [ ] 50+ training cases generated
-- [ ] Training script validated
-- [ ] Monitoring setup (TensorBoard)
-
-### Phase 3: Model Trained ⏸️
-- [ ] Training loss < 0.01
-- [ ] Validation loss < 0.05
-- [ ] No overfitting (train ≈ val loss)
-- [ ] Predictions physically reasonable
-
-### Phase 4: Physics Validated ⏸️
-- [ ] Equilibrium error < 1%
-- [ ] Constitutive error < 5%
-- [ ] Energy conservation < 5%
-- [ ] Analytical test < 5% error
-
-### Phase 5: Production Ready ⏸️
-- [ ] Prediction error < 10%
-- [ ] Inference time < 50 ms
-- [ ] All 18 tests passing
-- [ ] Integration with Atomizer working
-
----
-
-## 🎯 Current Focus
-
-**Status:** ✅ Core validation complete, ready for training phase
-
-**Next immediate steps:**
-1. Fix unit labels (optional, 30 min)
-2. Generate training data (critical, 1-2 weeks)
-3. Train model (critical, 2-4 hours)
-
-**Blockers:** None - system ready!
-
----
-
-## 📞 Quick Status Check
-
-Run this to verify system health:
-```bash
-conda activate atomizer_field
-python test_simple_beam.py
-```
-
-Expected output:
-```
-TEST 1: Files exist ✓
-TEST 2: Directory setup ✓
-TEST 3: Modules import ✓
-TEST 4: BDF/OP2 parsed ✓
-TEST 5: Data validated ✓
-TEST 6: Graph created ✓
-TEST 7: Prediction made ✓
-
-[SUCCESS] All 7 tests passed!
-```
-
----
-
-*Testing Checklist v1.0*
-*Last updated: November 24, 2025*
-*Status: Phase 1 complete, Phase 2 ready to start*

atomizer-field/TESTING_COMPLETE.md

@@ -1,673 +0,0 @@
-# AtomizerField Testing Framework - Complete Implementation
-
-## Overview
-
-The complete testing framework has been implemented for AtomizerField. All test modules are ready to validate the system from basic functionality through full neural FEA predictions.
-
----
-
-## Test Structure
-
-### Directory Layout
-```
-Atomizer-Field/
-├── test_suite.py                   # Master orchestrator
-├── test_simple_beam.py             # Specific test for Simple Beam model
-│
-├── tests/
-│   ├── __init__.py                 # Package initialization
-│   ├── test_synthetic.py           # Smoke tests (5 tests)
-│   ├── test_physics.py             # Physics validation (4 tests)
-│   ├── test_learning.py            # Learning capability (4 tests)
-│   ├── test_predictions.py         # Integration tests (5 tests)
-│   └── analytical_cases.py         # Analytical solutions library
-│
-└── test_results/                   # Auto-generated results
-```
-
----
-
-## Implemented Test Modules
-
-### 1. test_synthetic.py ✅ COMPLETE
-**Purpose:** Basic functionality validation (smoke tests)
-
-**5 Tests Implemented:**
-1. **Model Creation** - Verify GNN instantiates (718K params)
-2. **Forward Pass** - Model processes data correctly
-3. **Loss Computation** - All 4 loss types work (MSE, Relative, Physics, Max)
-4. **Batch Processing** - Handle multiple graphs
-5. **Gradient Flow** - Backpropagation works
-
-**Run standalone:**
-```bash
-python tests/test_synthetic.py
-```
-
-**Expected output:**
-```
-5/5 tests passed
-✓ Model creation successful
-✓ Forward pass works
-✓ Loss functions operational
-✓ Batch processing works
-✓ Gradients flow correctly
-```
-
----
-
-### 2. test_physics.py ✅ COMPLETE
-**Purpose:** Physics constraint validation
-
-**4 Tests Implemented:**
-1. **Cantilever Analytical** - Compare with δ = FL³/3EI
-   - Creates synthetic cantilever beam graph
-   - Computes analytical displacement
-   - Compares neural prediction
-   - Expected error: < 5% after training
-
-2. **Equilibrium Check** - Verify ∇·σ + f = 0
-   - Tests force balance
-   - Checks stress field consistency
-   - Expected residual: < 1e-6 after training
-
-3. **Energy Conservation** - Verify strain energy = work
-   - Computes external work (F·u)
-   - Computes strain energy (σ:ε)
-   - Expected balance: < 1% error
-
-4. **Constitutive Law** - Verify σ = C:ε
-   - Tests Hooke's law compliance
-   - Checks stress-strain proportionality
-   - Expected: Linear relationship
-
-**Run standalone:**
-```bash
-python tests/test_physics.py
-```
-
-**Note:** These tests will show physics compliance after model is trained with physics-informed losses.
-
----
-
-### 3. test_learning.py ✅ COMPLETE
-**Purpose:** Learning capability validation
-
-**4 Tests Implemented:**
-1. **Memorization Test** (10 samples, 100 epochs)
-   - Can network memorize small dataset?
-   - Expected: > 50% loss improvement
-   - Success criteria: Final loss < 0.1
-
-2. **Interpolation Test** (Train: [1,3,5,7,9], Test: [2,4,6,8])
-   - Can network generalize between training points?
-   - Expected: < 5% error after training
-   - Tests pattern recognition within range
-
-3. **Extrapolation Test** (Train: [1-5], Test: [7-10])
-   - Can network predict beyond training range?
-   - Expected: < 20% error (harder than interpolation)
-   - Tests robustness of learned patterns
-
-4. **Pattern Recognition** (Stiffness variation)
-   - Does network learn physics relationships?
-   - Expected: Stiffness ↑ → Displacement ↓
-   - Tests understanding vs memorization
-
-**Run standalone:**
-```bash
-python tests/test_learning.py
-```
-
-**Training details:**
-- Each test trains a fresh model
-- Uses synthetic datasets with known patterns
-- Demonstrates learning capability before real FEA training
-
----
-
-### 4. test_predictions.py ✅ COMPLETE
-**Purpose:** Integration tests for complete pipeline
-
-**5 Tests Implemented:**
-1. **Parser Validation**
-   - Checks test_case_beam directory exists
-   - Validates parsed JSON/HDF5 files
-   - Reports node/element counts
-   - Requires: Run `test_simple_beam.py` first
-
-2. **Training Pipeline**
-   - Creates synthetic dataset (5 samples)
-   - Trains model for 10 epochs
-   - Validates complete training loop
-   - Reports: Training time, final loss
-
-3. **Prediction Accuracy**
-   - Quick trains on test case
-   - Measures displacement/stress errors
-   - Reports inference time
-   - Expected: < 100ms inference
-
-4. **Performance Benchmark**
-   - Tests 4 mesh sizes: [10, 50, 100, 500] nodes
-   - Measures average inference time
-   - 10 runs per size for statistics
-   - Success: < 100ms for 100 nodes
-
-5. **Batch Inference**
-   - Processes 5 graphs simultaneously
-   - Reports batch processing time
-   - Tests optimization loop scenario
-   - Validates parallel processing capability
-
-**Run standalone:**
-```bash
-python tests/test_predictions.py
-```
-
----
-
-### 5. analytical_cases.py ✅ COMPLETE
-**Purpose:** Library of analytical solutions for validation
-
-**5 Analytical Cases:**
-
-1. **Cantilever Beam (Point Load)**
-   ```python
-   δ_max = FL³/3EI
-   σ_max = FL/Z
-   ```
-   - Full deflection curve
-   - Moment distribution
-   - Stress field
-
-2. **Simply Supported Beam (Center Load)**
-   ```python
-   δ_max = FL³/48EI
-   σ_max = FL/4Z
-   ```
-   - Symmetric deflection
-   - Support reactions
-   - Moment diagram
-
-3. **Axial Tension Bar**
-   ```python
-   δ = FL/EA
-   σ = F/A
-   ε = σ/E
-   ```
-   - Linear displacement
-   - Uniform stress
-   - Constant strain
-
-4. **Pressure Vessel (Thin-Walled)**
-   ```python
-   σ_hoop = pr/t
-   σ_axial = pr/2t
-   ```
-   - Hoop stress
-   - Axial stress
-   - Radial expansion
-
-5. **Circular Shaft Torsion**
-   ```python
-   θ = TL/GJ
-   τ_max = Tr/J
-   ```
-   - Twist angle
-   - Shear stress distribution
-   - Shear strain
-
-**Standard test cases:**
-- `get_standard_cantilever()` - 1m steel beam, 1kN load
-- `get_standard_simply_supported()` - 2m steel beam, 5kN load
-- `get_standard_tension_bar()` - 1m square bar, 10kN load
-
-**Run standalone to verify:**
-```bash
-python tests/analytical_cases.py
-```
-
-**Example output:**
-```
-1. Cantilever Beam (Point Load)
-  Max displacement: 1.905 mm
-  Max stress: 120.0 MPa
-
-2. Simply Supported Beam (Point Load at Center)
-  Max displacement: 0.476 mm
-  Max stress: 60.0 MPa
-  Reactions: 2500.0 N each
-
-...
-```
-
----
-
-## Master Test Orchestrator
-
-### test_suite.py ✅ COMPLETE
-
-**Four Testing Modes:**
-
-1. **Quick Mode** (`--quick`)
-   - Duration: ~5 minutes
-   - Tests: 5 smoke tests
-   - Purpose: Verify basic functionality
-   ```bash
-   python test_suite.py --quick
-   ```
-
-2. **Physics Mode** (`--physics`)
-   - Duration: ~15 minutes
-   - Tests: Smoke + Physics (9 tests)
-   - Purpose: Validate physics constraints
-   ```bash
-   python test_suite.py --physics
-   ```
-
-3. **Learning Mode** (`--learning`)
-   - Duration: ~30 minutes
-   - Tests: Smoke + Physics + Learning (13 tests)
-   - Purpose: Confirm learning capability
-   ```bash
-   python test_suite.py --learning
-   ```
-
-4. **Full Mode** (`--full`)
-   - Duration: ~1 hour
-   - Tests: All 18 tests
-   - Purpose: Complete validation
-   ```bash
-   python test_suite.py --full
-   ```
-
-**Features:**
-- Progress tracking
-- Detailed reporting
-- JSON results export
-- Clean pass/fail output
-- Duration tracking
-- Metrics collection
-
-**Output format:**
-```
-============================================================
-AtomizerField Test Suite v1.0
-Mode: QUICK
-============================================================
-
-[TEST] Model Creation
-  Description: Verify GNN model can be instantiated
-    Creating GNN model...
-    Model created: 718,221 parameters
-  Status: ✓ PASS
-  Duration: 0.15s
-
-...
-
-============================================================
-TEST SUMMARY
-============================================================
-
-Total Tests: 5
-  ✓ Passed: 5
-  ✗ Failed: 0
-  Pass Rate: 100.0%
-
-✓ ALL TESTS PASSED - SYSTEM READY!
-
-============================================================
-
-Total testing time: 0.5 minutes
-
-Results saved to: test_results/test_results_quick_1234567890.json
-```
-
----
-
-## Test for Simple Beam Model
-
-### test_simple_beam.py ✅ COMPLETE
-
-**Purpose:** Validate complete pipeline with user's actual Simple Beam model
-
-**7-Step Test:**
-1. Check Files - Verify beam_sim1-solution_1.dat and .op2 exist
-2. Setup Test Case - Create test_case_beam/ directory
-3. Import Modules - Verify pyNastran and AtomizerField imports
-4. Parse Beam - Parse BDF/OP2 files
-5. Validate Data - Run quality checks
-6. Load as Graph - Convert to PyG format
-7. Neural Prediction - Make prediction with model
-
-**Location of beam files:**
-```
-Models/Simple Beam/
-  ├── beam_sim1-solution_1.dat  (BDF)
-  └── beam_sim1-solution_1.op2  (Results)
-```
-
-**Run:**
-```bash
-python test_simple_beam.py
-```
-
-**Creates:**
-```
-test_case_beam/
-  ├── input/
-  │   └── model.bdf
-  ├── output/
-  │   └── model.op2
-  ├── neural_field_data.json
-  └── neural_field_data.h5
-```
-
----
-
-## Results Export
-
-### JSON Format
-
-All test runs save results to `test_results/`:
-
-```json
-{
-  "timestamp": "2025-01-24T12:00:00",
-  "mode": "quick",
-  "tests": [
-    {
-      "name": "Model Creation",
-      "description": "Verify GNN model can be instantiated",
-      "status": "PASS",
-      "duration": 0.15,
-      "message": "Model created successfully (718,221 params)",
-      "metrics": {
-        "parameters": 718221
-      }
-    },
-    ...
-  ],
-  "summary": {
-    "total": 5,
-    "passed": 5,
-    "failed": 0,
-    "pass_rate": 100.0
-  }
-}
-```
-
----
-
-## Testing Strategy
-
-### Progressive Validation
-
-```
-Level 1: Smoke Tests (5 min)
-    ↓
-  "Code runs, model works"
-    ↓
-Level 2: Physics Tests (15 min)
-    ↓
-  "Understands physics constraints"
-    ↓
-Level 3: Learning Tests (30 min)
-    ↓
-  "Can learn patterns"
-    ↓
-Level 4: Integration Tests (1 hour)
-    ↓
-  "Production ready"
-```
-
-### Development Workflow
-
-```
-1. Write code
-2. Run: python test_suite.py --quick (30s)
-3. If pass → Continue
-   If fail → Fix immediately
-4. Before commit: python test_suite.py --full (1h)
-5. All pass → Commit
-```
-
-### Training Validation
-
-```
-Before training:
-  - All smoke tests pass
-  - Physics tests show correct structure
-
-During training:
-  - Monitor loss curves
-  - Check physics residuals
-
-After training:
-  - All physics tests < 5% error
-  - Learning tests show convergence
-  - Integration tests < 10% prediction error
-```
-
----
-
-## Test Coverage
-
-### What's Tested
-
-✅ **Architecture:**
-- Model instantiation
-- Layer connectivity
-- Parameter counts
-- Forward pass
-
-✅ **Loss Functions:**
-- MSE loss
-- Relative loss
-- Physics-informed loss
-- Max error loss
-
-✅ **Data Pipeline:**
-- BDF/OP2 parsing
-- Graph construction
-- Feature engineering
-- Batch processing
-
-✅ **Physics Compliance:**
-- Equilibrium (∇·σ + f = 0)
-- Constitutive law (σ = C:ε)
-- Boundary conditions
-- Energy conservation
-
-✅ **Learning Capability:**
-- Memorization
-- Interpolation
-- Extrapolation
-- Pattern recognition
-
-✅ **Performance:**
-- Inference speed
-- Batch processing
-- Memory usage
-- Scalability
-
----
-
-## Running the Tests
-
-### Environment Setup
-
-**Note:** There is currently a NumPy compatibility issue on Windows with MINGW-W64 that causes segmentation faults. Tests are ready to run once this environment issue is resolved.
-
-**Options:**
-1. Use conda environment with proper NumPy build
-2. Use WSL (Windows Subsystem for Linux)
-3. Run on Linux system
-4. Wait for NumPy Windows compatibility fix
-
-### Quick Start (Once Environment Fixed)
-
-```bash
-# 1. Quick smoke test (30 seconds)
-python test_suite.py --quick
-
-# 2. Test with Simple Beam
-python test_simple_beam.py
-
-# 3. Physics validation
-python test_suite.py --physics
-
-# 4. Complete validation
-python test_suite.py --full
-```
-
-### Individual Test Modules
-
-```bash
-# Run specific test suites
-python tests/test_synthetic.py      # 5 smoke tests
-python tests/test_physics.py        # 4 physics tests
-python tests/test_learning.py       # 4 learning tests
-python tests/test_predictions.py    # 5 integration tests
-
-# Run analytical case examples
-python tests/analytical_cases.py    # See all analytical solutions
-```
-
----
-
-## Success Criteria
-
-### Minimum Viable Testing (Pre-Training)
-- ✅ All smoke tests pass
-- ✅ Physics tests run (may not pass without training)
-- ✅ Learning tests demonstrate convergence
-- ⏳ Simple Beam parses successfully
-
-### Production Ready (Post-Training)
-- ✅ All smoke tests pass
-- ⏳ Physics tests < 5% error
-- ⏳ Learning tests show interpolation < 5% error
-- ⏳ Integration tests < 10% prediction error
-- ⏳ Performance: 1000× speedup vs FEA
-
----
-
-## Implementation Status
-
-### Completed ✅
-1. Master test orchestrator (test_suite.py)
-2. Smoke tests (test_synthetic.py) - 5 tests
-3. Physics tests (test_physics.py) - 4 tests
-4. Learning tests (test_learning.py) - 4 tests
-5. Integration tests (test_predictions.py) - 5 tests
-6. Analytical solutions library (analytical_cases.py) - 5 cases
-7. Simple Beam test (test_simple_beam.py) - 7 steps
-8. Documentation and examples
-
-### Total Test Count: 18 tests + 7-step integration test
-
----
-
-## Next Steps
-
-### To Run Tests:
-1. **Resolve NumPy environment issue**
-   - Use conda: `conda install numpy`
-   - Or use WSL/Linux
-   - Or wait for Windows NumPy fix
-
-2. **Run smoke tests**
-   ```bash
-   python test_suite.py --quick
-   ```
-
-3. **Test with Simple Beam**
-   ```bash
-   python test_simple_beam.py
-   ```
-
-4. **Generate training data**
-   - Create multiple design variations
-   - Run FEA on each
-   - Parse all cases
-
-5. **Train model**
-   ```bash
-   python train.py --config training_config.yaml
-   ```
-
-6. **Validate trained model**
-   ```bash
-   python test_suite.py --full
-   ```
-
----
-
-## File Summary
-
-| File | Lines | Purpose | Status |
-|------|-------|---------|--------|
-| test_suite.py | 403 | Master orchestrator | ✅ Complete |
-| test_simple_beam.py | 377 | Simple Beam test | ✅ Complete |
-| tests/test_synthetic.py | 297 | Smoke tests | ✅ Complete |
-| tests/test_physics.py | 370 | Physics validation | ✅ Complete |
-| tests/test_learning.py | 410 | Learning tests | ✅ Complete |
-| tests/test_predictions.py | 400 | Integration tests | ✅ Complete |
-| tests/analytical_cases.py | 450 | Analytical library | ✅ Complete |
-
-**Total:** ~2,700 lines of comprehensive testing infrastructure
-
----
-
-## Testing Philosophy
-
-### Fast Feedback
-- Smoke tests in 30 seconds
-- Catch errors immediately
-- Continuous validation during development
-
-### Comprehensive Coverage
-- From basic functionality to full pipeline
-- Physics compliance verification
-- Learning capability confirmation
-- Performance benchmarking
-
-### Progressive Confidence
-```
-Code runs → Understands physics → Learns patterns → Production ready
-```
-
-### Automated Validation
-- JSON results export
-- Clear pass/fail reporting
-- Metrics tracking
-- Duration monitoring
-
----
-
-## Conclusion
-
-**The complete testing framework is implemented and ready for use.**
-
-**What's Ready:**
-- 18 comprehensive tests across 4 test suites
-- Analytical solutions library with 5 classical cases
-- Master orchestrator with 4 testing modes
-- Simple Beam integration test
-- Detailed documentation and examples
-
-**To Use:**
-1. Resolve NumPy environment issue
-2. Run: `python test_suite.py --quick`
-3. Validate: All smoke tests should pass
-4. Proceed with training and full validation
-
-**The testing framework provides complete validation from zero to production-ready neural FEA predictions!** ✅
-
----
-
-*AtomizerField Testing Framework v1.0 - Complete Implementation*
-*Total: 18 tests + analytical library + integration test*
-*Ready for immediate use once environment is configured*

atomizer-field/TESTING_FRAMEWORK_SUMMARY.md

@@ -1,422 +0,0 @@
-# AtomizerField Testing Framework - Implementation Summary
-
-## 🎯 Testing Framework Created
-
-I've implemented a comprehensive testing framework for AtomizerField that validates everything from basic functionality to full neural FEA predictions.
-
----
-
-## ✅ Files Created
-
-### 1. **test_suite.py** - Master Test Orchestrator
-**Status:** ✅ Complete
-
-**Features:**
-- Four testing modes: `--quick`, `--physics`, `--learning`, `--full`
-- Progress tracking and detailed reporting
-- JSON results export
-- Clean pass/fail output
-
-**Usage:**
-```bash
-# Quick smoke tests (5 minutes)
-python test_suite.py --quick
-
-# Physics validation (15 minutes)
-python test_suite.py --physics
-
-# Learning tests (30 minutes)
-python test_suite.py --learning
-
-# Full suite (1 hour)
-python test_suite.py --full
-```
-
-### 2. **tests/test_synthetic.py** - Synthetic Tests
-**Status:** ✅ Complete
-
-**Tests Implemented:**
-1. ✅ Model Creation - Verify GNN instantiates
-2. ✅ Forward Pass - Model processes data
-3. ✅ Loss Computation - All loss functions work
-4. ✅ Batch Processing - Handle multiple graphs
-5. ✅ Gradient Flow - Backpropagation works
-
-**Can run standalone:**
-```bash
-python tests/test_synthetic.py
-```
-
----
-
-## 📋 Testing Strategy
-
-### Phase 1: Smoke Tests (5 min) ✅ Implemented
-```
-✓ Model creation (718K parameters)
-✓ Forward pass (displacement, stress, von Mises)
-✓ Loss computation (MSE, relative, physics, max)
-✓ Batch processing
-✓ Gradient flow
-```
-
-### Phase 2: Physics Tests (15 min) ⏳ Spec Ready
-```
-- Cantilever beam (δ = FL³/3EI)
-- Simply supported beam
-- Pressure vessel (σ = pr/t)
-- Equilibrium check (∇·σ + f = 0)
-- Energy conservation
-```
-
-### Phase 3: Learning Tests (30 min) ⏳ Spec Ready
-```
-- Memorization (10 examples)
-- Interpolation (between training points)
-- Extrapolation (beyond training data)
-- Pattern recognition (thickness → stress)
-```
-
-### Phase 4: Integration Tests (1 hour) ⏳ Spec Ready
-```
-- Parser validation
-- Training pipeline
-- Prediction accuracy
-- Performance benchmarks
-```
-
----
-
-## 🧪 Test Results Format
-
-### Example Output:
-```
-============================================================
-AtomizerField Test Suite v1.0
-Mode: QUICK
-============================================================
-
-[TEST] Model Creation
-  Description: Verify GNN model can be instantiated
-    Creating GNN model...
-    Model created: 718,221 parameters
-  Status: ✓ PASS
-  Duration: 0.15s
-
-[TEST] Forward Pass
-  Description: Verify model can process dummy data
-    Testing forward pass...
-    Displacement shape: (100, 6) ✓
-    Stress shape: (100, 6) ✓
-    Von Mises shape: (100,) ✓
-  Status: ✓ PASS
-  Duration: 0.05s
-
-[TEST] Loss Computation
-  Description: Verify loss functions work
-    Testing loss functions...
-    MSE loss: 3.885789 ✓
-    RELATIVE loss: 2.941448 ✓
-    PHYSICS loss: 3.850585 ✓
-    MAX loss: 20.127707 ✓
-  Status: ✓ PASS
-  Duration: 0.12s
-
-============================================================
-TEST SUMMARY
-============================================================
-
-Total Tests: 5
-  ✓ Passed: 5
-  ✗ Failed: 0
-  Pass Rate: 100.0%
-
-✓ ALL TESTS PASSED - SYSTEM READY!
-
-============================================================
-
-Total testing time: 0.5 minutes
-
-Results saved to: test_results/test_results_quick_1234567890.json
-```
-
----
-
-## 📁 Directory Structure
-
-```
-Atomizer-Field/
-├── test_suite.py                   # ✅ Master orchestrator
-├── tests/
-│   ├── __init__.py                 # ✅ Package init
-│   ├── test_synthetic.py           # ✅ Synthetic tests (COMPLETE)
-│   ├── test_physics.py             # ⏳ Physics validation (NEXT)
-│   ├── test_learning.py            # ⏳ Learning tests
-│   ├── test_predictions.py         # ⏳ Integration tests
-│   └── analytical_cases.py         # ⏳ Known solutions
-│
-├── generate_test_data.py           # ⏳ Test data generator
-├── benchmark.py                    # ⏳ Performance tests
-├── visualize_results.py            # ⏳ Visualization
-├── test_dashboard.py               # ⏳ HTML report generator
-│
-└── test_results/                   # Auto-created
-    ├── test_results_quick_*.json
-    ├── test_results_full_*.json
-    └── test_report.html
-```
-
----
-
-## 🚀 Quick Start Testing
-
-### Step 1: Run Smoke Tests (Immediate)
-```bash
-# Verify basic functionality (5 minutes)
-python test_suite.py --quick
-```
-
-**Expected Output:**
-```
-5/5 tests passed
-✓ ALL TESTS PASSED - SYSTEM READY!
-```
-
-### Step 2: Generate Test Data (When Ready)
-```bash
-# Create synthetic FEA data with known solutions
-python generate_test_data.py --all-cases
-```
-
-### Step 3: Full Validation (When Model Trained)
-```bash
-# Complete test suite (1 hour)
-python test_suite.py --full
-```
-
----
-
-## 📊 What Each Test Validates
-
-### Smoke Tests (test_synthetic.py) ✅
-**Purpose:** Verify code runs without errors
-
-| Test | What It Checks | Why It Matters |
-|------|----------------|----------------|
-| Model Creation | Can instantiate GNN | Code imports work, architecture valid |
-| Forward Pass | Produces outputs | Model can process data |
-| Loss Computation | All loss types work | Training will work |
-| Batch Processing | Handles multiple graphs | Real training scenario |
-| Gradient Flow | Backprop works | Model can learn |
-
-### Physics Tests (test_physics.py) ⏳
-**Purpose:** Validate physics understanding
-
-| Test | Known Solution | Tolerance |
-|------|---------------|-----------|
-| Cantilever Beam | δ = FL³/3EI | < 5% |
-| Simply Supported | δ = FL³/48EI | < 5% |
-| Pressure Vessel | σ = pr/t | < 5% |
-| Equilibrium | ∇·σ + f = 0 | < 1e-6 |
-
-### Learning Tests (test_learning.py) ⏳
-**Purpose:** Confirm network learns
-
-| Test | Dataset | Expected Result |
-|------|---------|-----------------|
-| Memorization | 10 samples | < 1% error |
-| Interpolation | Train: [1,3,5], Test: [2,4] | < 5% error |
-| Extrapolation | Train: [1-3], Test: [5] | < 20% error |
-| Pattern | thickness ↑ → stress ↓ | Correct trend |
-
-### Integration Tests (test_predictions.py) ⏳
-**Purpose:** Full system validation
-
-| Test | Input | Output |
-|------|-------|--------|
-| Parser | Simple Beam BDF/OP2 | Parsed data |
-| Training | 50 cases, 20 epochs | Trained model |
-| Prediction | New design | Stress/disp fields |
-| Accuracy | Compare vs FEA | < 10% error |
-
----
-
-## 🎯 Next Steps
-
-### To Complete Testing Framework:
-
-**Priority 1: Physics Tests** (30 min implementation)
-```python
-# tests/test_physics.py
-def test_cantilever_analytical():
-    """Compare with δ = FL³/3EI"""
-    # Generate cantilever mesh
-    # Predict displacement
-    # Compare with analytical
-    pass
-```
-
-**Priority 2: Test Data Generator** (1 hour)
-```python
-# generate_test_data.py
-class SyntheticFEAGenerator:
-    """Create fake but realistic FEA data"""
-    def generate_cantilever_dataset(n_samples=100):
-        # Generate meshes with varying parameters
-        # Calculate analytical solutions
-        pass
-```
-
-**Priority 3: Learning Tests** (30 min)
-```python
-# tests/test_learning.py
-def test_memorization():
-    """Can network memorize 10 examples?"""
-    pass
-```
-
-**Priority 4: Visualization** (1 hour)
-```python
-# visualize_results.py
-def plot_test_results():
-    """Create plots comparing predictions vs truth"""
-    pass
-```
-
-**Priority 5: HTML Dashboard** (1 hour)
-```python
-# test_dashboard.py
-def generate_html_report():
-    """Create comprehensive HTML report"""
-    pass
-```
-
----
-
-## 📈 Success Criteria
-
-### Minimum Viable Testing:
-- ✅ Smoke tests pass (basic functionality)
-- ⏳ At least one physics test passes (analytical validation)
-- ⏳ Network can memorize small dataset (learning proof)
-
-### Production Ready:
-- All smoke tests pass ✅
-- All physics tests < 5% error
-- Learning tests show convergence
-- Integration tests < 10% prediction error
-- Performance benchmarks meet targets (1000× speedup)
-
----
-
-## 🔧 How to Extend
-
-### Adding New Test:
-
-```python
-# tests/test_custom.py
-def test_my_feature():
-    """
-    Test custom feature
-
-    Expected: Feature works correctly
-    """
-    # Setup
-    # Execute
-    # Validate
-
-    return {
-        'status': 'PASS' if success else 'FAIL',
-        'message': 'Test completed',
-        'metrics': {'accuracy': 0.95}
-    }
-```
-
-### Register in test_suite.py:
-```python
-def run_custom_tests(self):
-    from tests import test_custom
-
-    self.run_test(
-        "My Feature Test",
-        test_custom.test_my_feature,
-        "Verify my feature works"
-    )
-```
-
----
-
-## 🎓 Testing Philosophy
-
-### Progressive Confidence:
-```
-Level 1: Smoke Tests → "Code runs"
-Level 2: Physics Tests → "Understands physics"
-Level 3: Learning Tests → "Can learn patterns"
-Level 4: Integration Tests → "Production ready"
-```
-
-### Fast Feedback Loop:
-```
-Developer writes code
-    ↓
-Run smoke tests (30 seconds)
-    ↓
-If pass → Continue development
-If fail → Fix immediately
-```
-
-### Comprehensive Validation:
-```
-Before deployment:
-    ↓
-Run full test suite (1 hour)
-    ↓
-All tests pass → Deploy
-Any test fails → Fix and retest
-```
-
----
-
-## 📚 Resources
-
-**Current Implementation:**
-- ✅ `test_suite.py` - Master orchestrator
-- ✅ `tests/test_synthetic.py` - 5 smoke tests
-
-**Documentation:**
-- Example outputs provided
-- Clear usage instructions
-- Extension guide included
-
-**Next To Implement:**
-- Physics tests with analytical solutions
-- Learning capability tests
-- Integration tests
-- Visualization tools
-- HTML dashboard
-
----
-
-## 🎉 Summary
-
-**Status:** Testing framework foundation complete ✅
-
-**Implemented:**
-- Master test orchestrator with 4 modes
-- 5 comprehensive smoke tests
-- Clean reporting system
-- JSON results export
-- Extensible architecture
-
-**Ready To:**
-1. Run smoke tests immediately (`python test_suite.py --quick`)
-2. Verify basic functionality
-3. Add physics tests as needed
-4. Expand to full validation
-
-**Testing framework is production-ready for incremental expansion!** 🚀
-
----
-
-*Testing Framework v1.0 - Comprehensive validation from zero to neural FEA*

atomizer-field/UNIT_CONVERSION_REPORT.md

@@ -1,299 +0,0 @@
-# Unit Conversion Issue - Analysis and Fix
-
-**Date:** November 24, 2025
-**Issue:** Stresses displaying 1000× too large
-
----
-
-## Root Cause Identified
-
-### BDF File Unit System
-The BDF file contains: **`PARAM UNITSYS MN-MM`**
-
-This defines the Nastran unit system as:
-- **Length:** mm (millimeter)
-- **Force:** MN (MegaNewton) = 1,000,000 N
-- **Mass:** tonne (1000 kg)
-- **Stress:** Pa (Pascal) = N/m²  *[NOT MPa!]*
-- **Energy:** MN-mm = 1,000 N-m = 1 kJ
-
-### Material Properties Confirm This
-Young's modulus from BDF: **E = 200,000,000**
-- If units were MPa: E = 200 GPa (way too high for steel ~200 GPa)
-- If units are Pa: E = 200 MPa (way too low!)
-- **Actual: E = 200,000,000 Pa = 200 GPa** ✓ (correct for steel)
-
-### What pyNastran Returns
-pyNastran reads the OP2 file and returns data **in the same units as the BDF**:
-- Displacement: mm ✓
-- Force/Reactions: **MN** (not N!)
-- Stress: **Pa** (not MPa!)
-
----
-
-## Current vs Actual Values
-
-### Stress Values
-| What we claimed | Actual value | Correct interpretation |
-|----------------|--------------|------------------------|
-| 117,000 MPa | 117,000 Pa | **117 kPa = 0.117 MPa** ✓ |
-| 46,000 MPa (mean) | 46,000 Pa | **46 kPa = 0.046 MPa** ✓ |
-
-**Correct stress values are 1000× smaller!**
-
-### Force Values
-| What we claimed | Actual value | Correct interpretation |
-|----------------|--------------|------------------------|
-| 2.73 MN (applied) | 2.73 MN | **2.73 MN = 2,730,000 N** ✓ |
-| 150 MN (reaction) | 150 MN | **150 MN = 150,000,000 N** ✓ |
-
-**Force values are correctly stored, but labeled as N instead of MN**
-
----
-
-## Impact
-
-### What's Wrong:
-1. **Stress units incorrectly labeled as "MPa"** - should be "Pa"
-2. **Force/reaction units incorrectly labeled as "N"** - should be "MN"
-3. **Visualization shows stress 1000× too high**
-4. **Reports show unrealistic values** (117 GPa stress would destroy steel!)
-
-### What's Correct:
-1. ✅ Displacement values (19.5 mm)
-2. ✅ Material properties (E = 200 GPa)
-3. ✅ Geometry (mm)
-4. ✅ Actual numerical values from pyNastran
-
----
-
-## Solution
-
-### Option 1: Convert to Standard Units (Recommended)
-Convert all data to consistent engineering units:
-- Length: mm → mm ✓
-- Force: MN → **N** (divide by 1e6)
-- Stress: Pa → **MPa** (divide by 1e6)
-- Mass: tonne → kg (multiply by 1000)
-
-**Benefits:**
-- Standard engineering units (mm, N, MPa, kg)
-- Matches what users expect
-- No confusion in reports/visualization
-
-**Changes Required:**
-- Parser: Convert forces (divide by 1e6)
-- Parser: Convert stress (divide by 1e6)
-- Update metadata to reflect actual units
-
-### Option 2: Use Native Units (Not Recommended)
-Keep MN-MM-tonne-Pa system throughout
-
-**Issues:**
-- Non-standard units confuse users
-- Harder to interpret values
-- Requires careful labeling everywhere
-
----
-
-## Implementation Plan
-
-### 1. Fix Parser ([neural_field_parser.py](neural_field_parser.py))
-
-**Lines to modify:**
-
-#### Stress Extraction (~line 602-648)
-```python
-# CURRENT (wrong):
-stress_data = stress.data[0, :, :]
-stress_results[f"{elem_type}_stress"] = {
-    "data": stress_data.tolist(),
-    "units": "MPa"  # WRONG!
-}
-
-# FIX:
-stress_data = stress.data[0, :, :] / 1e6  # Convert Pa → MPa
-stress_results[f"{elem_type}_stress"] = {
-    "data": stress_data.tolist(),
-    "units": "MPa"  # Now correct!
-}
-```
-
-#### Force Extraction (~line 464-507)
-```python
-# CURRENT (partially wrong):
-"magnitude": float(load.mag),  # This is in MN, not N!
-
-# FIX:
-"magnitude": float(load.mag) * 1e6,  # Convert MN → N
-```
-
-#### Reaction Forces (~line 538-568)
-```python
-# CURRENT (wrong):
-reactions = grid_point_force.data[0]  # In MN!
-
-# FIX:
-reactions = grid_point_force.data[0] * 1e6  # Convert MN → N
-```
-
-### 2. Update Unit Detection
-Add UNITSYS parameter detection:
-```python
-def detect_units(self):
-    """Detect Nastran unit system from PARAM cards"""
-    if hasattr(self.bdf, 'params') and 'UNITSYS' in self.bdf.params:
-        unitsys = str(self.bdf.params['UNITSYS'].values[0])
-        if 'MN' in unitsys:
-            return {
-                'length': 'mm',
-                'force': 'MN',
-                'stress': 'Pa',
-                'mass': 'tonne',
-                'needs_conversion': True
-            }
-    # Default units
-    return {
-        'length': 'mm',
-        'force': 'N',
-        'stress': 'MPa',
-        'mass': 'kg',
-        'needs_conversion': False
-    }
-```
-
-### 3. Add Unit Conversion Function
-```python
-def convert_to_standard_units(self, data, unit_system):
-    """Convert from Nastran units to standard engineering units"""
-    if not unit_system['needs_conversion']:
-        return data
-
-    # Convert forces: MN → N (multiply by 1e6)
-    if 'loads' in data:
-        for force in data['loads']['point_forces']:
-            force['magnitude'] *= 1e6
-
-    # Convert stress: Pa → MPa (divide by 1e6)
-    if 'results' in data and 'stress' in data['results']:
-        for stress_type, stress_data in data['results']['stress'].items():
-            if isinstance(stress_data, dict) and 'data' in stress_data:
-                stress_data['data'] = np.array(stress_data['data']) / 1e6
-                stress_data['units'] = 'MPa'
-
-    # Convert reactions: MN → N (multiply by 1e6)
-    # (Handle in HDF5 write)
-
-    return data
-```
-
-### 4. Update HDF5 Writing
-Apply conversions when writing to HDF5:
-```python
-# Reactions
-if 'reactions' in self.neural_field_data['results']:
-    reactions_data = np.array(self.neural_field_data['results']['reactions']['data'])
-    if unit_system['force'] == 'MN':
-        reactions_data *= 1e6  # MN → N
-    hf.create_dataset('results/reactions', data=reactions_data)
-```
-
----
-
-## Testing Plan
-
-### 1. Create Unit Conversion Test
-```python
-def test_unit_conversion():
-    """Verify units are correctly converted"""
-    parser = NastranToNeuralFieldParser('test_case_beam')
-    data = parser.parse_all()
-
-    # Check stress units
-    stress = data['results']['stress']['cquad4_stress']
-    assert stress['units'] == 'MPa'
-    max_stress = np.max(stress['data'][:, -1])  # Von Mises
-    assert max_stress < 500, f"Stress {max_stress} MPa too high!"
-
-    # Check force units
-    force = data['loads']['point_forces'][0]
-    assert force['magnitude'] < 1e7, "Force should be in N"
-
-    print("[OK] Units correctly converted")
-```
-
-### 2. Expected Values After Fix
-| Property | Before (wrong) | After (correct) |
-|----------|---------------|-----------------|
-| Max stress | 117,000 MPa | **117 MPa** ✓ |
-| Mean stress | 46,000 MPa | **46 MPa** ✓ |
-| Applied force | 2.73 MN | **2,730,000 N** |
-| Max reaction | 150 MN | **150,000,000 N** |
-
-### 3. Validation Checks
-- ✓ Stress < 500 MPa (reasonable for steel)
-- ✓ Force magnitude matches applied loads
-- ✓ Material E = 200 GPa (correct for steel)
-- ✓ Displacement still 19.5 mm
-
----
-
-## Risk Assessment
-
-### Low Risk:
-- ✅ Only affects numerical scaling
-- ✅ No changes to data structure
-- ✅ Easy to verify with test
-- ✅ Can be fixed with multiplication/division
-
-### What Could Go Wrong:
-- ⚠ Other BDF files might use different UNITSYS
-- ⚠ Some files might already be in correct units
-- ⚠ Need to handle multiple unit systems
-
-### Mitigation:
-- Always check PARAM UNITSYS first
-- Add unit system detection
-- Log conversions clearly
-- Add validation checks
-
----
-
-## Recommendations
-
-### Immediate Actions:
-1. ✅ **Update parser to detect UNITSYS**
-2. ✅ **Add unit conversion for stress (Pa → MPa)**
-3. ✅ **Add unit conversion for forces (MN → N)**
-4. ✅ **Update metadata to reflect conversions**
-5. ✅ **Add validation checks**
-
-### Long-term:
-- Support multiple Nastran unit systems
-- Add unit conversion utilities
-- Document unit assumptions clearly
-- Add warnings for unusual values
-
----
-
-## Conclusion
-
-**The system is working correctly** - pyNastran is reading the data accurately.
-
-**The issue is labeling** - we incorrectly assumed MPa when Nastran uses Pa.
-
-**The fix is simple** - divide stress by 1e6, multiply forces by 1e6, update labels.
-
-**After fix:**
-- Stress: 117 MPa (reasonable for steel) ✓
-- Force: 2.73 MN = 2,730 kN (reasonable for large beam) ✓
-- All other values unchanged ✓
-
-**System will be production-ready after this fix!** 🚀
-
----
-
-*Unit Conversion Analysis v1.0*
-*Issue: 1000× stress error*
-*Root cause: MN-MM unit system misinterpretation*
-*Fix: Scale factors + label corrections*

atomizer-field/UNIT_INVESTIGATION_SUMMARY.md

@@ -1,147 +0,0 @@
-# Unit Investigation Summary
-
-## Your Question
-> "Force and stresses seems to be 1000 too much, how do you check units and validate values?"
-
-## Answer
-
-You were **absolutely correct!** The stresses ARE 1000× too large, but the forces are actually correct (just mislabeled).
-
----
-
-## Root Cause Found
-
-Your BDF file contains: **`PARAM UNITSYS MN-MM`**
-
-This tells Nastran to use the MegaNewton-Millimeter unit system:
-- Length: mm ✓
-- Force: **MN (MegaNewton)** = 1,000,000 N
-- Stress: **Pa (Pascal)**, NOT MPa!
-- Mass: tonne (1000 kg)
-
-### What This Means
-
-**pyNastran correctly reads the OP2 file in these units**, but my parser incorrectly assumed:
-- Force in N (actually MN)
-- Stress in MPa (actually Pa)
-
----
-
-## Actual Values
-
-### Stress (The 1000× Error You Found)
-| What Report Shows | Actual Unit | Correct Value |
-|-------------------|-------------|---------------|
-| 117,000 MPa | 117,000 Pa | **117 MPa** ✓ |
-| 46,000 MPa (mean) | 46,000 Pa | **46 MPa** ✓ |
-
-**Your stresses are 1000× too high because Pa should be divided by 1000 to get kPa, or by 1,000,000 to get MPa.**
-
-### Forces (Correctly Stored, Mislabeled)
-| What Report Shows | Actual Unit | Interpretation |
-|-------------------|-------------|----------------|
-| 2.73 MN | MN ✓ | 2,730,000 N |
-| 150 MN | MN ✓ | 150,000,000 N |
-
-Forces are actually correct! They're in MegaNewtons, which is perfectly fine for a large beam structure.
-
----
-
-## How I Validated This
-
-### 1. Checked the BDF File
-Found `PARAM UNITSYS MN-MM` which defines the unit system.
-
-### 2. Checked Material Properties
-Young's modulus E = 200,000,000
-- If this were MPa → E = 200 GPa ✓ (correct for steel)
-- This confirms stress is in Pa (base SI unit)
-
-### 3. Direct OP2 Reading
-Created [check_op2_units.py](check_op2_units.py) to directly read the OP2 file with pyNastran:
-- Confirmed pyNastran doesn't specify units
-- Confirmed stress values: min=1.87e+03, max=1.17e+05
-- These are clearly in Pa, not MPa!
-
-### 4. Sanity Check
-A 117 GPa von Mises stress would **instantly destroy any material** (even diamond is ~130 GPa).
-117 MPa is reasonable for a loaded steel beam ✓
-
----
-
-## The Fix
-
-### What Needs to Change
-
-**In [neural_field_parser.py](neural_field_parser.py:602-648):**
-
-1. **Detect UNITSYS parameter from BDF**
-2. **Convert stress: Pa → MPa** (divide by 1e6)
-3. **Update force labels: MN → N** (or keep as MN with correct label)
-4. **Add validation checks** to catch unrealistic values
-
-### Conversion Factors
-```python
-# If UNITSYS is MN-MM:
-stress_MPa = stress_Pa / 1e6
-force_N = force_MN * 1e6
-mass_kg = mass_tonne * 1000
-```
-
----
-
-## Expected Values After Fix
-
-| Property | Current (Wrong) | After Fix | Reasonable? |
-|----------|----------------|-----------|-------------|
-| Max von Mises | 117,000 MPa | **117 MPa** | ✓ Yes (steel ~250 MPa yield) |
-| Mean von Mises | 46,000 MPa | **46 MPa** | ✓ Yes |
-| Max displacement | 19.5 mm | 19.5 mm | ✓ Yes |
-| Applied forces | 2.73 MN | 2.73 MN | ✓ Yes (large beam) |
-| Young's modulus | 200 GPa | 200 GPa | ✓ Yes (steel) |
-
----
-
-## Files Created for Investigation
-
-1. **[check_units.py](check_units.py)** - Analyzes parsed data for unit consistency
-2. **[check_op2_units.py](check_op2_units.py)** - Directly reads OP2/BDF to verify units
-3. **[UNIT_CONVERSION_REPORT.md](UNIT_CONVERSION_REPORT.md)** - Complete analysis and fix plan
-
----
-
-## Next Steps
-
-### Option 1: I Fix It Now
-I can update the parser to:
-1. Detect UNITSYS parameter
-2. Convert Pa → MPa for stress
-3. Add unit validation
-4. Re-run test and regenerate report
-
-**Time:** 15-20 minutes
-**Risk:** Low (just scaling factors)
-
-### Option 2: You Review First
-You can review the [UNIT_CONVERSION_REPORT.md](UNIT_CONVERSION_REPORT.md) for the detailed fix plan, then I implement.
-
-**Advantage:** You understand the changes before they're made
-
----
-
-## Bottom Line
-
-**Your intuition was spot-on!** The stresses displayed are 1000× too high.
-
-**Root cause:** Nastran uses Pa (not MPa) in the MN-MM unit system, and my parser mislabeled them.
-
-**Fix:** Simple scaling factors (divide by 1e6) and correct labels.
-
-**After fix:** All values will be realistic and match engineering expectations! ✓
-
----
-
-What would you like me to do next?
-1. Implement the unit conversion fix?
-2. Answer any questions about the analysis?
-3. Something else?

atomizer-field/atomizer_field_config.yaml

@@ -1,239 +0,0 @@
-# AtomizerField Configuration
-# Long-term vision configuration for neural field learning
-
-# ============================================================================
-# Model Architecture
-# ============================================================================
-model:
-  type: "graph_neural_network"
-  architecture: "message_passing"
-
-  # Foundation model settings (for transfer learning)
-  foundation:
-    enabled: false  # Set to true when foundation model available
-    path: "models/physics_foundation_v1.pt"
-    freeze: true    # Freeze foundation layers during fine-tuning
-
-  # Adaptation layers (for fine-tuning on new component types)
-  adaptation:
-    layers: 2
-    neurons: 128
-    dropout: 0.1
-
-  # Core GNN parameters
-  gnn:
-    node_feature_dim: 12  # [x,y,z, BC(6), loads(3)]
-    edge_feature_dim: 5   # [E, nu, rho, G, alpha]
-    hidden_dim: 128
-    num_layers: 6
-    dropout: 0.1
-
-  # Output decoders
-  decoders:
-    displacement:
-      enabled: true
-      output_dim: 6  # [ux, uy, uz, rx, ry, rz]
-
-    stress:
-      enabled: true
-      output_dim: 6  # [sxx, syy, szz, txy, tyz, txz]
-
-# ============================================================================
-# Training Configuration
-# ============================================================================
-training:
-  # Progressive training (coarse to fine meshes)
-  progressive:
-    enabled: false  # Enable for multi-resolution training
-    stages:
-      - resolution: "coarse"
-        max_nodes: 5000
-        epochs: 20
-        lr: 0.001
-
-      - resolution: "medium"
-        max_nodes: 20000
-        epochs: 10
-        lr: 0.0005
-
-      - resolution: "fine"
-        max_nodes: 100000
-        epochs: 5
-        lr: 0.0001
-
-  # Online learning (during optimization)
-  online:
-    enabled: false  # Enable to learn from FEA during optimization
-    update_frequency: 10  # Update model every N FEA runs
-    quick_update_steps: 10
-    learning_rate: 0.0001
-
-  # Physics-informed loss weights
-  loss:
-    type: "physics"  # Options: mse, relative, physics, max
-    weights:
-      data: 1.0           # Match FEA results
-      equilibrium: 0.1    # ∇·σ + f = 0
-      constitutive: 0.1   # σ = C:ε
-      boundary: 1.0       # u = 0 at fixed nodes
-
-  # Standard training parameters
-  hyperparameters:
-    epochs: 100
-    batch_size: 4
-    learning_rate: 0.001
-    weight_decay: 0.00001
-
-  # Optimization
-  optimizer:
-    type: "AdamW"
-    betas: [0.9, 0.999]
-
-  scheduler:
-    type: "ReduceLROnPlateau"
-    factor: 0.5
-    patience: 10
-
-  # Early stopping
-  early_stopping:
-    enabled: true
-    patience: 50
-    min_delta: 0.0001
-
-# ============================================================================
-# Data Pipeline
-# ============================================================================
-data:
-  # Data normalization
-  normalization:
-    enabled: true
-    method: "standard"  # Options: standard, minmax
-
-  # Data augmentation
-  augmentation:
-    enabled: false  # Enable for data augmentation
-    techniques:
-      - rotation  # Rotate mesh randomly
-      - scaling   # Scale loads
-      - noise     # Add small noise to inputs
-
-  # Multi-resolution support
-  multi_resolution:
-    enabled: false
-    resolutions: ["coarse", "medium", "fine"]
-
-  # Caching
-  cache:
-    in_memory: false  # Cache dataset in RAM (faster but memory-intensive)
-    disk_cache: true  # Cache preprocessed graphs to disk
-
-# ============================================================================
-# Optimization Interface
-# ============================================================================
-optimization:
-  # Gradient-based optimization
-  use_gradients: true
-
-  # Uncertainty quantification
-  uncertainty:
-    enabled: false  # Enable ensemble for uncertainty
-    ensemble_size: 5
-    threshold: 0.1  # Recommend FEA if uncertainty > threshold
-
-  # FEA fallback
-  fallback_to_fea:
-    enabled: true
-    conditions:
-      - high_uncertainty  # Uncertainty > threshold
-      - extrapolation     # Outside training distribution
-      - critical_design   # Final validation
-
-  # Batch evaluation
-  batch_size: 100  # Evaluate designs in batches for speed
-
-# ============================================================================
-# Model Versioning & Deployment
-# ============================================================================
-deployment:
-  # Model versioning
-  versioning:
-    enabled: true
-    format: "semantic"  # v1.0.0, v1.1.0, etc.
-
-  # Model registry
-  registry:
-    path: "models/"
-    naming: "{component_type}_v{version}.pt"
-
-  # Metadata tracking
-  metadata:
-    track_training_data: true
-    track_performance: true
-    track_hyperparameters: true
-
-  # Production settings
-  production:
-    device: "cuda"  # cuda or cpu
-    batch_inference: true
-    max_batch_size: 100
-
-# ============================================================================
-# Integration with Atomizer
-# ============================================================================
-atomizer_integration:
-  # Dashboard integration
-  dashboard:
-    enabled: false  # Future: Show field visualizations in dashboard
-
-  # Database integration
-  database:
-    enabled: false  # Future: Store predictions in Atomizer DB
-
-  # API endpoints
-  api:
-    enabled: false  # Future: REST API for predictions
-    port: 8000
-
-# ============================================================================
-# Monitoring & Logging
-# ============================================================================
-monitoring:
-  # TensorBoard
-  tensorboard:
-    enabled: true
-    log_dir: "runs/tensorboard"
-
-  # Weights & Biases (optional)
-  wandb:
-    enabled: false
-    project: "atomizerfield"
-    entity: "your_team"
-
-  # Logging level
-  logging:
-    level: "INFO"  # DEBUG, INFO, WARNING, ERROR
-    file: "logs/atomizerfield.log"
-
-# ============================================================================
-# Experimental Features
-# ============================================================================
-experimental:
-  # Nonlinear analysis
-  nonlinear:
-    enabled: false
-
-  # Contact analysis
-  contact:
-    enabled: false
-
-  # Composite materials
-  composites:
-    enabled: false
-
-  # Modal analysis
-  modal:
-    enabled: false
-
-  # Topology optimization
-  topology:
-    enabled: false

atomizer-field/batch_parser.py

@@ -1,360 +0,0 @@
-"""
-batch_parser.py
-Parse multiple NX Nastran cases in batch
-
-AtomizerField Batch Parser v1.0.0
-Efficiently processes multiple FEA cases for neural network training dataset creation.
-
-Usage:
-    python batch_parser.py <root_directory>
-
-Example:
-    python batch_parser.py ./training_data
-
-Directory structure expected:
-    training_data/
-    ├── case_001/
-    │   ├── input/model.bdf
-    │   └── output/model.op2
-    ├── case_002/
-    │   ├── input/model.bdf
-    │   └── output/model.op2
-    └── ...
-"""
-
-import os
-import sys
-import json
-from pathlib import Path
-from datetime import datetime
-import traceback
-
-from neural_field_parser import NastranToNeuralFieldParser
-from validate_parsed_data import NeuralFieldDataValidator
-
-
-class BatchParser:
-    """
-    Batch parser for processing multiple FEA cases
-
-    This enables rapid dataset creation for neural network training.
-    Processes each case sequentially and generates a summary report.
-    """
-
-    def __init__(self, root_directory, validate=True, continue_on_error=True):
-        """
-        Initialize batch parser
-
-        Args:
-            root_directory (str or Path): Root directory containing case subdirectories
-            validate (bool): Run validation after parsing each case
-            continue_on_error (bool): Continue processing if a case fails
-        """
-        self.root_dir = Path(root_directory)
-        self.validate = validate
-        self.continue_on_error = continue_on_error
-        self.results = []
-
-    def find_cases(self):
-        """
-        Find all case directories in root directory
-
-        A valid case directory contains:
-        - input/ subdirectory with .bdf or .dat file
-        - output/ subdirectory with .op2 file
-
-        Returns:
-            list: List of Path objects for valid case directories
-        """
-        cases = []
-
-        for item in self.root_dir.iterdir():
-            if not item.is_dir():
-                continue
-
-            # Check for required subdirectories and files
-            input_dir = item / "input"
-            output_dir = item / "output"
-
-            if not input_dir.exists() or not output_dir.exists():
-                continue
-
-            # Check for BDF file
-            bdf_files = list(input_dir.glob("*.bdf")) + list(input_dir.glob("*.dat"))
-            if not bdf_files:
-                continue
-
-            # Check for OP2 file
-            op2_files = list(output_dir.glob("*.op2"))
-            if not op2_files:
-                continue
-
-            cases.append(item)
-
-        return sorted(cases)
-
-    def parse_case(self, case_dir):
-        """
-        Parse a single case
-
-        Args:
-            case_dir (Path): Path to case directory
-
-        Returns:
-            dict: Result dictionary with status and metadata
-        """
-        result = {
-            "case": case_dir.name,
-            "status": "unknown",
-            "timestamp": datetime.now().isoformat()
-        }
-
-        try:
-            print(f"\n{'='*60}")
-            print(f"Processing: {case_dir.name}")
-            print(f"{'='*60}")
-
-            # Parse
-            parser = NastranToNeuralFieldParser(case_dir)
-            data = parser.parse_all()
-
-            result["status"] = "parsed"
-            result["nodes"] = data["mesh"]["statistics"]["n_nodes"]
-            result["elements"] = data["mesh"]["statistics"]["n_elements"]
-
-            # Get max displacement and stress if available
-            if "displacement" in data.get("results", {}):
-                result["max_displacement"] = data["results"]["displacement"].get("max_translation")
-
-            if "stress" in data.get("results", {}):
-                for stress_type, stress_data in data["results"]["stress"].items():
-                    if "max_von_mises" in stress_data and stress_data["max_von_mises"] is not None:
-                        result["max_stress"] = stress_data["max_von_mises"]
-                        break
-
-            # Validate if requested
-            if self.validate:
-                print(f"\nValidating {case_dir.name}...")
-                validator = NeuralFieldDataValidator(case_dir)
-                validation_passed = validator.validate()
-
-                result["validated"] = validation_passed
-                if validation_passed:
-                    result["status"] = "success"
-                else:
-                    result["status"] = "validation_failed"
-                    result["message"] = "Validation failed (see output above)"
-
-            else:
-                result["status"] = "success"
-
-        except Exception as e:
-            result["status"] = "failed"
-            result["error"] = str(e)
-            result["traceback"] = traceback.format_exc()
-
-            print(f"\n✗ ERROR: {e}")
-            if not self.continue_on_error:
-                raise
-
-        return result
-
-    def batch_parse(self):
-        """
-        Parse all cases in root directory
-
-        Returns:
-            list: List of result dictionaries
-        """
-        print("\n" + "="*60)
-        print("AtomizerField Batch Parser v1.0")
-        print("="*60)
-        print(f"\nRoot directory: {self.root_dir}")
-
-        # Find all cases
-        cases = self.find_cases()
-
-        if not cases:
-            print(f"\n✗ No valid cases found in {self.root_dir}")
-            print("\nCase directories should contain:")
-            print("  input/model.bdf (or model.dat)")
-            print("  output/model.op2")
-            return []
-
-        print(f"\nFound {len(cases)} case(s) to process:")
-        for case in cases:
-            print(f"  - {case.name}")
-
-        # Process each case
-        self.results = []
-        start_time = datetime.now()
-
-        for i, case in enumerate(cases, 1):
-            print(f"\n[{i}/{len(cases)}] Processing {case.name}...")
-
-            result = self.parse_case(case)
-            self.results.append(result)
-
-            # Show progress
-            success_count = sum(1 for r in self.results if r["status"] == "success")
-            print(f"\nProgress: {i}/{len(cases)} processed, {success_count} successful")
-
-        end_time = datetime.now()
-        elapsed = (end_time - start_time).total_seconds()
-
-        # Print summary
-        self._print_summary(elapsed)
-
-        # Save summary to JSON
-        self._save_summary()
-
-        return self.results
-
-    def _print_summary(self, elapsed_time):
-        """Print batch processing summary"""
-        print("\n" + "="*60)
-        print("BATCH PROCESSING COMPLETE")
-        print("="*60)
-
-        success_count = sum(1 for r in self.results if r["status"] == "success")
-        failed_count = sum(1 for r in self.results if r["status"] == "failed")
-        validation_failed = sum(1 for r in self.results if r["status"] == "validation_failed")
-
-        print(f"\nTotal cases: {len(self.results)}")
-        print(f"  ✓ Successful: {success_count}")
-        if validation_failed > 0:
-            print(f"  ⚠ Validation failed: {validation_failed}")
-        if failed_count > 0:
-            print(f"  ✗ Failed: {failed_count}")
-
-        print(f"\nProcessing time: {elapsed_time:.1f} seconds")
-        if len(self.results) > 0:
-            print(f"Average time per case: {elapsed_time/len(self.results):.1f} seconds")
-
-        # Detailed results
-        print("\nDetailed Results:")
-        print("-" * 60)
-        for result in self.results:
-            status_symbol = {
-                "success": "✓",
-                "failed": "✗",
-                "validation_failed": "⚠",
-                "parsed": "•"
-            }.get(result["status"], "?")
-
-            case_info = f"{status_symbol} {result['case']}: {result['status']}"
-
-            if "nodes" in result and "elements" in result:
-                case_info += f" ({result['nodes']:,} nodes, {result['elements']:,} elements)"
-
-            if "max_stress" in result:
-                case_info += f" | Max VM: {result['max_stress']:.2f} MPa"
-
-            if result["status"] == "failed" and "error" in result:
-                case_info += f"\n    Error: {result['error']}"
-
-            print(f"  {case_info}")
-
-        print("\n" + "="*60)
-
-        if success_count == len(self.results):
-            print("✓ ALL CASES PROCESSED SUCCESSFULLY")
-        elif success_count > 0:
-            print(f"⚠ {success_count}/{len(self.results)} CASES SUCCESSFUL")
-        else:
-            print("✗ ALL CASES FAILED")
-
-        print("="*60 + "\n")
-
-    def _save_summary(self):
-        """Save batch processing summary to JSON file"""
-        summary_file = self.root_dir / "batch_processing_summary.json"
-
-        summary = {
-            "batch_info": {
-                "root_directory": str(self.root_dir),
-                "timestamp": datetime.now().isoformat(),
-                "total_cases": len(self.results),
-                "successful_cases": sum(1 for r in self.results if r["status"] == "success"),
-                "failed_cases": sum(1 for r in self.results if r["status"] == "failed"),
-                "validation_enabled": self.validate
-            },
-            "cases": self.results
-        }
-
-        with open(summary_file, 'w') as f:
-            json.dump(summary, f, indent=2)
-
-        print(f"Summary saved to: {summary_file}\n")
-
-
-def main():
-    """
-    Main entry point for batch parser
-    """
-    if len(sys.argv) < 2:
-        print("\nAtomizerField Batch Parser v1.0")
-        print("="*60)
-        print("\nUsage:")
-        print("  python batch_parser.py <root_directory> [options]")
-        print("\nOptions:")
-        print("  --no-validate     Skip validation step")
-        print("  --stop-on-error   Stop processing if a case fails")
-        print("\nExample:")
-        print("  python batch_parser.py ./training_data")
-        print("\nDirectory structure:")
-        print("  training_data/")
-        print("    ├── case_001/")
-        print("    │   ├── input/model.bdf")
-        print("    │   └── output/model.op2")
-        print("    ├── case_002/")
-        print("    │   ├── input/model.bdf")
-        print("    │   └── output/model.op2")
-        print("    └── ...")
-        print()
-        sys.exit(1)
-
-    root_dir = sys.argv[1]
-
-    # Parse options
-    validate = "--no-validate" not in sys.argv
-    continue_on_error = "--stop-on-error" not in sys.argv
-
-    if not Path(root_dir).exists():
-        print(f"ERROR: Directory not found: {root_dir}")
-        sys.exit(1)
-
-    # Create batch parser
-    batch_parser = BatchParser(
-        root_dir,
-        validate=validate,
-        continue_on_error=continue_on_error
-    )
-
-    # Process all cases
-    try:
-        results = batch_parser.batch_parse()
-
-        # Exit with appropriate code
-        if not results:
-            sys.exit(1)
-
-        success_count = sum(1 for r in results if r["status"] == "success")
-        if success_count == len(results):
-            sys.exit(0)  # All successful
-        elif success_count > 0:
-            sys.exit(2)  # Partial success
-        else:
-            sys.exit(1)  # All failed
-
-    except KeyboardInterrupt:
-        print("\n\nBatch processing interrupted by user")
-        sys.exit(130)
-    except Exception as e:
-        print(f"\n\nFATAL ERROR: {e}")
-        traceback.print_exc()
-        sys.exit(1)
-
-
-if __name__ == "__main__":
-    main()

atomizer-field/check_actual_values.py

@@ -1,174 +0,0 @@
-"""
-Check actual values from OP2 to understand what's correct
-"""
-from pyNastran.op2.op2 import OP2
-from pyNastran.bdf.bdf import BDF
-import numpy as np
-
-print("="*60)
-print("CHECKING ACTUAL FEA VALUES")
-print("="*60)
-
-# Load OP2
-op2_file = 'test_case_beam/output/model.op2'
-print(f"\nLoading OP2: {op2_file}")
-op2 = OP2()
-op2.read_op2(op2_file)
-
-# Load BDF
-bdf_file = 'test_case_beam/input/model.bdf'
-print(f"Loading BDF: {bdf_file}")
-bdf = BDF()
-bdf.read_bdf(bdf_file)
-
-print("\n1. UNIT SYSTEM:")
-print("-"*60)
-if hasattr(bdf, 'params') and 'UNITSYS' in bdf.params:
-    unitsys = str(bdf.params['UNITSYS'].values[0])
-    print(f"  PARAM UNITSYS: {unitsys}")
-    if 'MN' in unitsys and 'MM' in unitsys:
-        print("  This is MegaNewton-Millimeter system:")
-        print("    - Length: mm")
-        print("    - Force: MN (MegaNewton)")
-        print("    - Stress: Pa (base SI)")
-        print("    - Mass: tonne")
-else:
-    print("  No UNITSYS parameter found")
-
-print("\n2. MATERIAL PROPERTIES:")
-print("-"*60)
-if hasattr(bdf, 'materials') and bdf.materials:
-    mat = list(bdf.materials.values())[0]
-    print(f"  Material ID: {mat.mid}")
-    print(f"  Type: {mat.type}")
-    if hasattr(mat, 'e') and mat.e:
-        print(f"  Young's modulus E: {mat.e:.2e}")
-        print(f"    -> E = {mat.e/1e9:.1f} GPa (if units are Pa)")
-        print(f"    -> E = {mat.e/1e6:.1f} GPa (if units are kPa)")
-        print(f"    -> E = {mat.e/1e3:.1f} GPa (if units are MPa)")
-        print(f"    Steel E ~= 200 GPa, so units must be Pa")
-
-print("\n3. APPLIED FORCES FROM BDF:")
-print("-"*60)
-total_force = 0
-n_forces = 0
-if hasattr(bdf, 'loads') and bdf.loads:
-    for load_id, load_list in bdf.loads.items():
-        for load in load_list:
-            if hasattr(load, 'mag'):
-                print(f"  Load ID {load_id}, Node {load.node}: {load.mag:.2e} (unit depends on UNITSYS)")
-                total_force += abs(load.mag)
-                n_forces += 1
-                if n_forces >= 3:
-                    break
-        if n_forces >= 3:
-            break
-    print(f"  Total applied force (first 3): {total_force:.2e}")
-    print(f"  In MN: {total_force:.2e} MN")
-    print(f"  In N: {total_force*1e6:.2e} N")
-
-print("\n4. DISPLACEMENT FROM OP2:")
-print("-"*60)
-if hasattr(op2, 'displacements') and op2.displacements:
-    for subcase_id, disp in op2.displacements.items():
-        # Get translation only (DOF 1-3)
-        translations = disp.data[0, :, :3]
-        max_trans = np.max(np.abs(translations))
-        max_idx = np.unravel_index(np.argmax(np.abs(translations)), translations.shape)
-
-        print(f"  Subcase {subcase_id}:")
-        print(f"    Max translation: {max_trans:.6f} mm")
-        print(f"    Location: node index {max_idx[0]}, DOF {max_idx[1]}")
-
-print("\n5. STRESS FROM OP2 (RAW VALUES):")
-print("-"*60)
-# Try new API
-stress_dict = None
-if hasattr(op2, 'op2_results') and hasattr(op2.op2_results, 'stress'):
-    if hasattr(op2.op2_results.stress, 'cquad4_stress'):
-        stress_dict = op2.op2_results.stress.cquad4_stress
-elif hasattr(op2, 'cquad4_stress'):
-    try:
-        stress_dict = op2.cquad4_stress
-    except:
-        pass
-
-if stress_dict:
-    for subcase_id, stress in stress_dict.items():
-        # Stress data columns depend on element type
-        # For CQUAD4: typically [fiber_distance, oxx, oyy, txy, angle, major, minor, von_mises]
-        stress_data = stress.data[0, :, :]
-
-        print(f"  Subcase {subcase_id}:")
-        print(f"    Data shape: {stress_data.shape} (elements × stress_components)")
-        print(f"    Stress components: {stress_data.shape[1]}")
-
-        # Von Mises is usually last column
-        von_mises = stress_data[:, -1]
-        print(f"\n  Von Mises stress (column {stress_data.shape[1]-1}):")
-        print(f"    Min: {np.min(von_mises):.2e}")
-        print(f"    Max: {np.max(von_mises):.2e}")
-        print(f"    Mean: {np.mean(von_mises):.2e}")
-        print(f"    Median: {np.median(von_mises):.2e}")
-
-        print(f"\n  Principal stresses (columns 5-6 typically):")
-        if stress_data.shape[1] >= 7:
-            major = stress_data[:, -3]
-            minor = stress_data[:, -2]
-            print(f"    Major max: {np.max(major):.2e}")
-            print(f"    Minor min: {np.min(minor):.2e}")
-
-        print(f"\n  Direct stresses (columns 1-2 typically):")
-        if stress_data.shape[1] >= 3:
-            sxx = stress_data[:, 1]
-            syy = stress_data[:, 2]
-            print(f"    sigmaxx range: {np.min(sxx):.2e} to {np.max(sxx):.2e}")
-            print(f"    sigmayy range: {np.min(syy):.2e} to {np.max(syy):.2e}")
-
-print("\n6. REACTIONS FROM OP2:")
-print("-"*60)
-if hasattr(op2, 'grid_point_forces') and op2.grid_point_forces:
-    for subcase_id, gpf in op2.grid_point_forces.items():
-        forces = gpf.data[0]
-        print(f"  Subcase {subcase_id}:")
-        print(f"    Data shape: {forces.shape}")
-        print(f"    Max reaction (all DOF): {np.max(np.abs(forces)):.2e}")
-
-        # Get force components (first 3 columns usually Fx, Fy, Fz)
-        if forces.shape[1] >= 3:
-            fx = forces[:, 0]
-            fy = forces[:, 1]
-            fz = forces[:, 2]
-            print(f"    Fx range: {np.min(fx):.2e} to {np.max(fx):.2e}")
-            print(f"    Fy range: {np.min(fy):.2e} to {np.max(fy):.2e}")
-            print(f"    Fz range: {np.min(fz):.2e} to {np.max(fz):.2e}")
-
-print("\n7. YOUR STATED VALUES:")
-print("-"*60)
-print("  You said:")
-print("    - Stress around 117 MPa")
-print("    - Force around 152,200 N")
-print("\n  From OP2 raw data above:")
-print("    - If Von Mises max = 1.17e+05, this is:")
-print("      -> 117,000 Pa = 117 kPa = 0.117 MPa (if UNITSYS=MN-MM)")
-print("      -> OR 117,000 MPa (if somehow in MPa already)")
-print("\n  For force 152,200 N:")
-print("    - If reactions max = 1.52e+08 from OP2:")
-print("      -> 152,000,000 Pa or N·mm⁻² (if MN-MM system)")
-print("      -> 152 MN = 152,000,000 N (conversion)")
-print("      -> OR your expected value is 0.1522 MN = 152,200 N")
-
-print("\n8. DIRECTIONS AND TENSORS:")
-print("-"*60)
-print("  Stress tensor (symmetric 3×3):")
-print("    sigma = [sigmaxx  tauxy  tauxz]")
-print("        [tauxy  sigmayy  tauyz]")
-print("        [tauxz  tauyz  sigmazz]")
-print("\n  Stored in OP2 for shells (CQUAD4) as:")
-print("    [fiber_dist, sigmaxx, sigmayy, tauxy, angle, sigma_major, sigma_minor, von_mises]")
-print("\n  Displacement vector (6 DOF per node):")
-print("    [Tx, Ty, Tz, Rx, Ry, Rz]")
-print("\n  Force/Reaction vector (6 DOF per node):")
-print("    [Fx, Fy, Fz, Mx, My, Mz]")
-
-print("\n" + "="*60)

atomizer-field/check_op2_units.py

@@ -1,122 +0,0 @@
-"""
-Check actual units from pyNastran OP2 reader
-"""
-from pyNastran.op2.op2 import OP2
-import numpy as np
-
-print("="*60)
-print("CHECKING OP2 FILE UNITS")
-print("="*60)
-
-# Load OP2 file
-op2_file = 'test_case_beam/output/model.op2'
-print(f"\nLoading: {op2_file}")
-
-op2 = OP2()
-op2.read_op2(op2_file)
-
-print("\n1. DISPLACEMENT DATA:")
-print("-"*60)
-if hasattr(op2, 'displacements') and op2.displacements:
-    for subcase_id, disp in op2.displacements.items():
-        print(f"  Subcase {subcase_id}:")
-        print(f"    Data shape: {disp.data.shape}")
-        print(f"    Max displacement (all DOF): {np.max(np.abs(disp.data)):.6f}")
-        print(f"    Translation max (DOF 1-3): {np.max(np.abs(disp.data[0, :, :3])):.6f}")
-
-        # Check if pyNastran has unit info
-        if hasattr(disp, 'units'):
-            print(f"    Units: {disp.units}")
-        else:
-            print(f"    Units: Not specified by pyNastran")
-
-print("\n2. STRESS DATA:")
-print("-"*60)
-# Try new API first
-stress_dict = None
-if hasattr(op2, 'op2_results') and hasattr(op2.op2_results, 'stress'):
-    if hasattr(op2.op2_results.stress, 'cquad4_stress'):
-        stress_dict = op2.op2_results.stress.cquad4_stress
-elif hasattr(op2, 'cquad4_stress'):
-    try:
-        stress_dict = op2.cquad4_stress
-    except:
-        stress_dict = None
-
-if stress_dict:
-    for subcase_id, stress in stress_dict.items():
-        print(f"  Subcase {subcase_id}:")
-        print(f"    Data shape: {stress.data.shape}")
-
-        # Get von Mises stress (last column)
-        von_mises = stress.data[0, :, -1]
-        print(f"    Von Mises min: {np.min(von_mises):.2e}")
-        print(f"    Von Mises max: {np.max(von_mises):.2e}")
-        print(f"    Von Mises mean: {np.mean(von_mises):.2e}")
-
-        # Check if pyNastran has unit info
-        if hasattr(stress, 'units'):
-            print(f"    Units: {stress.units}")
-        else:
-            print(f"    Units: Not specified by pyNastran")
-
-        # Check data type names
-        if hasattr(stress, 'data_names'):
-            print(f"    Data names: {stress.data_names}")
-else:
-    print("  No CQUAD4 stress data found")
-
-print("\n3. REACTION FORCES:")
-print("-"*60)
-if hasattr(op2, 'grid_point_forces') and op2.grid_point_forces:
-    for subcase_id, forces in op2.grid_point_forces.items():
-        print(f"  Subcase {subcase_id}:")
-        print(f"    Data shape: {forces.data.shape}")
-        print(f"    Max force: {np.max(np.abs(forces.data)):.2e}")
-
-        if hasattr(forces, 'units'):
-            print(f"    Units: {forces.units}")
-        else:
-            print(f"    Units: Not specified by pyNastran")
-
-print("\n4. BDF FILE UNITS:")
-print("-"*60)
-# Try to read BDF to check units
-from pyNastran.bdf.bdf import BDF
-bdf_file = 'test_case_beam/input/model.bdf'
-print(f"Loading: {bdf_file}")
-
-bdf = BDF()
-bdf.read_bdf(bdf_file)
-
-# Check for PARAM cards that define units
-if hasattr(bdf, 'params') and bdf.params:
-    print("  PARAM cards found:")
-    for param_name, param in bdf.params.items():
-        if 'UNIT' in param_name.upper() or 'WTMASS' in param_name.upper():
-            print(f"    {param_name}: {param}")
-
-# Check material properties (can infer units from magnitude)
-if hasattr(bdf, 'materials') and bdf.materials:
-    print("\n  Material properties (first material):")
-    mat = list(bdf.materials.values())[0]
-    print(f"    Type: {mat.type}")
-    if hasattr(mat, 'e') and mat.e:
-        print(f"    Young's modulus E: {mat.e:.2e}")
-        print(f"      If E~200,000 then units are MPa (steel)")
-        print(f"      If E~200,000,000 then units are Pa (steel)")
-        print(f"      If E~29,000,000 then units are psi (steel)")
-
-print("\n5. NASTRAN UNIT SYSTEM ANALYSIS:")
-print("-"*60)
-print("  Common Nastran unit systems:")
-print("    - SI: m, kg, N, Pa, s")
-print("    - mm-tonne-N: mm, tonne, N, MPa, s")
-print("    - mm-kg-N: mm, kg, N, MPa, s")
-print("    - in-lb-s: in, lb, lbf, psi, s")
-print("")
-print("  Our metadata claims: mm, kg, N, MPa")
-print("  But pyNastran might return stress in Pa (base SI)")
-print("  This would explain the 1000× error!")
-
-print("\n" + "="*60)

atomizer-field/check_units.py

@@ -1,104 +0,0 @@
-"""
-Script to investigate unit conversion issues in AtomizerField
-"""
-import json
-import h5py
-import numpy as np
-
-print("="*60)
-print("UNIT VALIDATION CHECK")
-print("="*60)
-
-# Load JSON metadata
-with open('test_case_beam/neural_field_data.json', 'r') as f:
-    data = json.load(f)
-
-# Check units
-print("\n1. UNITS FROM METADATA:")
-print("-"*60)
-units = data['metadata']['units']
-for key, value in units.items():
-    print(f"  {key}: {value}")
-
-# Check loads
-print("\n2. APPLIED LOADS:")
-print("-"*60)
-loads = data['loads']
-print(f"  Available load types: {list(loads.keys())}")
-
-if 'point_forces' in loads:
-    point_forces = loads['point_forces']
-    print(f"  Point forces: {len(point_forces)} applied")
-
-    if point_forces:
-        print("\n  Sample forces (first 3):")
-        for i in range(min(3, len(point_forces))):
-            force = point_forces[i]
-            print(f"    Force {i+1}:")
-            print(f"      Node: {force['node']}")
-            print(f"      Magnitude: {force['magnitude']:.2e} N")
-            print(f"      Direction: {force['direction']}")
-
-# Load HDF5 data
-print("\n3. REACTION FORCES FROM HDF5:")
-print("-"*60)
-with h5py.File('test_case_beam/neural_field_data.h5', 'r') as f:
-    reactions = f['results/reactions'][:]
-
-    # Get statistics
-    non_zero_reactions = reactions[np.abs(reactions) > 1e-10]
-    print(f"  Shape: {reactions.shape}")
-    print(f"  Min: {np.min(reactions):.2e}")
-    print(f"  Max: {np.max(reactions):.2e}")
-    print(f"  Mean (non-zero): {np.mean(np.abs(non_zero_reactions)):.2e}")
-    print(f"  Max absolute: {np.max(np.abs(reactions)):.2e}")
-
-    # Check displacement for comparison
-    displacement = f['results/displacement'][:]
-    max_disp = np.max(np.abs(displacement[:, :3]))  # Translation only
-    print(f"\n  Max displacement: {max_disp:.6f} mm")
-
-# Check stress
-print("\n4. STRESS VALUES FROM HDF5:")
-print("-"*60)
-with h5py.File('test_case_beam/neural_field_data.h5', 'r') as f:
-    stress = f['results/stress/cquad4_stress/data'][:]
-
-    # Von Mises stress is in column 7 (0-indexed)
-    von_mises = stress[:, 7]
-
-    print(f"  Shape: {stress.shape}")
-    print(f"  Von Mises min: {np.min(von_mises):.2e} MPa")
-    print(f"  Von Mises max: {np.max(von_mises):.2e} MPa")
-    print(f"  Von Mises mean: {np.mean(von_mises):.2e} MPa")
-
-# Check if values make sense
-print("\n5. SANITY CHECK:")
-print("-"*60)
-print(f"  Units claimed: force=N, stress=MPa, length=mm")
-print(f"  Max reaction force: {np.max(np.abs(reactions)):.2e} N")
-print(f"  Max von Mises: {np.max(von_mises):.2e} MPa")
-print(f"  Max displacement: {max_disp:.6f} mm")
-
-# Typical beam: if force is 1000 N, stress should be ~10-100 MPa
-# If reaction is 152 million N, that's 152,000 kN - VERY high!
-max_reaction = np.max(np.abs(reactions))
-max_stress_val = np.max(von_mises)
-
-print(f"\n  If force unit is actually kN instead of N:")
-print(f"    Max reaction: {max_reaction/1000:.2e} kN")
-print(f"  If stress unit is actually Pa instead of MPa:")
-print(f"    Max stress: {max_stress_val/1e6:.2e} MPa")
-
-print("\n6. HYPOTHESIS:")
-print("-"*60)
-if max_reaction > 1e6:
-    print("  [!] Reaction forces seem TOO LARGE (>1 MN)")
-    print("  [!] Possible issue: pyNastran returns forces in different units")
-    print("  [!] Check: Nastran may export in base units (N) while expecting kN")
-
-if max_stress_val > 1e6:
-    print("  [!] Stresses seem TOO LARGE (>1000 MPa)")
-    print("  [!] Possible issue: pyNastran returns stress in Pa, not MPa")
-
-print("\n" + "="*60)

atomizer-field/neural_field_parser.py

@@ -1,921 +0,0 @@
-"""
-neural_field_parser.py
-Parses NX Nastran files into Neural Field training data
-
-AtomizerField Data Parser v1.0.0
-Converts NX Nastran BDF/OP2 files into standardized neural field training format.
-This format is designed to be future-proof for years of neural network training.
-
-Usage:
-    python neural_field_parser.py <case_directory>
-
-Example:
-    python neural_field_parser.py training_case_001
-"""
-
-import json
-import numpy as np
-import h5py
-from pathlib import Path
-from datetime import datetime
-import hashlib
-import warnings
-
-# pyNastran imports
-try:
-    from pyNastran.bdf.bdf import BDF
-    from pyNastran.op2.op2 import OP2
-except ImportError:
-    print("ERROR: pyNastran is required. Install with: pip install pyNastran")
-    raise
-
-
-class NastranToNeuralFieldParser:
-    """
-    Parses Nastran BDF/OP2 files into Neural Field data structure v1.0
-
-    This parser extracts complete field data (stress, displacement, strain at every node/element)
-    rather than just scalar maximum values. This enables neural networks to learn complete
-    physics fields for 1000x faster structural optimization.
-
-    Data Structure v1.0:
-    -------------------
-    - metadata: Version, timestamps, analysis info, units
-    - mesh: Complete node coordinates, element connectivity
-    - materials: Full material properties (E, nu, rho, etc.)
-    - boundary_conditions: All constraints (SPC, MPC)
-    - loads: All loading conditions (forces, pressures, gravity, thermal)
-    - results: Complete field results (displacement, stress, strain at ALL points)
-
-    Attributes:
-        case_dir (Path): Directory containing input/output subdirectories
-        bdf_file (Path): Path to Nastran input deck (.bdf or .dat)
-        op2_file (Path): Path to Nastran binary results (.op2)
-        bdf (BDF): pyNastran BDF reader object
-        op2 (OP2): pyNastran OP2 reader object
-        neural_field_data (dict): Complete parsed data structure
-    """
-
-    def __init__(self, case_directory):
-        """
-        Initialize parser with case directory
-
-        Args:
-            case_directory (str or Path): Path to case directory containing:
-                - input/model.bdf (or model.dat)
-                - output/model.op2
-        """
-        self.case_dir = Path(case_directory)
-
-        # Find BDF file (try both .bdf and .dat extensions)
-        bdf_candidates = list((self.case_dir / "input").glob("model.bdf")) + \
-                        list((self.case_dir / "input").glob("model.dat"))
-        if not bdf_candidates:
-            raise FileNotFoundError(
-                f"No model.bdf or model.dat found in {self.case_dir / 'input'}/"
-            )
-        self.bdf_file = bdf_candidates[0]
-
-        # Find OP2 file
-        op2_candidates = list((self.case_dir / "output").glob("model.op2"))
-        if not op2_candidates:
-            raise FileNotFoundError(
-                f"No model.op2 found in {self.case_dir / 'output'}/"
-            )
-        self.op2_file = op2_candidates[0]
-
-        print(f"Found BDF: {self.bdf_file.name}")
-        print(f"Found OP2: {self.op2_file.name}")
-
-        # Initialize readers with minimal debug output
-        self.bdf = BDF(debug=False)
-        self.op2 = OP2(debug=False)
-
-        # Initialize data structure v1.0
-        self.neural_field_data = {
-            "metadata": {},
-            "geometry": {},
-            "mesh": {},
-            "materials": {},
-            "boundary_conditions": {},
-            "loads": {},
-            "results": {}
-        }
-
-    def parse_all(self):
-        """
-        Main parsing function - extracts all data from BDF/OP2 files
-
-        Returns:
-            dict: Complete neural field data structure
-        """
-        print("\n" + "="*60)
-        print("Starting AtomizerField Neural Field Parser v1.0")
-        print("="*60)
-
-        # Parse input deck
-        print("\n[1/6] Reading BDF file...")
-        self.bdf.read_bdf(str(self.bdf_file))
-        print(f"      Loaded {len(self.bdf.nodes)} nodes, {len(self.bdf.elements)} elements")
-
-        # Parse results
-        print("\n[2/6] Reading OP2 file...")
-        self.op2.read_op2(str(self.op2_file))
-        # Check for sol attribute (may not exist in all pyNastran versions)
-        sol_num = getattr(self.op2, 'sol', 'Unknown')
-        print(f"      Loaded solution: SOL {sol_num}")
-
-        # Extract all data
-        print("\n[3/6] Extracting metadata...")
-        self.extract_metadata()
-
-        print("\n[4/6] Extracting mesh data...")
-        self.extract_mesh()
-
-        print("\n[5/6] Extracting materials, BCs, and loads...")
-        self.extract_materials()
-        self.extract_boundary_conditions()
-        self.extract_loads()
-
-        print("\n[6/6] Extracting field results...")
-        self.extract_results()
-
-        # Save to file
-        print("\nSaving data to disk...")
-        self.save_data()
-
-        print("\n" + "="*60)
-        print("Parsing complete! [OK]")
-        print("="*60)
-        return self.neural_field_data
-
-    def extract_metadata(self):
-        """
-        Extract metadata and analysis information
-
-        This includes:
-        - Data format version (v1.0.0)
-        - Timestamps
-        - Analysis type (SOL 101, 103, etc.)
-        - Units system
-        - File hashes for provenance
-        """
-        # Generate file hash for data provenance
-        with open(self.bdf_file, 'rb') as f:
-            bdf_hash = hashlib.sha256(f.read()).hexdigest()
-        with open(self.op2_file, 'rb') as f:
-            op2_hash = hashlib.sha256(f.read()).hexdigest()
-
-        # Extract title if available
-        title = ""
-        if hasattr(self.bdf, 'case_control_deck') and self.bdf.case_control_deck:
-            if hasattr(self.bdf.case_control_deck, 'title'):
-                title = str(self.bdf.case_control_deck.title)
-
-        # Get solution type if available
-        sol_num = getattr(self.op2, 'sol', 'Unknown')
-
-        self.neural_field_data["metadata"] = {
-            "version": "1.0.0",
-            "created_at": datetime.now().isoformat(),
-            "source": "NX_Nastran",
-            "case_directory": str(self.case_dir),
-            "case_name": self.case_dir.name,
-            "analysis_type": f"SOL_{sol_num}",
-            "title": title,
-            "file_hashes": {
-                "bdf": bdf_hash,
-                "op2": op2_hash
-            },
-            "units": {
-                "length": "mm",  # Standard NX units
-                "force": "N",
-                "stress": "MPa",
-                "mass": "kg",
-                "temperature": "C"
-            },
-            "parser_version": "1.0.0",
-            "notes": "Complete field data for neural network training"
-        }
-        print(f"      Analysis: {self.neural_field_data['metadata']['analysis_type']}")
-
-    def extract_mesh(self):
-        """
-        Extract complete mesh data from BDF
-
-        This preserves:
-        - All node coordinates (global coordinate system)
-        - All element connectivity
-        - Element types (solid, shell, beam, rigid)
-        - Material and property IDs for each element
-        """
-        print("      Extracting nodes...")
-
-        # Nodes - store in sorted order for consistent indexing
-        nodes = []
-        node_ids = []
-        for nid, node in sorted(self.bdf.nodes.items()):
-            node_ids.append(nid)
-            # Get position in global coordinate system
-            pos = node.get_position()
-            nodes.append([pos[0], pos[1], pos[2]])
-
-        nodes_array = np.array(nodes, dtype=np.float64)
-
-        print(f"      Extracted {len(nodes)} nodes")
-        print(f"      Extracting elements...")
-
-        # Elements - organize by type for efficient neural network processing
-        element_data = {
-            "solid": [],
-            "shell": [],
-            "beam": [],
-            "rigid": []
-        }
-
-        element_type_counts = {}
-
-        for eid, elem in sorted(self.bdf.elements.items()):
-            elem_type = elem.type
-            element_type_counts[elem_type] = element_type_counts.get(elem_type, 0) + 1
-
-            # Solid elements (3D stress states)
-            if elem_type in ['CTETRA', 'CHEXA', 'CPENTA', 'CTETRA10', 'CHEXA20', 'CPENTA15']:
-                element_data["solid"].append({
-                    "id": eid,
-                    "type": elem_type,
-                    "nodes": list(elem.node_ids),
-                    "material_id": elem.pid,  # Property ID which links to material
-                    "property_id": elem.pid if hasattr(elem, 'pid') else None
-                })
-
-            # Shell elements (2D plane stress)
-            elif elem_type in ['CQUAD4', 'CTRIA3', 'CQUAD8', 'CTRIA6', 'CQUAD', 'CTRIA']:
-                thickness = None
-                try:
-                    # Get thickness from property
-                    if hasattr(elem, 'pid') and elem.pid in self.bdf.properties:
-                        prop = self.bdf.properties[elem.pid]
-                        if hasattr(prop, 't'):
-                            thickness = prop.t
-                except:
-                    pass
-
-                element_data["shell"].append({
-                    "id": eid,
-                    "type": elem_type,
-                    "nodes": list(elem.node_ids),
-                    "material_id": elem.pid,
-                    "property_id": elem.pid,
-                    "thickness": thickness
-                })
-
-            # Beam elements (1D elements)
-            elif elem_type in ['CBAR', 'CBEAM', 'CROD', 'CONROD']:
-                element_data["beam"].append({
-                    "id": eid,
-                    "type": elem_type,
-                    "nodes": list(elem.node_ids),
-                    "material_id": elem.pid if hasattr(elem, 'pid') else None,
-                    "property_id": elem.pid if hasattr(elem, 'pid') else None
-                })
-
-            # Rigid elements (kinematic constraints)
-            elif elem_type in ['RBE2', 'RBE3', 'RBAR', 'RROD']:
-                element_data["rigid"].append({
-                    "id": eid,
-                    "type": elem_type,
-                    "nodes": list(elem.node_ids)
-                })
-
-        print(f"      Extracted {len(self.bdf.elements)} elements:")
-        for etype, count in element_type_counts.items():
-            print(f"        {etype}: {count}")
-
-        # Calculate mesh bounding box for reference
-        bbox_min = nodes_array.min(axis=0)
-        bbox_max = nodes_array.max(axis=0)
-        bbox_size = bbox_max - bbox_min
-
-        # Store mesh data
-        self.neural_field_data["mesh"] = {
-            "statistics": {
-                "n_nodes": len(nodes),
-                "n_elements": len(self.bdf.elements),
-                "element_types": {
-                    "solid": len(element_data["solid"]),
-                    "shell": len(element_data["shell"]),
-                    "beam": len(element_data["beam"]),
-                    "rigid": len(element_data["rigid"])
-                },
-                "element_type_breakdown": element_type_counts
-            },
-            "bounding_box": {
-                "min": bbox_min.tolist(),
-                "max": bbox_max.tolist(),
-                "size": bbox_size.tolist()
-            },
-            "nodes": {
-                "ids": node_ids,
-                "coordinates": nodes_array.tolist(),  # Will be stored in HDF5
-                "shape": list(nodes_array.shape),
-                "dtype": str(nodes_array.dtype)
-            },
-            "elements": element_data
-        }
-
-    def extract_materials(self):
-        """
-        Extract all material properties
-
-        Captures complete material definitions including:
-        - Isotropic (MAT1): E, nu, rho, G, alpha
-        - Orthotropic (MAT8, MAT9): directional properties
-        - Stress limits for validation
-        """
-        print("      Extracting materials...")
-
-        materials = []
-        for mid, mat in sorted(self.bdf.materials.items()):
-            mat_data = {
-                "id": mid,
-                "type": mat.type
-            }
-
-            if mat.type == 'MAT1':  # Isotropic material
-                mat_data.update({
-                    "E": float(mat.e) if mat.e is not None else None,      # Young's modulus
-                    "nu": float(mat.nu) if mat.nu is not None else None,   # Poisson's ratio
-                    "rho": float(mat.rho) if mat.rho is not None else None,# Density
-                    "G": float(mat.g) if mat.g is not None else None,      # Shear modulus
-                    "alpha": float(mat.a) if hasattr(mat, 'a') and mat.a is not None else None,  # Thermal expansion
-                    "tref": float(mat.tref) if hasattr(mat, 'tref') and mat.tref is not None else None,
-                })
-
-                # Stress limits (if defined)
-                try:
-                    if hasattr(mat, 'St') and callable(mat.St):
-                        mat_data["ST"] = float(mat.St()) if mat.St() is not None else None
-                    if hasattr(mat, 'Sc') and callable(mat.Sc):
-                        mat_data["SC"] = float(mat.Sc()) if mat.Sc() is not None else None
-                    if hasattr(mat, 'Ss') and callable(mat.Ss):
-                        mat_data["SS"] = float(mat.Ss()) if mat.Ss() is not None else None
-                except:
-                    pass
-
-            elif mat.type == 'MAT8':  # Orthotropic shell material
-                mat_data.update({
-                    "E1": float(mat.e11) if hasattr(mat, 'e11') and mat.e11 is not None else None,
-                    "E2": float(mat.e22) if hasattr(mat, 'e22') and mat.e22 is not None else None,
-                    "nu12": float(mat.nu12) if hasattr(mat, 'nu12') and mat.nu12 is not None else None,
-                    "G12": float(mat.g12) if hasattr(mat, 'g12') and mat.g12 is not None else None,
-                    "G1z": float(mat.g1z) if hasattr(mat, 'g1z') and mat.g1z is not None else None,
-                    "G2z": float(mat.g2z) if hasattr(mat, 'g2z') and mat.g2z is not None else None,
-                    "rho": float(mat.rho) if hasattr(mat, 'rho') and mat.rho is not None else None,
-                })
-
-            materials.append(mat_data)
-
-        self.neural_field_data["materials"] = materials
-        print(f"      Extracted {len(materials)} materials")
-
-    def extract_boundary_conditions(self):
-        """
-        Extract all boundary conditions
-
-        Includes:
-        - SPC: Single point constraints (fixed DOFs)
-        - MPC: Multi-point constraints (equations)
-        - SUPORT: Free body supports
-        """
-        print("      Extracting boundary conditions...")
-
-        bcs = {
-            "spc": [],      # Single point constraints
-            "mpc": [],      # Multi-point constraints
-            "suport": []    # Free body supports
-        }
-
-        # SPC (fixed DOFs) - critical for neural network to understand support conditions
-        spc_count = 0
-        for spc_id, spc_list in self.bdf.spcs.items():
-            for spc in spc_list:
-                try:
-                    # Handle different SPC types
-                    if hasattr(spc, 'node_ids'):
-                        nodes = spc.node_ids
-                    elif hasattr(spc, 'node'):
-                        nodes = [spc.node]
-                    else:
-                        continue
-
-                    for node in nodes:
-                        bcs["spc"].append({
-                            "id": spc_id,
-                            "node": int(node),
-                            "dofs": str(spc.components) if hasattr(spc, 'components') else "123456",
-                            "enforced_motion": float(spc.enforced) if hasattr(spc, 'enforced') and spc.enforced is not None else 0.0
-                        })
-                        spc_count += 1
-                except Exception as e:
-                    warnings.warn(f"Could not parse SPC {spc_id}: {e}")
-
-        # MPC equations
-        mpc_count = 0
-        for mpc_id, mpc_list in self.bdf.mpcs.items():
-            for mpc in mpc_list:
-                try:
-                    bcs["mpc"].append({
-                        "id": mpc_id,
-                        "nodes": list(mpc.node_ids) if hasattr(mpc, 'node_ids') else [],
-                        "coefficients": list(mpc.coefficients) if hasattr(mpc, 'coefficients') else [],
-                        "components": list(mpc.components) if hasattr(mpc, 'components') else []
-                    })
-                    mpc_count += 1
-                except Exception as e:
-                    warnings.warn(f"Could not parse MPC {mpc_id}: {e}")
-
-        self.neural_field_data["boundary_conditions"] = bcs
-        print(f"      Extracted {spc_count} SPCs, {mpc_count} MPCs")
-
-    def extract_loads(self):
-        """
-        Extract all loading conditions
-
-        Includes:
-        - Point forces and moments
-        - Distributed pressures
-        - Gravity loads
-        - Thermal loads
-        """
-        print("      Extracting loads...")
-
-        loads = {
-            "point_forces": [],
-            "pressure": [],
-            "gravity": [],
-            "thermal": []
-        }
-
-        force_count = 0
-        pressure_count = 0
-        gravity_count = 0
-
-        # Point forces, moments, and pressures
-        for load_id, load_list in self.bdf.loads.items():
-            for load in load_list:
-                try:
-                    if load.type == 'FORCE':
-                        loads["point_forces"].append({
-                            "id": load_id,
-                            "type": "force",
-                            "node": int(load.node),
-                            "magnitude": float(load.mag),
-                            "direction": [float(load.xyz[0]), float(load.xyz[1]), float(load.xyz[2])],
-                            "coord_system": int(load.cid) if hasattr(load, 'cid') else 0
-                        })
-                        force_count += 1
-
-                    elif load.type == 'MOMENT':
-                        loads["point_forces"].append({
-                            "id": load_id,
-                            "type": "moment",
-                            "node": int(load.node),
-                            "magnitude": float(load.mag),
-                            "direction": [float(load.xyz[0]), float(load.xyz[1]), float(load.xyz[2])],
-                            "coord_system": int(load.cid) if hasattr(load, 'cid') else 0
-                        })
-                        force_count += 1
-
-                    elif load.type in ['PLOAD', 'PLOAD2', 'PLOAD4']:
-                        pressure_data = {
-                            "id": load_id,
-                            "type": load.type
-                        }
-
-                        if hasattr(load, 'eids'):
-                            pressure_data["elements"] = list(load.eids)
-                        elif hasattr(load, 'eid'):
-                            pressure_data["elements"] = [int(load.eid)]
-
-                        if hasattr(load, 'pressures'):
-                            pressure_data["pressure"] = [float(p) for p in load.pressures]
-                        elif hasattr(load, 'pressure'):
-                            pressure_data["pressure"] = float(load.pressure)
-
-                        loads["pressure"].append(pressure_data)
-                        pressure_count += 1
-
-                    elif load.type == 'GRAV':
-                        loads["gravity"].append({
-                            "id": load_id,
-                            "acceleration": float(load.scale),
-                            "direction": [float(load.N[0]), float(load.N[1]), float(load.N[2])],
-                            "coord_system": int(load.cid) if hasattr(load, 'cid') else 0
-                        })
-                        gravity_count += 1
-
-                except Exception as e:
-                    warnings.warn(f"Could not parse load {load_id} type {load.type}: {e}")
-
-        # Temperature loads (if available)
-        thermal_count = 0
-        if hasattr(self.bdf, 'temps'):
-            for temp_id, temp_list in self.bdf.temps.items():
-                for temp in temp_list:
-                    try:
-                        loads["thermal"].append({
-                            "id": temp_id,
-                            "node": int(temp.node),
-                            "temperature": float(temp.temperature)
-                        })
-                        thermal_count += 1
-                    except Exception as e:
-                        warnings.warn(f"Could not parse thermal load {temp_id}: {e}")
-
-        self.neural_field_data["loads"] = loads
-        print(f"      Extracted {force_count} forces, {pressure_count} pressures, {gravity_count} gravity, {thermal_count} thermal")
-
-    def extract_results(self):
-        """
-        Extract complete field results from OP2
-
-        This is the CRITICAL function for neural field learning.
-        We extract COMPLETE fields, not just maximum values:
-        - Displacement at every node (6 DOF)
-        - Stress at every element (full tensor)
-        - Strain at every element (full tensor)
-        - Reaction forces at constrained nodes
-
-        This complete field data enables the neural network to learn
-        the physics of how structures respond to loads.
-        """
-        print("      Extracting field results...")
-
-        results = {}
-
-        # Determine subcase ID (usually 1 for linear static)
-        subcase_id = 1
-        if hasattr(self.op2, 'isubcase_name_map'):
-            available_subcases = list(self.op2.isubcase_name_map.keys())
-            if available_subcases:
-                subcase_id = available_subcases[0]
-
-        print(f"      Using subcase ID: {subcase_id}")
-
-        # Displacement - complete field at all nodes
-        if hasattr(self.op2, 'displacements') and subcase_id in self.op2.displacements:
-            print("      Processing displacement field...")
-            disp = self.op2.displacements[subcase_id]
-            disp_data = disp.data[0, :, :]  # [itime=0, all_nodes, 6_dofs]
-
-            # Extract node IDs
-            node_ids = disp.node_gridtype[:, 0].tolist()
-
-            # Calculate magnitudes for quick reference
-            translation_mag = np.linalg.norm(disp_data[:, :3], axis=1)
-            rotation_mag = np.linalg.norm(disp_data[:, 3:], axis=1)
-
-            results["displacement"] = {
-                "node_ids": node_ids,
-                "data": disp_data.tolist(),  # Will be stored in HDF5
-                "shape": list(disp_data.shape),
-                "dtype": str(disp_data.dtype),
-                "max_translation": float(np.max(translation_mag)),
-                "max_rotation": float(np.max(rotation_mag)),
-                "units": "mm and radians"
-            }
-            print(f"        Displacement: {len(node_ids)} nodes, max={results['displacement']['max_translation']:.6f} mm")
-
-        # Stress - handle different element types
-        stress_results = {}
-
-        # Solid element stress (CTETRA, CHEXA, etc.)
-        stress_attrs = ['ctetra_stress', 'chexa_stress', 'cpenta_stress']
-        for attr in stress_attrs:
-            if hasattr(self.op2, attr):
-                stress_obj = getattr(self.op2, attr)
-                if subcase_id in stress_obj:
-                    elem_type = attr.replace('_stress', '')
-                    print(f"      Processing {elem_type} stress...")
-                    stress = stress_obj[subcase_id]
-                    stress_data = stress.data[0, :, :]
-
-                    # Extract element IDs
-                    element_ids = stress.element_node[:, 0].tolist()
-
-                    # Von Mises stress is usually the last column
-                    von_mises = None
-                    if stress_data.shape[1] >= 7:  # Has von Mises
-                        von_mises = stress_data[:, -1]
-                        max_vm = float(np.max(von_mises))
-                        von_mises = von_mises.tolist()
-                    else:
-                        max_vm = None
-
-                    stress_results[f"{elem_type}_stress"] = {
-                        "element_ids": element_ids,
-                        "data": stress_data.tolist(),  # Full stress tensor
-                        "shape": list(stress_data.shape),
-                        "dtype": str(stress_data.dtype),
-                        "von_mises": von_mises,
-                        "max_von_mises": max_vm,
-                        "units": "MPa"
-                    }
-                    print(f"        {elem_type}: {len(element_ids)} elements, max VM={max_vm:.2f} MPa" if max_vm else f"        {elem_type}: {len(element_ids)} elements")
-
-        # Shell element stress
-        shell_stress_attrs = ['cquad4_stress', 'ctria3_stress', 'cquad8_stress', 'ctria6_stress']
-        for attr in shell_stress_attrs:
-            if hasattr(self.op2, attr):
-                stress_obj = getattr(self.op2, attr)
-                if subcase_id in stress_obj:
-                    elem_type = attr.replace('_stress', '')
-                    print(f"      Processing {elem_type} stress...")
-                    stress = stress_obj[subcase_id]
-                    stress_data = stress.data[0, :, :]
-
-                    element_ids = stress.element_node[:, 0].tolist()
-
-                    stress_results[f"{elem_type}_stress"] = {
-                        "element_ids": element_ids,
-                        "data": stress_data.tolist(),
-                        "shape": list(stress_data.shape),
-                        "dtype": str(stress_data.dtype),
-                        "units": "MPa"
-                    }
-                    print(f"        {elem_type}: {len(element_ids)} elements")
-
-        results["stress"] = stress_results
-
-        # Strain - similar to stress
-        strain_results = {}
-        strain_attrs = ['ctetra_strain', 'chexa_strain', 'cpenta_strain',
-                       'cquad4_strain', 'ctria3_strain']
-        for attr in strain_attrs:
-            if hasattr(self.op2, attr):
-                strain_obj = getattr(self.op2, attr)
-                if subcase_id in strain_obj:
-                    elem_type = attr.replace('_strain', '')
-                    strain = strain_obj[subcase_id]
-                    strain_data = strain.data[0, :, :]
-                    element_ids = strain.element_node[:, 0].tolist()
-
-                    strain_results[f"{elem_type}_strain"] = {
-                        "element_ids": element_ids,
-                        "data": strain_data.tolist(),
-                        "shape": list(strain_data.shape),
-                        "dtype": str(strain_data.dtype),
-                        "units": "mm/mm"
-                    }
-
-        if strain_results:
-            results["strain"] = strain_results
-            print(f"      Extracted strain for {len(strain_results)} element types")
-
-        # SPC Forces (reaction forces at constraints)
-        if hasattr(self.op2, 'spc_forces') and subcase_id in self.op2.spc_forces:
-            print("      Processing reaction forces...")
-            spc = self.op2.spc_forces[subcase_id]
-            spc_data = spc.data[0, :, :]
-            node_ids = spc.node_gridtype[:, 0].tolist()
-
-            # Calculate total reaction force magnitude
-            force_mag = np.linalg.norm(spc_data[:, :3], axis=1)
-            moment_mag = np.linalg.norm(spc_data[:, 3:], axis=1)
-
-            results["reactions"] = {
-                "node_ids": node_ids,
-                "forces": spc_data.tolist(),
-                "shape": list(spc_data.shape),
-                "dtype": str(spc_data.dtype),
-                "max_force": float(np.max(force_mag)),
-                "max_moment": float(np.max(moment_mag)),
-                "units": "N and N-mm"
-            }
-            print(f"        Reactions: {len(node_ids)} nodes, max force={results['reactions']['max_force']:.2f} N")
-
-        self.neural_field_data["results"] = results
-
-    def save_data(self):
-        """
-        Save parsed data to JSON and HDF5 files
-
-        Data structure:
-        - neural_field_data.json: Metadata, structure, small arrays
-        - neural_field_data.h5: Large arrays (node coordinates, field results)
-
-        HDF5 is used for efficient storage and loading of large numerical arrays.
-        JSON provides human-readable metadata and structure.
-        """
-        # Save JSON metadata
-        json_file = self.case_dir / "neural_field_data.json"
-
-        # Create a copy for JSON (will remove large arrays)
-        json_data = self._prepare_json_data()
-
-        with open(json_file, 'w') as f:
-            json.dump(json_data, f, indent=2, default=str)
-
-        print(f"  [OK] Saved metadata to: {json_file.name}")
-
-        # Save HDF5 for large arrays
-        h5_file = self.case_dir / "neural_field_data.h5"
-        with h5py.File(h5_file, 'w') as f:
-            # Metadata attributes
-            f.attrs['version'] = '1.0.0'
-            f.attrs['created_at'] = self.neural_field_data['metadata']['created_at']
-            f.attrs['case_name'] = self.neural_field_data['metadata']['case_name']
-
-            # Save mesh data
-            mesh_grp = f.create_group('mesh')
-            node_coords = np.array(self.neural_field_data["mesh"]["nodes"]["coordinates"])
-            mesh_grp.create_dataset('node_coordinates',
-                                   data=node_coords,
-                                   compression='gzip',
-                                   compression_opts=4)
-            mesh_grp.create_dataset('node_ids',
-                                   data=np.array(self.neural_field_data["mesh"]["nodes"]["ids"]))
-
-            # Save results
-            if "results" in self.neural_field_data:
-                results_grp = f.create_group('results')
-
-                # Displacement
-                if "displacement" in self.neural_field_data["results"]:
-                    disp_data = np.array(self.neural_field_data["results"]["displacement"]["data"])
-                    results_grp.create_dataset('displacement',
-                                             data=disp_data,
-                                             compression='gzip',
-                                             compression_opts=4)
-                    results_grp.create_dataset('displacement_node_ids',
-                                             data=np.array(self.neural_field_data["results"]["displacement"]["node_ids"]))
-
-                # Stress fields
-                if "stress" in self.neural_field_data["results"]:
-                    stress_grp = results_grp.create_group('stress')
-                    for stress_type, stress_data in self.neural_field_data["results"]["stress"].items():
-                        type_grp = stress_grp.create_group(stress_type)
-                        type_grp.create_dataset('data',
-                                              data=np.array(stress_data["data"]),
-                                              compression='gzip',
-                                              compression_opts=4)
-                        type_grp.create_dataset('element_ids',
-                                              data=np.array(stress_data["element_ids"]))
-
-                # Strain fields
-                if "strain" in self.neural_field_data["results"]:
-                    strain_grp = results_grp.create_group('strain')
-                    for strain_type, strain_data in self.neural_field_data["results"]["strain"].items():
-                        type_grp = strain_grp.create_group(strain_type)
-                        type_grp.create_dataset('data',
-                                              data=np.array(strain_data["data"]),
-                                              compression='gzip',
-                                              compression_opts=4)
-                        type_grp.create_dataset('element_ids',
-                                              data=np.array(strain_data["element_ids"]))
-
-                # Reactions
-                if "reactions" in self.neural_field_data["results"]:
-                    reactions_data = np.array(self.neural_field_data["results"]["reactions"]["forces"])
-                    results_grp.create_dataset('reactions',
-                                             data=reactions_data,
-                                             compression='gzip',
-                                             compression_opts=4)
-                    results_grp.create_dataset('reaction_node_ids',
-                                             data=np.array(self.neural_field_data["results"]["reactions"]["node_ids"]))
-
-        print(f"  [OK] Saved field data to: {h5_file.name}")
-
-        # Calculate and display file sizes
-        json_size = json_file.stat().st_size / 1024  # KB
-        h5_size = h5_file.stat().st_size / 1024  # KB
-        print(f"\n  File sizes:")
-        print(f"    JSON: {json_size:.1f} KB")
-        print(f"    HDF5: {h5_size:.1f} KB")
-        print(f"    Total: {json_size + h5_size:.1f} KB")
-
-    def _prepare_json_data(self):
-        """
-        Prepare data for JSON export by removing large arrays
-        (they go to HDF5 instead)
-        """
-        import copy
-        json_data = copy.deepcopy(self.neural_field_data)
-
-        # Remove large arrays from nodes (keep metadata)
-        if "mesh" in json_data and "nodes" in json_data["mesh"]:
-            json_data["mesh"]["nodes"]["coordinates"] = f"<stored in HDF5: shape {json_data['mesh']['nodes']['shape']}>"
-
-        # Remove large result arrays
-        if "results" in json_data:
-            if "displacement" in json_data["results"]:
-                shape = json_data["results"]["displacement"]["shape"]
-                json_data["results"]["displacement"]["data"] = f"<stored in HDF5: shape {shape}>"
-
-            if "stress" in json_data["results"]:
-                for stress_type in json_data["results"]["stress"]:
-                    shape = json_data["results"]["stress"][stress_type]["shape"]
-                    json_data["results"]["stress"][stress_type]["data"] = f"<stored in HDF5: shape {shape}>"
-
-            if "strain" in json_data["results"]:
-                for strain_type in json_data["results"]["strain"]:
-                    shape = json_data["results"]["strain"][strain_type]["shape"]
-                    json_data["results"]["strain"][strain_type]["data"] = f"<stored in HDF5: shape {shape}>"
-
-            if "reactions" in json_data["results"]:
-                shape = json_data["results"]["reactions"]["shape"]
-                json_data["results"]["reactions"]["forces"] = f"<stored in HDF5: shape {shape}>"
-
-        return json_data
-
-
-# ============================================================================
-# MAIN ENTRY POINT
-# ============================================================================
-
-def main():
-    """
-    Main function to run the parser from command line
-
-    Usage:
-        python neural_field_parser.py <case_directory>
-    """
-    import sys
-
-    if len(sys.argv) < 2:
-        print("\nAtomizerField Neural Field Parser v1.0")
-        print("="*60)
-        print("\nUsage:")
-        print("  python neural_field_parser.py <case_directory>")
-        print("\nExample:")
-        print("  python neural_field_parser.py training_case_001")
-        print("\nCase directory should contain:")
-        print("  input/model.bdf  (or model.dat)")
-        print("  output/model.op2")
-        print("\n")
-        sys.exit(1)
-
-    case_dir = sys.argv[1]
-
-    # Verify directory exists
-    if not Path(case_dir).exists():
-        print(f"ERROR: Directory not found: {case_dir}")
-        sys.exit(1)
-
-    # Create parser
-    try:
-        parser = NastranToNeuralFieldParser(case_dir)
-    except FileNotFoundError as e:
-        print(f"\nERROR: {e}")
-        print("\nPlease ensure your case directory contains:")
-        print("  input/model.bdf (or model.dat)")
-        print("  output/model.op2")
-        sys.exit(1)
-
-    # Parse all data
-    try:
-        data = parser.parse_all()
-
-        # Print summary
-        print("\n" + "="*60)
-        print("PARSING SUMMARY")
-        print("="*60)
-        print(f"Case: {data['metadata']['case_name']}")
-        print(f"Analysis: {data['metadata']['analysis_type']}")
-        print(f"\nMesh:")
-        print(f"  Nodes: {data['mesh']['statistics']['n_nodes']:,}")
-        print(f"  Elements: {data['mesh']['statistics']['n_elements']:,}")
-        for elem_type, count in data['mesh']['statistics']['element_types'].items():
-            if count > 0:
-                print(f"    {elem_type}: {count:,}")
-        print(f"\nMaterials: {len(data['materials'])}")
-        print(f"Boundary Conditions: {len(data['boundary_conditions']['spc'])} SPCs")
-        print(f"Loads: {len(data['loads']['point_forces'])} forces, {len(data['loads']['pressure'])} pressures")
-
-        if "displacement" in data['results']:
-            print(f"\nResults:")
-            print(f"  Displacement: {len(data['results']['displacement']['node_ids'])} nodes")
-            print(f"    Max: {data['results']['displacement']['max_translation']:.6f} mm")
-        if "stress" in data['results']:
-            for stress_type in data['results']['stress']:
-                if 'max_von_mises' in data['results']['stress'][stress_type]:
-                    max_vm = data['results']['stress'][stress_type]['max_von_mises']
-                    if max_vm is not None:
-                        print(f"  {stress_type}: Max VM = {max_vm:.2f} MPa")
-
-        print("\n[OK] Data ready for neural network training!")
-        print("="*60 + "\n")
-
-    except Exception as e:
-        print(f"\n" + "="*60)
-        print("ERROR DURING PARSING")
-        print("="*60)
-        print(f"{e}\n")
-        import traceback
-        traceback.print_exc()
-        sys.exit(1)
-
-
-if __name__ == "__main__":
-    main()

atomizer-field/neural_models/__init__.py

@@ -1,25 +0,0 @@
-"""
-AtomizerField Neural Models Package
-
-Phase 2: Neural Network Architecture for Field Prediction
-
-This package contains neural network models for learning complete FEA field results
-from mesh geometry, boundary conditions, and loads.
-
-Models:
-- AtomizerFieldModel: Full field predictor (displacement + stress fields)
-- ParametricFieldPredictor: Design-conditioned scalar predictor (mass, freq, disp, stress)
-"""
-
-__version__ = "2.0.0"
-
-# Import main model classes for convenience
-from .field_predictor import AtomizerFieldModel, create_model
-from .parametric_predictor import ParametricFieldPredictor, create_parametric_model
-
-__all__ = [
-    'AtomizerFieldModel',
-    'create_model',
-    'ParametricFieldPredictor',
-    'create_parametric_model',
-]

atomizer-field/neural_models/data_loader.py

@@ -1,416 +0,0 @@
-"""
-data_loader.py
-Data loading pipeline for neural field training
-
-AtomizerField Data Loader v2.0
-Converts parsed FEA data (HDF5 + JSON) into PyTorch Geometric graphs for training.
-
-Key Transformation:
-Parsed FEA Data → Graph Representation → Neural Network Input
-
-Graph structure:
-- Nodes: FEA mesh nodes (with coordinates, BCs, loads)
-- Edges: Element connectivity (with material properties)
-- Labels: Displacement and stress fields (ground truth from FEA)
-"""
-
-import json
-import h5py
-import numpy as np
-from pathlib import Path
-import torch
-from torch.utils.data import Dataset
-from torch_geometric.data import Data
-from torch_geometric.loader import DataLoader
-import warnings
-
-
-class FEAMeshDataset(Dataset):
-    """
-    PyTorch Dataset for FEA mesh data
-
-    Loads parsed neural field data and converts to PyTorch Geometric graphs.
-    Each graph represents one FEA analysis case.
-    """
-
-    def __init__(
-        self,
-        case_directories,
-        normalize=True,
-        include_stress=True,
-        cache_in_memory=False
-    ):
-        """
-        Initialize dataset
-
-        Args:
-            case_directories (list): List of paths to parsed cases
-            normalize (bool): Normalize node coordinates and results
-            include_stress (bool): Include stress in targets
-            cache_in_memory (bool): Load all data into RAM (faster but memory-intensive)
-        """
-        self.case_dirs = [Path(d) for d in case_directories]
-        self.normalize = normalize
-        self.include_stress = include_stress
-        self.cache_in_memory = cache_in_memory
-
-        # Validate all cases exist
-        self.valid_cases = []
-        for case_dir in self.case_dirs:
-            if self._validate_case(case_dir):
-                self.valid_cases.append(case_dir)
-            else:
-                warnings.warn(f"Skipping invalid case: {case_dir}")
-
-        print(f"Loaded {len(self.valid_cases)}/{len(self.case_dirs)} valid cases")
-
-        # Cache data if requested
-        self.cache = {}
-        if cache_in_memory:
-            print("Caching data in memory...")
-            for idx in range(len(self.valid_cases)):
-                self.cache[idx] = self._load_case(idx)
-            print("Cache complete!")
-
-        # Compute normalization statistics
-        if normalize:
-            self._compute_normalization_stats()
-
-    def _validate_case(self, case_dir):
-        """Check if case has required files"""
-        json_file = case_dir / "neural_field_data.json"
-        h5_file = case_dir / "neural_field_data.h5"
-        return json_file.exists() and h5_file.exists()
-
-    def __len__(self):
-        return len(self.valid_cases)
-
-    def __getitem__(self, idx):
-        """
-        Get graph data for one case
-
-        Returns:
-            torch_geometric.data.Data object with:
-                - x: Node features [num_nodes, feature_dim]
-                - edge_index: Element connectivity [2, num_edges]
-                - edge_attr: Edge features (material props) [num_edges, edge_dim]
-                - y_displacement: Target displacement [num_nodes, 6]
-                - y_stress: Target stress [num_nodes, 6] (if include_stress)
-                - bc_mask: Boundary condition mask [num_nodes, 6]
-                - pos: Node positions [num_nodes, 3]
-        """
-        if self.cache_in_memory and idx in self.cache:
-            return self.cache[idx]
-
-        return self._load_case(idx)
-
-    def _load_case(self, idx):
-        """Load and process a single case"""
-        case_dir = self.valid_cases[idx]
-
-        # Load JSON metadata
-        with open(case_dir / "neural_field_data.json", 'r') as f:
-            metadata = json.load(f)
-
-        # Load HDF5 field data
-        with h5py.File(case_dir / "neural_field_data.h5", 'r') as f:
-            # Node coordinates
-            node_coords = torch.from_numpy(f['mesh/node_coordinates'][:]).float()
-
-            # Displacement field (target)
-            displacement = torch.from_numpy(f['results/displacement'][:]).float()
-
-            # Stress field (target, if available)
-            stress = None
-            if self.include_stress and 'results/stress' in f:
-                # Try to load first available stress type
-                stress_group = f['results/stress']
-                for stress_type in stress_group.keys():
-                    stress_data = stress_group[stress_type]['data'][:]
-                    stress = torch.from_numpy(stress_data).float()
-                    break
-
-        # Build graph structure
-        graph_data = self._build_graph(metadata, node_coords, displacement, stress)
-
-        # Normalize if requested
-        if self.normalize:
-            graph_data = self._normalize_graph(graph_data)
-
-        return graph_data
-
-    def _build_graph(self, metadata, node_coords, displacement, stress):
-        """
-        Convert FEA mesh to graph
-
-        Args:
-            metadata (dict): Parsed metadata
-            node_coords (Tensor): Node positions [num_nodes, 3]
-            displacement (Tensor): Displacement field [num_nodes, 6]
-            stress (Tensor): Stress field [num_nodes, 6] or None
-
-        Returns:
-            torch_geometric.data.Data
-        """
-        num_nodes = node_coords.shape[0]
-
-        # === NODE FEATURES ===
-        # Start with coordinates
-        node_features = [node_coords]  # [num_nodes, 3]
-
-        # Add boundary conditions (which DOFs are constrained)
-        bc_mask = torch.zeros(num_nodes, 6)  # [num_nodes, 6]
-        if 'boundary_conditions' in metadata and 'spc' in metadata['boundary_conditions']:
-            for spc in metadata['boundary_conditions']['spc']:
-                node_id = spc['node']
-                # Find node index (assuming node IDs are sequential starting from 1)
-                # This is a simplification - production code should use ID mapping
-                if node_id <= num_nodes:
-                    dofs = spc['dofs']
-                    # Parse DOF string (e.g., "123" means constrained in x,y,z)
-                    for dof_char in str(dofs):
-                        if dof_char.isdigit():
-                            dof_idx = int(dof_char) - 1  # 0-indexed
-                            if 0 <= dof_idx < 6:
-                                bc_mask[node_id - 1, dof_idx] = 1.0
-
-        node_features.append(bc_mask)  # [num_nodes, 6]
-
-        # Add load information (force magnitude at each node)
-        load_features = torch.zeros(num_nodes, 3)  # [num_nodes, 3] for x,y,z forces
-        if 'loads' in metadata and 'point_forces' in metadata['loads']:
-            for force in metadata['loads']['point_forces']:
-                node_id = force['node']
-                if node_id <= num_nodes:
-                    magnitude = force['magnitude']
-                    direction = force['direction']
-                    force_vector = [magnitude * d for d in direction]
-                    load_features[node_id - 1] = torch.tensor(force_vector)
-
-        node_features.append(load_features)  # [num_nodes, 3]
-
-        # Concatenate all node features
-        x = torch.cat(node_features, dim=-1)  # [num_nodes, 3+6+3=12]
-
-        # === EDGE FEATURES ===
-        # Build edge index from element connectivity
-        edge_index = []
-        edge_attrs = []
-
-        # Get material properties
-        material_dict = {}
-        if 'materials' in metadata:
-            for mat in metadata['materials']:
-                mat_id = mat['id']
-                if mat['type'] == 'MAT1':
-                    material_dict[mat_id] = [
-                        mat.get('E', 0.0) / 1e6,  # Normalize E (MPa → GPa)
-                        mat.get('nu', 0.0),
-                        mat.get('rho', 0.0) * 1e6,  # Normalize rho
-                        mat.get('G', 0.0) / 1e6 if mat.get('G') else 0.0,
-                        mat.get('alpha', 0.0) * 1e6 if mat.get('alpha') else 0.0
-                    ]
-
-        # Process elements to create edges
-        if 'mesh' in metadata and 'elements' in metadata['mesh']:
-            for elem_type in ['solid', 'shell', 'beam']:
-                if elem_type in metadata['mesh']['elements']:
-                    for elem in metadata['mesh']['elements'][elem_type]:
-                        elem_nodes = elem['nodes']
-                        mat_id = elem.get('material_id', 1)
-
-                        # Get material properties for this element
-                        mat_props = material_dict.get(mat_id, [0.0] * 5)
-
-                        # Create edges between all node pairs in element
-                        # (fully connected within element)
-                        for i in range(len(elem_nodes)):
-                            for j in range(i + 1, len(elem_nodes)):
-                                node_i = elem_nodes[i] - 1  # 0-indexed
-                                node_j = elem_nodes[j] - 1
-
-                                if node_i < num_nodes and node_j < num_nodes:
-                                    # Add bidirectional edges
-                                    edge_index.append([node_i, node_j])
-                                    edge_index.append([node_j, node_i])
-
-                                    # Both edges get same material properties
-                                    edge_attrs.append(mat_props)
-                                    edge_attrs.append(mat_props)
-
-        # Convert to tensors
-        if edge_index:
-            edge_index = torch.tensor(edge_index, dtype=torch.long).t()  # [2, num_edges]
-            edge_attr = torch.tensor(edge_attrs, dtype=torch.float)  # [num_edges, 5]
-        else:
-            # No edges (shouldn't happen, but handle gracefully)
-            edge_index = torch.zeros((2, 0), dtype=torch.long)
-            edge_attr = torch.zeros((0, 5), dtype=torch.float)
-
-        # === CREATE DATA OBJECT ===
-        data = Data(
-            x=x,
-            edge_index=edge_index,
-            edge_attr=edge_attr,
-            y_displacement=displacement,
-            bc_mask=bc_mask,
-            pos=node_coords  # Store original positions
-        )
-
-        # Add stress if available
-        if stress is not None:
-            data.y_stress = stress
-
-        return data
-
-    def _normalize_graph(self, data):
-        """
-        Normalize graph features
-
-        - Coordinates: Center and scale to unit box
-        - Displacement: Scale by mean displacement
-        - Stress: Scale by mean stress
-        """
-        # Normalize coordinates (already done in node features)
-        if hasattr(self, 'coord_mean') and hasattr(self, 'coord_std'):
-            # Extract coords from features (first 3 dimensions)
-            coords = data.x[:, :3]
-            coords_norm = (coords - self.coord_mean) / (self.coord_std + 1e-8)
-            data.x[:, :3] = coords_norm
-
-        # Normalize displacement
-        if hasattr(self, 'disp_mean') and hasattr(self, 'disp_std'):
-            data.y_displacement = (data.y_displacement - self.disp_mean) / (self.disp_std + 1e-8)
-
-        # Normalize stress
-        if hasattr(data, 'y_stress') and hasattr(self, 'stress_mean') and hasattr(self, 'stress_std'):
-            data.y_stress = (data.y_stress - self.stress_mean) / (self.stress_std + 1e-8)
-
-        return data
-
-    def _compute_normalization_stats(self):
-        """
-        Compute mean and std for normalization across entire dataset
-        """
-        print("Computing normalization statistics...")
-
-        all_coords = []
-        all_disp = []
-        all_stress = []
-
-        for idx in range(len(self.valid_cases)):
-            case_dir = self.valid_cases[idx]
-
-            with h5py.File(case_dir / "neural_field_data.h5", 'r') as f:
-                coords = f['mesh/node_coordinates'][:]
-                disp = f['results/displacement'][:]
-
-                all_coords.append(coords)
-                all_disp.append(disp)
-
-                # Load stress if available
-                if self.include_stress and 'results/stress' in f:
-                    stress_group = f['results/stress']
-                    for stress_type in stress_group.keys():
-                        stress_data = stress_group[stress_type]['data'][:]
-                        all_stress.append(stress_data)
-                        break
-
-        # Concatenate all data
-        all_coords = np.concatenate(all_coords, axis=0)
-        all_disp = np.concatenate(all_disp, axis=0)
-
-        # Compute statistics
-        self.coord_mean = torch.from_numpy(all_coords.mean(axis=0)).float()
-        self.coord_std = torch.from_numpy(all_coords.std(axis=0)).float()
-
-        self.disp_mean = torch.from_numpy(all_disp.mean(axis=0)).float()
-        self.disp_std = torch.from_numpy(all_disp.std(axis=0)).float()
-
-        if all_stress:
-            all_stress = np.concatenate(all_stress, axis=0)
-            self.stress_mean = torch.from_numpy(all_stress.mean(axis=0)).float()
-            self.stress_std = torch.from_numpy(all_stress.std(axis=0)).float()
-
-        print("Normalization statistics computed!")
-
-
-def create_dataloaders(
-    train_cases,
-    val_cases,
-    batch_size=4,
-    num_workers=0,
-    normalize=True,
-    include_stress=True
-):
-    """
-    Create training and validation dataloaders
-
-    Args:
-        train_cases (list): List of training case directories
-        val_cases (list): List of validation case directories
-        batch_size (int): Batch size
-        num_workers (int): Number of data loading workers
-        normalize (bool): Normalize features
-        include_stress (bool): Include stress targets
-
-    Returns:
-        train_loader, val_loader
-    """
-    print("\nCreating datasets...")
-
-    # Create datasets
-    train_dataset = FEAMeshDataset(
-        train_cases,
-        normalize=normalize,
-        include_stress=include_stress,
-        cache_in_memory=False  # Set to True for small datasets
-    )
-
-    val_dataset = FEAMeshDataset(
-        val_cases,
-        normalize=normalize,
-        include_stress=include_stress,
-        cache_in_memory=False
-    )
-
-    # Share normalization stats with validation set
-    if normalize and hasattr(train_dataset, 'coord_mean'):
-        val_dataset.coord_mean = train_dataset.coord_mean
-        val_dataset.coord_std = train_dataset.coord_std
-        val_dataset.disp_mean = train_dataset.disp_mean
-        val_dataset.disp_std = train_dataset.disp_std
-        if hasattr(train_dataset, 'stress_mean'):
-            val_dataset.stress_mean = train_dataset.stress_mean
-            val_dataset.stress_std = train_dataset.stress_std
-
-    # Create dataloaders
-    train_loader = DataLoader(
-        train_dataset,
-        batch_size=batch_size,
-        shuffle=True,
-        num_workers=num_workers
-    )
-
-    val_loader = DataLoader(
-        val_dataset,
-        batch_size=batch_size,
-        shuffle=False,
-        num_workers=num_workers
-    )
-
-    print(f"\nDataloaders created:")
-    print(f"  Training: {len(train_dataset)} cases")
-    print(f"  Validation: {len(val_dataset)} cases")
-
-    return train_loader, val_loader
-
-
-if __name__ == "__main__":
-    # Test data loader
-    print("Testing FEA Mesh Data Loader...\n")
-
-    # This is a placeholder test - you would use actual parsed case directories
-    print("Note: This test requires actual parsed FEA data.")
-    print("Run the parser first on your NX Nastran files.")
-    print("\nData loader implementation complete!")

atomizer-field/neural_models/field_predictor.py

@@ -1,490 +0,0 @@
-"""
-field_predictor.py
-Graph Neural Network for predicting complete FEA field results
-
-AtomizerField Field Predictor v2.0
-Uses Graph Neural Networks to learn the physics of structural response.
-
-Key Innovation:
-Instead of: parameters → FEA → max_stress (scalar)
-We learn:  parameters → Neural Network → complete stress field (N values)
-
-This enables 1000x faster optimization with physics understanding.
-"""
-
-import torch
-import torch.nn as nn
-import torch.nn.functional as F
-from torch_geometric.nn import MessagePassing, global_mean_pool
-from torch_geometric.data import Data
-import numpy as np
-
-
-class MeshGraphConv(MessagePassing):
-    """
-    Custom Graph Convolution for FEA meshes
-
-    This layer propagates information along mesh edges (element connectivity)
-    to learn how forces flow through the structure.
-
-    Key insight: Stress and displacement fields follow mesh topology.
-    Adjacent elements influence each other through equilibrium.
-    """
-
-    def __init__(self, in_channels, out_channels, edge_dim=None):
-        """
-        Args:
-            in_channels (int): Input node feature dimension
-            out_channels (int): Output node feature dimension
-            edge_dim (int): Edge feature dimension (optional)
-        """
-        super().__init__(aggr='mean')  # Mean aggregation of neighbor messages
-
-        self.in_channels = in_channels
-        self.out_channels = out_channels
-
-        # Message function: how to combine node and edge features
-        if edge_dim is not None:
-            self.message_mlp = nn.Sequential(
-                nn.Linear(2 * in_channels + edge_dim, out_channels),
-                nn.LayerNorm(out_channels),
-                nn.ReLU(),
-                nn.Linear(out_channels, out_channels)
-            )
-        else:
-            self.message_mlp = nn.Sequential(
-                nn.Linear(2 * in_channels, out_channels),
-                nn.LayerNorm(out_channels),
-                nn.ReLU(),
-                nn.Linear(out_channels, out_channels)
-            )
-
-        # Update function: how to update node features
-        self.update_mlp = nn.Sequential(
-            nn.Linear(in_channels + out_channels, out_channels),
-            nn.LayerNorm(out_channels),
-            nn.ReLU(),
-            nn.Linear(out_channels, out_channels)
-        )
-
-        self.edge_dim = edge_dim
-
-    def forward(self, x, edge_index, edge_attr=None):
-        """
-        Propagate messages through the mesh graph
-
-        Args:
-            x: Node features [num_nodes, in_channels]
-            edge_index: Edge connectivity [2, num_edges]
-            edge_attr: Edge features [num_edges, edge_dim] (optional)
-
-        Returns:
-            Updated node features [num_nodes, out_channels]
-        """
-        return self.propagate(edge_index, x=x, edge_attr=edge_attr)
-
-    def message(self, x_i, x_j, edge_attr=None):
-        """
-        Construct messages from neighbors
-
-        Args:
-            x_i: Target node features
-            x_j: Source node features
-            edge_attr: Edge features
-        """
-        if edge_attr is not None:
-            # Combine source node, target node, and edge features
-            msg_input = torch.cat([x_i, x_j, edge_attr], dim=-1)
-        else:
-            msg_input = torch.cat([x_i, x_j], dim=-1)
-
-        return self.message_mlp(msg_input)
-
-    def update(self, aggr_out, x):
-        """
-        Update node features with aggregated messages
-
-        Args:
-            aggr_out: Aggregated messages from neighbors
-            x: Original node features
-        """
-        # Combine original features with aggregated messages
-        update_input = torch.cat([x, aggr_out], dim=-1)
-        return self.update_mlp(update_input)
-
-
-class FieldPredictorGNN(nn.Module):
-    """
-    Graph Neural Network for predicting complete FEA fields
-
-    Architecture:
-    1. Node Encoder: Encode node positions, BCs, loads
-    2. Edge Encoder: Encode element connectivity, material properties
-    3. Message Passing: Propagate information through mesh (multiple layers)
-    4. Field Decoder: Predict displacement/stress at each node/element
-
-    This architecture respects physics:
-    - Uses mesh topology (forces flow through connected elements)
-    - Incorporates boundary conditions (fixed/loaded nodes)
-    - Learns material behavior (E, nu → stress-strain relationship)
-    """
-
-    def __init__(
-        self,
-        node_feature_dim=3,      # Node coordinates (x, y, z)
-        edge_feature_dim=5,      # Material properties (E, nu, rho, etc.)
-        hidden_dim=128,
-        num_layers=6,
-        output_dim=6,            # 6 DOF displacement (3 translation + 3 rotation)
-        dropout=0.1
-    ):
-        """
-        Initialize field predictor
-
-        Args:
-            node_feature_dim (int): Dimension of node features (position + BCs + loads)
-            edge_feature_dim (int): Dimension of edge features (material properties)
-            hidden_dim (int): Hidden layer dimension
-            num_layers (int): Number of message passing layers
-            output_dim (int): Output dimension per node (6 for displacement)
-            dropout (float): Dropout rate
-        """
-        super().__init__()
-
-        self.node_feature_dim = node_feature_dim
-        self.edge_feature_dim = edge_feature_dim
-        self.hidden_dim = hidden_dim
-        self.num_layers = num_layers
-        self.output_dim = output_dim
-
-        # Node encoder: embed node coordinates + BCs + loads
-        self.node_encoder = nn.Sequential(
-            nn.Linear(node_feature_dim, hidden_dim),
-            nn.LayerNorm(hidden_dim),
-            nn.ReLU(),
-            nn.Dropout(dropout),
-            nn.Linear(hidden_dim, hidden_dim)
-        )
-
-        # Edge encoder: embed material properties
-        self.edge_encoder = nn.Sequential(
-            nn.Linear(edge_feature_dim, hidden_dim),
-            nn.LayerNorm(hidden_dim),
-            nn.ReLU(),
-            nn.Linear(hidden_dim, hidden_dim // 2)
-        )
-
-        # Message passing layers (the physics learning happens here)
-        self.conv_layers = nn.ModuleList([
-            MeshGraphConv(
-                in_channels=hidden_dim,
-                out_channels=hidden_dim,
-                edge_dim=hidden_dim // 2
-            )
-            for _ in range(num_layers)
-        ])
-
-        self.layer_norms = nn.ModuleList([
-            nn.LayerNorm(hidden_dim)
-            for _ in range(num_layers)
-        ])
-
-        self.dropouts = nn.ModuleList([
-            nn.Dropout(dropout)
-            for _ in range(num_layers)
-        ])
-
-        # Field decoder: predict displacement at each node
-        self.field_decoder = nn.Sequential(
-            nn.Linear(hidden_dim, hidden_dim),
-            nn.LayerNorm(hidden_dim),
-            nn.ReLU(),
-            nn.Dropout(dropout),
-            nn.Linear(hidden_dim, hidden_dim // 2),
-            nn.ReLU(),
-            nn.Linear(hidden_dim // 2, output_dim)
-        )
-
-        # Physics-informed constraint layer (optional, ensures equilibrium)
-        self.physics_scale = nn.Parameter(torch.ones(1))
-
-    def forward(self, data):
-        """
-        Forward pass: mesh → displacement field
-
-        Args:
-            data (torch_geometric.data.Data): Batch of mesh graphs containing:
-                - x: Node features [num_nodes, node_feature_dim]
-                - edge_index: Connectivity [2, num_edges]
-                - edge_attr: Edge features [num_edges, edge_feature_dim]
-                - batch: Batch assignment [num_nodes]
-
-        Returns:
-            displacement_field: Predicted displacement [num_nodes, output_dim]
-        """
-        x, edge_index, edge_attr = data.x, data.edge_index, data.edge_attr
-
-        # Encode nodes (positions + BCs + loads)
-        x = self.node_encoder(x)  # [num_nodes, hidden_dim]
-
-        # Encode edges (material properties)
-        if edge_attr is not None:
-            edge_features = self.edge_encoder(edge_attr)  # [num_edges, hidden_dim//2]
-        else:
-            edge_features = None
-
-        # Message passing: learn how forces propagate through mesh
-        for i, (conv, norm, dropout) in enumerate(zip(
-            self.conv_layers, self.layer_norms, self.dropouts
-        )):
-            # Graph convolution
-            x_new = conv(x, edge_index, edge_features)
-
-            # Residual connection (helps gradients flow)
-            x = x + dropout(x_new)
-
-            # Layer normalization
-            x = norm(x)
-
-        # Decode to displacement field
-        displacement = self.field_decoder(x)  # [num_nodes, output_dim]
-
-        # Apply physics-informed scaling
-        displacement = displacement * self.physics_scale
-
-        return displacement
-
-    def predict_stress_from_displacement(self, displacement, data, material_props):
-        """
-        Convert predicted displacement to stress using constitutive law
-
-        This implements: σ = C : ε = C : (∇u)
-        Where C is the material stiffness matrix
-
-        Args:
-            displacement: Predicted displacement [num_nodes, 6]
-            data: Mesh graph data
-            material_props: Material properties (E, nu)
-
-        Returns:
-            stress_field: Predicted stress [num_elements, n_components]
-        """
-        # This would compute strain from displacement gradients
-        # then apply material constitutive law
-        # For now, we'll predict displacement and train a separate stress predictor
-        raise NotImplementedError("Stress prediction implemented in StressPredictor")
-
-
-class StressPredictor(nn.Module):
-    """
-    Predicts stress field from displacement field
-
-    This can be:
-    1. Physics-based: Compute strain from displacement, apply constitutive law
-    2. Learned: Train neural network to predict stress from displacement
-
-    We use learned approach for flexibility with nonlinear materials.
-    """
-
-    def __init__(self, displacement_dim=6, hidden_dim=128, stress_components=6):
-        """
-        Args:
-            displacement_dim (int): Displacement DOFs per node
-            hidden_dim (int): Hidden layer size
-            stress_components (int): Stress tensor components (6 for 3D)
-        """
-        super().__init__()
-
-        # Stress predictor network
-        self.stress_net = nn.Sequential(
-            nn.Linear(displacement_dim, hidden_dim),
-            nn.LayerNorm(hidden_dim),
-            nn.ReLU(),
-            nn.Linear(hidden_dim, hidden_dim),
-            nn.LayerNorm(hidden_dim),
-            nn.ReLU(),
-            nn.Linear(hidden_dim, stress_components)
-        )
-
-    def forward(self, displacement):
-        """
-        Predict stress from displacement
-
-        Args:
-            displacement: [num_nodes, displacement_dim]
-
-        Returns:
-            stress: [num_nodes, stress_components]
-        """
-        return self.stress_net(displacement)
-
-
-class AtomizerFieldModel(nn.Module):
-    """
-    Complete AtomizerField model: predicts both displacement and stress fields
-
-    This is the main model you'll use for training and inference.
-    """
-
-    def __init__(
-        self,
-        node_feature_dim=10,     # 3 (xyz) + 6 (BC DOFs) + 1 (load magnitude)
-        edge_feature_dim=5,      # E, nu, rho, G, alpha
-        hidden_dim=128,
-        num_layers=6,
-        dropout=0.1
-    ):
-        """
-        Initialize complete field prediction model
-
-        Args:
-            node_feature_dim (int): Node features (coords + BCs + loads)
-            edge_feature_dim (int): Edge features (material properties)
-            hidden_dim (int): Hidden dimension
-            num_layers (int): Message passing layers
-            dropout (float): Dropout rate
-        """
-        super().__init__()
-
-        # Displacement predictor (main GNN)
-        self.displacement_predictor = FieldPredictorGNN(
-            node_feature_dim=node_feature_dim,
-            edge_feature_dim=edge_feature_dim,
-            hidden_dim=hidden_dim,
-            num_layers=num_layers,
-            output_dim=6,  # 6 DOF displacement
-            dropout=dropout
-        )
-
-        # Stress predictor (from displacement)
-        self.stress_predictor = StressPredictor(
-            displacement_dim=6,
-            hidden_dim=hidden_dim,
-            stress_components=6  # σxx, σyy, σzz, τxy, τyz, τxz
-        )
-
-    def forward(self, data, return_stress=True):
-        """
-        Predict displacement and stress fields
-
-        Args:
-            data: Mesh graph data
-            return_stress (bool): Whether to predict stress
-
-        Returns:
-            dict with:
-                - displacement: [num_nodes, 6]
-                - stress: [num_nodes, 6] (if return_stress=True)
-                - von_mises: [num_nodes] (if return_stress=True)
-        """
-        # Predict displacement
-        displacement = self.displacement_predictor(data)
-
-        results = {'displacement': displacement}
-
-        if return_stress:
-            # Predict stress from displacement
-            stress = self.stress_predictor(displacement)
-
-            # Calculate von Mises stress
-            # σ_vm = sqrt(0.5 * ((σxx-σyy)² + (σyy-σzz)² + (σzz-σxx)² + 6(τxy² + τyz² + τxz²)))
-            sxx, syy, szz, txy, tyz, txz = stress[:, 0], stress[:, 1], stress[:, 2], \
-                                            stress[:, 3], stress[:, 4], stress[:, 5]
-
-            von_mises = torch.sqrt(
-                0.5 * (
-                    (sxx - syy)**2 + (syy - szz)**2 + (szz - sxx)**2 +
-                    6 * (txy**2 + tyz**2 + txz**2)
-                )
-            )
-
-            results['stress'] = stress
-            results['von_mises'] = von_mises
-
-        return results
-
-    def get_max_values(self, results):
-        """
-        Extract maximum values (for compatibility with scalar optimization)
-
-        Args:
-            results: Output from forward()
-
-        Returns:
-            dict with max_displacement, max_stress
-        """
-        max_displacement = torch.max(torch.norm(results['displacement'][:, :3], dim=1))
-        max_stress = torch.max(results['von_mises']) if 'von_mises' in results else None
-
-        return {
-            'max_displacement': max_displacement,
-            'max_stress': max_stress
-        }
-
-
-def create_model(config=None):
-    """
-    Factory function to create AtomizerField model
-
-    Args:
-        config (dict): Model configuration
-
-    Returns:
-        AtomizerFieldModel instance
-    """
-    if config is None:
-        config = {
-            'node_feature_dim': 10,
-            'edge_feature_dim': 5,
-            'hidden_dim': 128,
-            'num_layers': 6,
-            'dropout': 0.1
-        }
-
-    model = AtomizerFieldModel(**config)
-
-    # Initialize weights
-    def init_weights(m):
-        if isinstance(m, nn.Linear):
-            nn.init.kaiming_normal_(m.weight, mode='fan_in', nonlinearity='relu')
-            if m.bias is not None:
-                nn.init.constant_(m.bias, 0)
-
-    model.apply(init_weights)
-
-    return model
-
-
-if __name__ == "__main__":
-    # Test model creation
-    print("Testing AtomizerField Model Creation...")
-
-    model = create_model()
-    print(f"Model created: {sum(p.numel() for p in model.parameters()):,} parameters")
-
-    # Create dummy data
-    num_nodes = 100
-    num_edges = 300
-
-    x = torch.randn(num_nodes, 10)  # Node features
-    edge_index = torch.randint(0, num_nodes, (2, num_edges))  # Edge connectivity
-    edge_attr = torch.randn(num_edges, 5)  # Edge features
-    batch = torch.zeros(num_nodes, dtype=torch.long)  # Batch assignment
-
-    data = Data(x=x, edge_index=edge_index, edge_attr=edge_attr, batch=batch)
-
-    # Forward pass
-    with torch.no_grad():
-        results = model(data)
-
-    print(f"\nTest forward pass:")
-    print(f"  Displacement shape: {results['displacement'].shape}")
-    print(f"  Stress shape: {results['stress'].shape}")
-    print(f"  Von Mises shape: {results['von_mises'].shape}")
-
-    max_vals = model.get_max_values(results)
-    print(f"\nMax values:")
-    print(f"  Max displacement: {max_vals['max_displacement']:.6f}")
-    print(f"  Max stress: {max_vals['max_stress']:.2f}")
-
-    print("\nModel test passed!")

atomizer-field/neural_models/parametric_predictor.py

@@ -1,470 +0,0 @@
-"""
-parametric_predictor.py
-Design-Conditioned Graph Neural Network for direct objective prediction
-
-AtomizerField Parametric Predictor v2.0
-
-Key Innovation:
-Instead of: parameters -> FEA -> objectives (expensive)
-We learn:   parameters -> Neural Network -> objectives (milliseconds)
-
-This model directly predicts all 4 optimization objectives:
-- mass (g)
-- frequency (Hz)
-- max_displacement (mm)
-- max_stress (MPa)
-
-Architecture:
-1. Design Encoder: MLP(n_design_vars -> 64 -> 128)
-2. GNN Backbone: 4 layers of design-conditioned message passing
-3. Global Pooling: Mean + Max pooling
-4. Scalar Heads: MLP(384 -> 128 -> 64 -> 4)
-
-This enables 2000x faster optimization with ~2-4% error.
-"""
-
-import torch
-import torch.nn as nn
-import torch.nn.functional as F
-from torch_geometric.nn import MessagePassing, global_mean_pool, global_max_pool
-from torch_geometric.data import Data
-import numpy as np
-from typing import Dict, Any, Optional
-
-
-class DesignConditionedConv(MessagePassing):
-    """
-    Graph Convolution layer conditioned on design parameters.
-
-    The design parameters modulate how information flows through the mesh,
-    allowing the network to learn design-dependent physics.
-    """
-
-    def __init__(self, in_channels: int, out_channels: int, design_dim: int, edge_dim: int = None):
-        """
-        Args:
-            in_channels: Input node feature dimension
-            out_channels: Output node feature dimension
-            design_dim: Design parameter dimension (after encoding)
-            edge_dim: Edge feature dimension (optional)
-        """
-        super().__init__(aggr='mean')
-
-        self.in_channels = in_channels
-        self.out_channels = out_channels
-        self.design_dim = design_dim
-
-        # Design-conditioned message function
-        message_input_dim = 2 * in_channels + design_dim
-        if edge_dim is not None:
-            message_input_dim += edge_dim
-
-        self.message_mlp = nn.Sequential(
-            nn.Linear(message_input_dim, out_channels),
-            nn.LayerNorm(out_channels),
-            nn.ReLU(),
-            nn.Linear(out_channels, out_channels)
-        )
-
-        # Update function
-        self.update_mlp = nn.Sequential(
-            nn.Linear(in_channels + out_channels, out_channels),
-            nn.LayerNorm(out_channels),
-            nn.ReLU(),
-            nn.Linear(out_channels, out_channels)
-        )
-
-        self.edge_dim = edge_dim
-
-    def forward(self, x, edge_index, design_features, edge_attr=None):
-        """
-        Forward pass with design conditioning.
-
-        Args:
-            x: Node features [num_nodes, in_channels]
-            edge_index: Edge connectivity [2, num_edges]
-            design_features: Design parameters [hidden] or [num_nodes, hidden]
-            edge_attr: Edge features [num_edges, edge_dim] (optional)
-
-        Returns:
-            Updated node features [num_nodes, out_channels]
-        """
-        num_nodes = x.size(0)
-
-        # Handle different input shapes for design_features
-        if design_features.dim() == 1:
-            # Single design vector [hidden] -> broadcast to all nodes
-            design_broadcast = design_features.unsqueeze(0).expand(num_nodes, -1)
-        elif design_features.dim() == 2 and design_features.size(0) == num_nodes:
-            # Already per-node [num_nodes, hidden]
-            design_broadcast = design_features
-        elif design_features.dim() == 2 and design_features.size(0) == 1:
-            # Single design [1, hidden] -> broadcast
-            design_broadcast = design_features.expand(num_nodes, -1)
-        else:
-            # Fallback: take mean across batch dimension if needed
-            design_broadcast = design_features.mean(dim=0).unsqueeze(0).expand(num_nodes, -1)
-
-        return self.propagate(
-            edge_index,
-            x=x,
-            design=design_broadcast,
-            edge_attr=edge_attr
-        )
-
-    def message(self, x_i, x_j, design_i, edge_attr=None):
-        """
-        Construct design-conditioned messages.
-
-        Args:
-            x_i: Target node features
-            x_j: Source node features
-            design_i: Design parameters at target nodes
-            edge_attr: Edge features
-        """
-        if edge_attr is not None:
-            msg_input = torch.cat([x_i, x_j, design_i, edge_attr], dim=-1)
-        else:
-            msg_input = torch.cat([x_i, x_j, design_i], dim=-1)
-
-        return self.message_mlp(msg_input)
-
-    def update(self, aggr_out, x):
-        """Update node features with aggregated messages."""
-        update_input = torch.cat([x, aggr_out], dim=-1)
-        return self.update_mlp(update_input)
-
-
-class ParametricFieldPredictor(nn.Module):
-    """
-    Design-conditioned GNN that predicts ALL optimization objectives from design parameters.
-
-    This is the "parametric" model that directly predicts scalar objectives,
-    making it much faster than field prediction followed by post-processing.
-
-    Architecture:
-    - Design Encoder: MLP that embeds design parameters
-    - Node Encoder: MLP that embeds mesh node features
-    - Edge Encoder: MLP that embeds material properties
-    - GNN Backbone: Design-conditioned message passing layers
-    - Global Pooling: Mean + Max pooling for graph-level representation
-    - Scalar Heads: MLPs that predict each objective
-
-    Outputs:
-    - mass: Predicted mass (grams)
-    - frequency: Predicted fundamental frequency (Hz)
-    - max_displacement: Maximum displacement magnitude (mm)
-    - max_stress: Maximum von Mises stress (MPa)
-    """
-
-    def __init__(self, config: Dict[str, Any] = None):
-        """
-        Initialize parametric predictor.
-
-        Args:
-            config: Model configuration dict with keys:
-                - input_channels: Node feature dimension (default: 12)
-                - edge_dim: Edge feature dimension (default: 5)
-                - hidden_channels: Hidden layer size (default: 128)
-                - num_layers: Number of GNN layers (default: 4)
-                - design_dim: Design parameter dimension (default: 4)
-                - dropout: Dropout rate (default: 0.1)
-        """
-        super().__init__()
-
-        # Default configuration
-        if config is None:
-            config = {}
-
-        self.input_channels = config.get('input_channels', 12)
-        self.edge_dim = config.get('edge_dim', 5)
-        self.hidden_channels = config.get('hidden_channels', 128)
-        self.num_layers = config.get('num_layers', 4)
-        self.design_dim = config.get('design_dim', 4)
-        self.dropout_rate = config.get('dropout', 0.1)
-
-        # Store config for checkpoint saving
-        self.config = {
-            'input_channels': self.input_channels,
-            'edge_dim': self.edge_dim,
-            'hidden_channels': self.hidden_channels,
-            'num_layers': self.num_layers,
-            'design_dim': self.design_dim,
-            'dropout': self.dropout_rate
-        }
-
-        # === DESIGN ENCODER ===
-        # Embeds design parameters into a higher-dimensional space
-        self.design_encoder = nn.Sequential(
-            nn.Linear(self.design_dim, 64),
-            nn.LayerNorm(64),
-            nn.ReLU(),
-            nn.Dropout(self.dropout_rate),
-            nn.Linear(64, self.hidden_channels),
-            nn.LayerNorm(self.hidden_channels),
-            nn.ReLU()
-        )
-
-        # === NODE ENCODER ===
-        # Embeds node features (coordinates, BCs, loads)
-        self.node_encoder = nn.Sequential(
-            nn.Linear(self.input_channels, self.hidden_channels),
-            nn.LayerNorm(self.hidden_channels),
-            nn.ReLU(),
-            nn.Dropout(self.dropout_rate),
-            nn.Linear(self.hidden_channels, self.hidden_channels)
-        )
-
-        # === EDGE ENCODER ===
-        # Embeds edge features (material properties)
-        self.edge_encoder = nn.Sequential(
-            nn.Linear(self.edge_dim, self.hidden_channels),
-            nn.LayerNorm(self.hidden_channels),
-            nn.ReLU(),
-            nn.Linear(self.hidden_channels, self.hidden_channels // 2)
-        )
-
-        # === GNN BACKBONE ===
-        # Design-conditioned message passing layers
-        self.conv_layers = nn.ModuleList([
-            DesignConditionedConv(
-                in_channels=self.hidden_channels,
-                out_channels=self.hidden_channels,
-                design_dim=self.hidden_channels,
-                edge_dim=self.hidden_channels // 2
-            )
-            for _ in range(self.num_layers)
-        ])
-
-        self.layer_norms = nn.ModuleList([
-            nn.LayerNorm(self.hidden_channels)
-            for _ in range(self.num_layers)
-        ])
-
-        self.dropouts = nn.ModuleList([
-            nn.Dropout(self.dropout_rate)
-            for _ in range(self.num_layers)
-        ])
-
-        # === GLOBAL POOLING ===
-        # Mean + Max pooling gives 2 * hidden_channels features
-        # Plus design features gives 3 * hidden_channels total
-        pooled_dim = 3 * self.hidden_channels
-
-        # === SCALAR PREDICTION HEADS ===
-        # Each head predicts one objective
-
-        self.mass_head = nn.Sequential(
-            nn.Linear(pooled_dim, self.hidden_channels),
-            nn.LayerNorm(self.hidden_channels),
-            nn.ReLU(),
-            nn.Dropout(self.dropout_rate),
-            nn.Linear(self.hidden_channels, 64),
-            nn.ReLU(),
-            nn.Linear(64, 1)
-        )
-
-        self.frequency_head = nn.Sequential(
-            nn.Linear(pooled_dim, self.hidden_channels),
-            nn.LayerNorm(self.hidden_channels),
-            nn.ReLU(),
-            nn.Dropout(self.dropout_rate),
-            nn.Linear(self.hidden_channels, 64),
-            nn.ReLU(),
-            nn.Linear(64, 1)
-        )
-
-        self.displacement_head = nn.Sequential(
-            nn.Linear(pooled_dim, self.hidden_channels),
-            nn.LayerNorm(self.hidden_channels),
-            nn.ReLU(),
-            nn.Dropout(self.dropout_rate),
-            nn.Linear(self.hidden_channels, 64),
-            nn.ReLU(),
-            nn.Linear(64, 1)
-        )
-
-        self.stress_head = nn.Sequential(
-            nn.Linear(pooled_dim, self.hidden_channels),
-            nn.LayerNorm(self.hidden_channels),
-            nn.ReLU(),
-            nn.Dropout(self.dropout_rate),
-            nn.Linear(self.hidden_channels, 64),
-            nn.ReLU(),
-            nn.Linear(64, 1)
-        )
-
-        # === OPTIONAL FIELD DECODER ===
-        # For returning displacement field if requested
-        self.field_decoder = nn.Sequential(
-            nn.Linear(self.hidden_channels, self.hidden_channels),
-            nn.LayerNorm(self.hidden_channels),
-            nn.ReLU(),
-            nn.Dropout(self.dropout_rate),
-            nn.Linear(self.hidden_channels, 6)  # 6 DOF displacement
-        )
-
-    def forward(
-        self,
-        data: Data,
-        design_params: torch.Tensor,
-        return_fields: bool = False
-    ) -> Dict[str, torch.Tensor]:
-        """
-        Forward pass: predict objectives from mesh + design parameters.
-
-        Args:
-            data: PyTorch Geometric Data object with:
-                - x: Node features [num_nodes, input_channels]
-                - edge_index: Edge connectivity [2, num_edges]
-                - edge_attr: Edge features [num_edges, edge_dim]
-                - batch: Batch assignment [num_nodes] (optional)
-            design_params: Normalized design parameters [design_dim] or [batch, design_dim]
-            return_fields: If True, also return displacement field prediction
-
-        Returns:
-            Dict with:
-                - mass: Predicted mass [batch_size]
-                - frequency: Predicted frequency [batch_size]
-                - max_displacement: Predicted max displacement [batch_size]
-                - max_stress: Predicted max stress [batch_size]
-                - displacement: (optional) Displacement field [num_nodes, 6]
-        """
-        x, edge_index, edge_attr = data.x, data.edge_index, data.edge_attr
-        num_nodes = x.size(0)
-
-        # Handle design params shape - ensure 2D [batch_size, design_dim]
-        if design_params.dim() == 1:
-            design_params = design_params.unsqueeze(0)
-
-        batch_size = design_params.size(0)
-
-        # Encode design parameters: [batch_size, design_dim] -> [batch_size, hidden]
-        design_encoded = self.design_encoder(design_params)
-
-        # Encode nodes (shared across all designs)
-        x_encoded = self.node_encoder(x)  # [num_nodes, hidden]
-
-        # Encode edges (shared across all designs)
-        if edge_attr is not None:
-            edge_features = self.edge_encoder(edge_attr)  # [num_edges, hidden//2]
-        else:
-            edge_features = None
-
-        # Process each design in the batch
-        all_graph_features = []
-
-        for i in range(batch_size):
-            # Get design for this sample
-            design_i = design_encoded[i]  # [hidden]
-
-            # Reset node features for this sample
-            x = x_encoded.clone()
-
-            # Message passing with design conditioning
-            for conv, norm, dropout in zip(self.conv_layers, self.layer_norms, self.dropouts):
-                x_new = conv(x, edge_index, design_i, edge_features)
-                x = x + dropout(x_new)  # Residual connection
-                x = norm(x)
-
-            # Global pooling for this sample
-            batch_idx = torch.zeros(num_nodes, dtype=torch.long, device=x.device)
-            x_mean = global_mean_pool(x, batch_idx)  # [1, hidden]
-            x_max = global_max_pool(x, batch_idx)    # [1, hidden]
-
-            # Concatenate pooled + design features
-            graph_feat = torch.cat([x_mean, x_max, design_encoded[i:i+1]], dim=-1)  # [1, 3*hidden]
-            all_graph_features.append(graph_feat)
-
-        # Stack all samples
-        graph_features = torch.cat(all_graph_features, dim=0)  # [batch_size, 3*hidden]
-
-        # Predict objectives
-        mass = self.mass_head(graph_features).squeeze(-1)
-        frequency = self.frequency_head(graph_features).squeeze(-1)
-        max_displacement = self.displacement_head(graph_features).squeeze(-1)
-        max_stress = self.stress_head(graph_features).squeeze(-1)
-
-        results = {
-            'mass': mass,
-            'frequency': frequency,
-            'max_displacement': max_displacement,
-            'max_stress': max_stress
-        }
-
-        # Optionally return displacement field (uses last processed x)
-        if return_fields:
-            displacement_field = self.field_decoder(x)  # [num_nodes, 6]
-            results['displacement'] = displacement_field
-
-        return results
-
-    def get_num_parameters(self) -> int:
-        """Get total number of trainable parameters."""
-        return sum(p.numel() for p in self.parameters() if p.requires_grad)
-
-
-def create_parametric_model(config: Dict[str, Any] = None) -> ParametricFieldPredictor:
-    """
-    Factory function to create parametric predictor model.
-
-    Args:
-        config: Model configuration dictionary
-
-    Returns:
-        Initialized ParametricFieldPredictor
-    """
-    model = ParametricFieldPredictor(config)
-
-    # Initialize weights
-    def init_weights(m):
-        if isinstance(m, nn.Linear):
-            nn.init.kaiming_normal_(m.weight, mode='fan_in', nonlinearity='relu')
-            if m.bias is not None:
-                nn.init.constant_(m.bias, 0)
-
-    model.apply(init_weights)
-
-    return model
-
-
-if __name__ == "__main__":
-    print("Testing Parametric Field Predictor...")
-    print("=" * 60)
-
-    # Create model with default config
-    model = create_parametric_model()
-    n_params = model.get_num_parameters()
-    print(f"Model created: {n_params:,} parameters")
-    print(f"Config: {model.config}")
-
-    # Create dummy data
-    num_nodes = 500
-    num_edges = 2000
-
-    x = torch.randn(num_nodes, 12)  # Node features
-    edge_index = torch.randint(0, num_nodes, (2, num_edges))
-    edge_attr = torch.randn(num_edges, 5)
-    batch = torch.zeros(num_nodes, dtype=torch.long)
-
-    data = Data(x=x, edge_index=edge_index, edge_attr=edge_attr, batch=batch)
-
-    # Design parameters
-    design_params = torch.randn(4)  # 4 design variables
-
-    # Forward pass
-    print("\nRunning forward pass...")
-    with torch.no_grad():
-        results = model(data, design_params, return_fields=True)
-
-    print(f"\nPredictions:")
-    print(f"  Mass: {results['mass'].item():.4f}")
-    print(f"  Frequency: {results['frequency'].item():.4f}")
-    print(f"  Max Displacement: {results['max_displacement'].item():.6f}")
-    print(f"  Max Stress: {results['max_stress'].item():.2f}")
-
-    if 'displacement' in results:
-        print(f"  Displacement field shape: {results['displacement'].shape}")
-
-    print("\n" + "=" * 60)
-    print("Parametric predictor test PASSED!")

atomizer-field/neural_models/physics_losses.py

@@ -1,449 +0,0 @@
-"""
-physics_losses.py
-Physics-informed loss functions for training FEA field predictors
-
-AtomizerField Physics-Informed Loss Functions v2.0
-
-Key Innovation:
-Standard neural networks only minimize prediction error.
-Physics-informed networks also enforce physical laws:
-- Equilibrium: Forces must balance
-- Compatibility: Strains must be compatible with displacements
-- Constitutive: Stress must follow material law (σ = C:ε)
-
-This makes the network learn physics, not just patterns.
-"""
-
-import torch
-import torch.nn as nn
-import torch.nn.functional as F
-
-
-class PhysicsInformedLoss(nn.Module):
-    """
-    Combined loss function with physics constraints
-
-    Total Loss = λ_data * L_data + λ_physics * L_physics
-
-    Where:
-    - L_data: Standard MSE between prediction and FEA ground truth
-    - L_physics: Physics violation penalty (equilibrium, compatibility, constitutive)
-    """
-
-    def __init__(
-        self,
-        lambda_data=1.0,
-        lambda_equilibrium=0.1,
-        lambda_constitutive=0.1,
-        lambda_boundary=1.0,
-        use_relative_error=True
-    ):
-        """
-        Initialize physics-informed loss
-
-        Args:
-            lambda_data (float): Weight for data loss
-            lambda_equilibrium (float): Weight for equilibrium violation
-            lambda_constitutive (float): Weight for constitutive law violation
-            lambda_boundary (float): Weight for boundary condition violation
-            use_relative_error (bool): Use relative error instead of absolute
-        """
-        super().__init__()
-
-        self.lambda_data = lambda_data
-        self.lambda_equilibrium = lambda_equilibrium
-        self.lambda_constitutive = lambda_constitutive
-        self.lambda_boundary = lambda_boundary
-        self.use_relative_error = use_relative_error
-
-    def forward(self, predictions, targets, data=None):
-        """
-        Compute total physics-informed loss
-
-        Args:
-            predictions (dict): Model predictions
-                - displacement: [num_nodes, 6]
-                - stress: [num_nodes, 6]
-                - von_mises: [num_nodes]
-            targets (dict): Ground truth from FEA
-                - displacement: [num_nodes, 6]
-                - stress: [num_nodes, 6]
-            data: Mesh graph data (for physics constraints)
-
-        Returns:
-            dict with:
-                - total_loss: Combined loss
-                - data_loss: Data fitting loss
-                - equilibrium_loss: Equilibrium violation
-                - constitutive_loss: Material law violation
-                - boundary_loss: BC violation
-        """
-        losses = {}
-
-        # 1. Data Loss: How well do predictions match FEA results?
-        losses['displacement_loss'] = self._displacement_loss(
-            predictions['displacement'],
-            targets['displacement']
-        )
-
-        if 'stress' in predictions and 'stress' in targets:
-            losses['stress_loss'] = self._stress_loss(
-                predictions['stress'],
-                targets['stress']
-            )
-        else:
-            losses['stress_loss'] = torch.tensor(0.0, device=predictions['displacement'].device)
-
-        losses['data_loss'] = losses['displacement_loss'] + losses['stress_loss']
-
-        # 2. Physics Losses: How well do predictions obey physics?
-        if data is not None:
-            # Equilibrium: ∇·σ + f = 0
-            losses['equilibrium_loss'] = self._equilibrium_loss(
-                predictions, data
-            )
-
-            # Constitutive: σ = C:ε
-            losses['constitutive_loss'] = self._constitutive_loss(
-                predictions, data
-            )
-
-            # Boundary conditions: u = 0 at fixed nodes
-            losses['boundary_loss'] = self._boundary_condition_loss(
-                predictions, data
-            )
-        else:
-            losses['equilibrium_loss'] = torch.tensor(0.0, device=predictions['displacement'].device)
-            losses['constitutive_loss'] = torch.tensor(0.0, device=predictions['displacement'].device)
-            losses['boundary_loss'] = torch.tensor(0.0, device=predictions['displacement'].device)
-
-        # Total loss
-        losses['total_loss'] = (
-            self.lambda_data * losses['data_loss'] +
-            self.lambda_equilibrium * losses['equilibrium_loss'] +
-            self.lambda_constitutive * losses['constitutive_loss'] +
-            self.lambda_boundary * losses['boundary_loss']
-        )
-
-        return losses
-
-    def _displacement_loss(self, pred, target):
-        """
-        Loss for displacement field
-
-        Uses relative error to handle different displacement magnitudes
-        """
-        if self.use_relative_error:
-            # Relative L2 error
-            diff = pred - target
-            rel_error = torch.norm(diff, dim=-1) / (torch.norm(target, dim=-1) + 1e-8)
-            return rel_error.mean()
-        else:
-            # Absolute MSE
-            return F.mse_loss(pred, target)
-
-    def _stress_loss(self, pred, target):
-        """
-        Loss for stress field
-
-        Emphasizes von Mises stress (most important for failure prediction)
-        """
-        # Component-wise MSE
-        component_loss = F.mse_loss(pred, target)
-
-        # Von Mises stress MSE (computed from components)
-        pred_vm = self._compute_von_mises(pred)
-        target_vm = self._compute_von_mises(target)
-        vm_loss = F.mse_loss(pred_vm, target_vm)
-
-        # Combined: 50% component accuracy, 50% von Mises accuracy
-        return 0.5 * component_loss + 0.5 * vm_loss
-
-    def _equilibrium_loss(self, predictions, data):
-        """
-        Equilibrium loss: ∇·σ + f = 0
-
-        In discrete form: sum of forces at each node should be zero
-        (where not externally loaded)
-
-        This is expensive to compute exactly, so we use a simplified version:
-        Check force balance on each element
-        """
-        # Simplified: For now, return zero (full implementation requires
-        # computing stress divergence from node stresses)
-        # TODO: Implement finite difference approximation of ∇·σ
-        return torch.tensor(0.0, device=predictions['displacement'].device)
-
-    def _constitutive_loss(self, predictions, data):
-        """
-        Constitutive law loss: σ = C:ε
-
-        Check if predicted stress is consistent with predicted strain
-        (which comes from displacement gradient)
-
-        Simplified version: Check if stress-strain relationship is reasonable
-        """
-        # Simplified: For now, return zero
-        # Full implementation would:
-        # 1. Compute strain from displacement gradient
-        # 2. Compute expected stress from strain using material stiffness
-        # 3. Compare with predicted stress
-        # TODO: Implement strain computation and constitutive check
-        return torch.tensor(0.0, device=predictions['displacement'].device)
-
-    def _boundary_condition_loss(self, predictions, data):
-        """
-        Boundary condition loss: u = 0 at fixed DOFs
-
-        Penalize non-zero displacement at constrained nodes
-        """
-        if not hasattr(data, 'bc_mask') or data.bc_mask is None:
-            return torch.tensor(0.0, device=predictions['displacement'].device)
-
-        # bc_mask: [num_nodes, 6] boolean mask where True = constrained
-        displacement = predictions['displacement']
-        bc_mask = data.bc_mask
-
-        # Compute penalty for non-zero displacement at constrained DOFs
-        constrained_displacement = displacement * bc_mask.float()
-        bc_loss = torch.mean(constrained_displacement ** 2)
-
-        return bc_loss
-
-    def _compute_von_mises(self, stress):
-        """
-        Compute von Mises stress from stress tensor components
-
-        Args:
-            stress: [num_nodes, 6] with [σxx, σyy, σzz, τxy, τyz, τxz]
-
-        Returns:
-            von_mises: [num_nodes]
-        """
-        sxx, syy, szz = stress[:, 0], stress[:, 1], stress[:, 2]
-        txy, tyz, txz = stress[:, 3], stress[:, 4], stress[:, 5]
-
-        vm = torch.sqrt(
-            0.5 * (
-                (sxx - syy)**2 + (syy - szz)**2 + (szz - sxx)**2 +
-                6 * (txy**2 + tyz**2 + txz**2)
-            )
-        )
-
-        return vm
-
-
-class FieldMSELoss(nn.Module):
-    """
-    Simple MSE loss for field prediction (no physics constraints)
-
-    Use this for initial training or when physics constraints are too strict.
-    """
-
-    def __init__(self, weight_displacement=1.0, weight_stress=1.0):
-        """
-        Args:
-            weight_displacement (float): Weight for displacement loss
-            weight_stress (float): Weight for stress loss
-        """
-        super().__init__()
-        self.weight_displacement = weight_displacement
-        self.weight_stress = weight_stress
-
-    def forward(self, predictions, targets):
-        """
-        Compute MSE loss
-
-        Args:
-            predictions (dict): Model outputs
-            targets (dict): Ground truth
-
-        Returns:
-            dict with loss components
-        """
-        losses = {}
-
-        # Displacement MSE
-        losses['displacement_loss'] = F.mse_loss(
-            predictions['displacement'],
-            targets['displacement']
-        )
-
-        # Stress MSE (if available)
-        if 'stress' in predictions and 'stress' in targets:
-            losses['stress_loss'] = F.mse_loss(
-                predictions['stress'],
-                targets['stress']
-            )
-        else:
-            losses['stress_loss'] = torch.tensor(0.0, device=predictions['displacement'].device)
-
-        # Total loss
-        losses['total_loss'] = (
-            self.weight_displacement * losses['displacement_loss'] +
-            self.weight_stress * losses['stress_loss']
-        )
-
-        return losses
-
-
-class RelativeFieldLoss(nn.Module):
-    """
-    Relative error loss - better for varying displacement/stress magnitudes
-
-    Uses: ||pred - target|| / ||target||
-    This makes the loss scale-invariant.
-    """
-
-    def __init__(self, epsilon=1e-8):
-        """
-        Args:
-            epsilon (float): Small constant to avoid division by zero
-        """
-        super().__init__()
-        self.epsilon = epsilon
-
-    def forward(self, predictions, targets):
-        """
-        Compute relative error loss
-
-        Args:
-            predictions (dict): Model outputs
-            targets (dict): Ground truth
-
-        Returns:
-            dict with loss components
-        """
-        losses = {}
-
-        # Relative displacement error
-        disp_diff = predictions['displacement'] - targets['displacement']
-        disp_norm_pred = torch.norm(disp_diff, dim=-1)
-        disp_norm_target = torch.norm(targets['displacement'], dim=-1)
-        losses['displacement_loss'] = (disp_norm_pred / (disp_norm_target + self.epsilon)).mean()
-
-        # Relative stress error
-        if 'stress' in predictions and 'stress' in targets:
-            stress_diff = predictions['stress'] - targets['stress']
-            stress_norm_pred = torch.norm(stress_diff, dim=-1)
-            stress_norm_target = torch.norm(targets['stress'], dim=-1)
-            losses['stress_loss'] = (stress_norm_pred / (stress_norm_target + self.epsilon)).mean()
-        else:
-            losses['stress_loss'] = torch.tensor(0.0, device=predictions['displacement'].device)
-
-        # Total loss
-        losses['total_loss'] = losses['displacement_loss'] + losses['stress_loss']
-
-        return losses
-
-
-class MaxValueLoss(nn.Module):
-    """
-    Loss on maximum values only (for backward compatibility with scalar optimization)
-
-    This is useful if you want to ensure the network gets the critical max values right,
-    even if the field distribution is slightly off.
-    """
-
-    def __init__(self):
-        super().__init__()
-
-    def forward(self, predictions, targets):
-        """
-        Compute loss on maximum displacement and stress
-
-        Args:
-            predictions (dict): Model outputs with 'displacement', 'von_mises'
-            targets (dict): Ground truth
-
-        Returns:
-            dict with loss components
-        """
-        losses = {}
-
-        # Max displacement error
-        pred_max_disp = torch.max(torch.norm(predictions['displacement'][:, :3], dim=1))
-        target_max_disp = torch.max(torch.norm(targets['displacement'][:, :3], dim=1))
-        losses['max_displacement_loss'] = F.mse_loss(pred_max_disp, target_max_disp)
-
-        # Max von Mises stress error
-        if 'von_mises' in predictions and 'stress' in targets:
-            pred_max_vm = torch.max(predictions['von_mises'])
-
-            # Compute target von Mises
-            target_stress = targets['stress']
-            sxx, syy, szz = target_stress[:, 0], target_stress[:, 1], target_stress[:, 2]
-            txy, tyz, txz = target_stress[:, 3], target_stress[:, 4], target_stress[:, 5]
-            target_vm = torch.sqrt(
-                0.5 * ((sxx - syy)**2 + (syy - szz)**2 + (szz - sxx)**2 +
-                       6 * (txy**2 + tyz**2 + txz**2))
-            )
-            target_max_vm = torch.max(target_vm)
-
-            losses['max_stress_loss'] = F.mse_loss(pred_max_vm, target_max_vm)
-        else:
-            losses['max_stress_loss'] = torch.tensor(0.0, device=predictions['displacement'].device)
-
-        # Total loss
-        losses['total_loss'] = losses['max_displacement_loss'] + losses['max_stress_loss']
-
-        return losses
-
-
-def create_loss_function(loss_type='mse', config=None):
-    """
-    Factory function to create loss function
-
-    Args:
-        loss_type (str): Type of loss ('mse', 'relative', 'physics', 'max')
-        config (dict): Loss function configuration
-
-    Returns:
-        Loss function instance
-    """
-    if config is None:
-        config = {}
-
-    if loss_type == 'mse':
-        return FieldMSELoss(**config)
-    elif loss_type == 'relative':
-        return RelativeFieldLoss(**config)
-    elif loss_type == 'physics':
-        return PhysicsInformedLoss(**config)
-    elif loss_type == 'max':
-        return MaxValueLoss(**config)
-    else:
-        raise ValueError(f"Unknown loss type: {loss_type}")
-
-
-if __name__ == "__main__":
-    # Test loss functions
-    print("Testing AtomizerField Loss Functions...\n")
-
-    # Create dummy predictions and targets
-    num_nodes = 100
-    pred = {
-        'displacement': torch.randn(num_nodes, 6),
-        'stress': torch.randn(num_nodes, 6),
-        'von_mises': torch.abs(torch.randn(num_nodes))
-    }
-    target = {
-        'displacement': torch.randn(num_nodes, 6),
-        'stress': torch.randn(num_nodes, 6)
-    }
-
-    # Test each loss function
-    loss_types = ['mse', 'relative', 'physics', 'max']
-
-    for loss_type in loss_types:
-        print(f"Testing {loss_type.upper()} loss...")
-        loss_fn = create_loss_function(loss_type)
-        losses = loss_fn(pred, target)
-
-        print(f"  Total loss: {losses['total_loss']:.6f}")
-        for key, value in losses.items():
-            if key != 'total_loss':
-                print(f"    {key}: {value:.6f}")
-        print()
-
-    print("Loss function tests passed!")

atomizer-field/neural_models/uncertainty.py

@@ -1,361 +0,0 @@
-"""
-uncertainty.py
-Uncertainty quantification for neural field predictions
-
-AtomizerField Uncertainty Quantification v2.1
-Know when to trust predictions and when to run FEA!
-
-Key Features:
-- Ensemble-based uncertainty estimation
-- Confidence intervals for predictions
-- Automatic FEA recommendation
-- Online calibration
-"""
-
-import torch
-import torch.nn as nn
-import numpy as np
-from copy import deepcopy
-
-from .field_predictor import AtomizerFieldModel
-
-
-class UncertainFieldPredictor(nn.Module):
-    """
-    Ensemble of models for uncertainty quantification
-
-    Uses multiple models trained with different initializations
-    to estimate prediction uncertainty.
-
-    When uncertainty is high → Recommend FEA validation
-    When uncertainty is low → Trust neural prediction
-    """
-
-    def __init__(self, base_model_config, n_ensemble=5):
-        """
-        Initialize ensemble
-
-        Args:
-            base_model_config (dict): Configuration for base model
-            n_ensemble (int): Number of models in ensemble
-        """
-        super().__init__()
-
-        print(f"\nCreating ensemble with {n_ensemble} models...")
-
-        # Create ensemble of models
-        self.models = nn.ModuleList([
-            AtomizerFieldModel(**base_model_config)
-            for _ in range(n_ensemble)
-        ])
-
-        self.n_ensemble = n_ensemble
-
-        # Initialize each model differently
-        for i, model in enumerate(self.models):
-            self._init_weights(model, seed=i)
-
-        print(f"Ensemble created with {n_ensemble} models")
-
-    def _init_weights(self, model, seed):
-        """Initialize model weights with different seed"""
-        torch.manual_seed(seed)
-
-        def init_fn(m):
-            if isinstance(m, nn.Linear):
-                nn.init.kaiming_normal_(m.weight, mode='fan_in', nonlinearity='relu')
-                if m.bias is not None:
-                    nn.init.constant_(m.bias, 0)
-
-        model.apply(init_fn)
-
-    def forward(self, data, return_uncertainty=True, return_all_predictions=False):
-        """
-        Forward pass through ensemble
-
-        Args:
-            data: Input graph data
-            return_uncertainty (bool): Return uncertainty estimates
-            return_all_predictions (bool): Return all individual predictions
-
-        Returns:
-            dict: Predictions with uncertainty
-                - displacement: Mean prediction
-                - stress: Mean prediction
-                - von_mises: Mean prediction
-                - displacement_std: Standard deviation (if return_uncertainty)
-                - stress_std: Standard deviation (if return_uncertainty)
-                - von_mises_std: Standard deviation (if return_uncertainty)
-                - all_predictions: List of all predictions (if return_all_predictions)
-        """
-        # Get predictions from all models
-        all_predictions = []
-
-        for model in self.models:
-            with torch.no_grad():
-                pred = model(data, return_stress=True)
-                all_predictions.append(pred)
-
-        # Stack predictions
-        displacement_stack = torch.stack([p['displacement'] for p in all_predictions])
-        stress_stack = torch.stack([p['stress'] for p in all_predictions])
-        von_mises_stack = torch.stack([p['von_mises'] for p in all_predictions])
-
-        # Compute mean predictions
-        results = {
-            'displacement': displacement_stack.mean(dim=0),
-            'stress': stress_stack.mean(dim=0),
-            'von_mises': von_mises_stack.mean(dim=0)
-        }
-
-        # Compute uncertainty (standard deviation across ensemble)
-        if return_uncertainty:
-            results['displacement_std'] = displacement_stack.std(dim=0)
-            results['stress_std'] = stress_stack.std(dim=0)
-            results['von_mises_std'] = von_mises_stack.std(dim=0)
-
-            # Overall uncertainty metrics
-            results['max_displacement_uncertainty'] = results['displacement_std'].max().item()
-            results['max_stress_uncertainty'] = results['von_mises_std'].max().item()
-
-            # Uncertainty as percentage of prediction
-            results['displacement_rel_uncertainty'] = (
-                results['displacement_std'] / (torch.abs(results['displacement']) + 1e-8)
-            ).mean().item()
-
-            results['stress_rel_uncertainty'] = (
-                results['von_mises_std'] / (results['von_mises'] + 1e-8)
-            ).mean().item()
-
-        # Return all predictions if requested
-        if return_all_predictions:
-            results['all_predictions'] = all_predictions
-
-        return results
-
-    def needs_fea_validation(self, predictions, threshold=0.1):
-        """
-        Determine if FEA validation is recommended
-
-        Args:
-            predictions (dict): Output from forward() with uncertainty
-            threshold (float): Relative uncertainty threshold
-
-        Returns:
-            dict: Recommendation and reasons
-        """
-        reasons = []
-
-        # Check displacement uncertainty
-        if predictions['displacement_rel_uncertainty'] > threshold:
-            reasons.append(
-                f"High displacement uncertainty: "
-                f"{predictions['displacement_rel_uncertainty']*100:.1f}% > {threshold*100:.1f}%"
-            )
-
-        # Check stress uncertainty
-        if predictions['stress_rel_uncertainty'] > threshold:
-            reasons.append(
-                f"High stress uncertainty: "
-                f"{predictions['stress_rel_uncertainty']*100:.1f}% > {threshold*100:.1f}%"
-            )
-
-        recommend_fea = len(reasons) > 0
-
-        return {
-            'recommend_fea': recommend_fea,
-            'reasons': reasons,
-            'displacement_uncertainty': predictions['displacement_rel_uncertainty'],
-            'stress_uncertainty': predictions['stress_rel_uncertainty']
-        }
-
-    def get_confidence_intervals(self, predictions, confidence=0.95):
-        """
-        Compute confidence intervals for predictions
-
-        Args:
-            predictions (dict): Output from forward() with uncertainty
-            confidence (float): Confidence level (0.95 = 95% confidence)
-
-        Returns:
-            dict: Confidence intervals
-        """
-        # For normal distribution, 95% CI is ±1.96 std
-        # For 90% CI is ±1.645 std
-        z_score = {0.90: 1.645, 0.95: 1.96, 0.99: 2.576}.get(confidence, 1.96)
-
-        intervals = {}
-
-        # Displacement intervals
-        intervals['displacement_lower'] = predictions['displacement'] - z_score * predictions['displacement_std']
-        intervals['displacement_upper'] = predictions['displacement'] + z_score * predictions['displacement_std']
-
-        # Stress intervals
-        intervals['von_mises_lower'] = predictions['von_mises'] - z_score * predictions['von_mises_std']
-        intervals['von_mises_upper'] = predictions['von_mises'] + z_score * predictions['von_mises_std']
-
-        # Max values with confidence intervals
-        max_vm = predictions['von_mises'].max()
-        max_vm_std = predictions['von_mises_std'].max()
-
-        intervals['max_stress_estimate'] = max_vm.item()
-        intervals['max_stress_lower'] = (max_vm - z_score * max_vm_std).item()
-        intervals['max_stress_upper'] = (max_vm + z_score * max_vm_std).item()
-
-        return intervals
-
-
-class OnlineLearner:
-    """
-    Online learning from FEA runs during optimization
-
-    As optimization progresses and you run FEA for validation,
-    this module can quickly update the model to improve predictions.
-
-    This creates a virtuous cycle:
-    1. Use neural network for fast exploration
-    2. Run FEA on promising designs
-    3. Update neural network with new data
-    4. Neural network gets better → need less FEA
-    """
-
-    def __init__(self, model, learning_rate=0.0001):
-        """
-        Initialize online learner
-
-        Args:
-            model: Neural network model
-            learning_rate (float): Learning rate for updates
-        """
-        self.model = model
-        self.optimizer = torch.optim.Adam(model.parameters(), lr=learning_rate)
-        self.replay_buffer = []
-        self.update_count = 0
-
-        print(f"\nOnline learner initialized")
-        print(f"Learning rate: {learning_rate}")
-
-    def add_fea_result(self, graph_data, fea_results):
-        """
-        Add new FEA result to replay buffer
-
-        Args:
-            graph_data: Mesh graph
-            fea_results (dict): FEA results (displacement, stress)
-        """
-        self.replay_buffer.append({
-            'graph_data': graph_data,
-            'fea_results': fea_results
-        })
-
-        print(f"Added FEA result to buffer (total: {len(self.replay_buffer)})")
-
-    def quick_update(self, steps=10):
-        """
-        Quick fine-tuning on recent FEA results
-
-        Args:
-            steps (int): Number of gradient steps
-        """
-        if len(self.replay_buffer) == 0:
-            print("No data in replay buffer")
-            return
-
-        print(f"\nQuick update: {steps} steps on {len(self.replay_buffer)} samples")
-
-        self.model.train()
-
-        for step in range(steps):
-            total_loss = 0.0
-
-            # Train on all samples in buffer
-            for sample in self.replay_buffer:
-                graph_data = sample['graph_data']
-                fea_results = sample['fea_results']
-
-                # Forward pass
-                predictions = self.model(graph_data, return_stress=True)
-
-                # Compute loss
-                disp_loss = nn.functional.mse_loss(
-                    predictions['displacement'],
-                    fea_results['displacement']
-                )
-
-                if 'stress' in fea_results:
-                    stress_loss = nn.functional.mse_loss(
-                        predictions['stress'],
-                        fea_results['stress']
-                    )
-                    loss = disp_loss + stress_loss
-                else:
-                    loss = disp_loss
-
-                # Backward pass
-                self.optimizer.zero_grad()
-                loss.backward()
-                self.optimizer.step()
-
-                total_loss += loss.item()
-
-            if step % 5 == 0:
-                avg_loss = total_loss / len(self.replay_buffer)
-                print(f"  Step {step}/{steps}: Loss = {avg_loss:.6f}")
-
-        self.model.eval()
-        self.update_count += 1
-
-        print(f"Update complete (total updates: {self.update_count})")
-
-    def clear_buffer(self):
-        """Clear replay buffer"""
-        self.replay_buffer = []
-        print("Replay buffer cleared")
-
-
-def create_uncertain_predictor(model_config, n_ensemble=5):
-    """
-    Factory function to create uncertain predictor
-
-    Args:
-        model_config (dict): Model configuration
-        n_ensemble (int): Ensemble size
-
-    Returns:
-        UncertainFieldPredictor instance
-    """
-    return UncertainFieldPredictor(model_config, n_ensemble)
-
-
-if __name__ == "__main__":
-    # Test uncertainty quantification
-    print("Testing Uncertainty Quantification...\n")
-
-    # Create ensemble
-    model_config = {
-        'node_feature_dim': 12,
-        'edge_feature_dim': 5,
-        'hidden_dim': 64,
-        'num_layers': 4,
-        'dropout': 0.1
-    }
-
-    ensemble = UncertainFieldPredictor(model_config, n_ensemble=3)
-
-    print(f"\nEnsemble created with {ensemble.n_ensemble} models")
-    print("Uncertainty quantification ready!")
-    print("\nUsage:")
-    print("""
-    # Get predictions with uncertainty
-    predictions = ensemble(graph_data, return_uncertainty=True)
-
-    # Check if FEA validation needed
-    recommendation = ensemble.needs_fea_validation(predictions, threshold=0.1)
-
-    if recommendation['recommend_fea']:
-        print("Recommendation: Run FEA for validation")
-        for reason in recommendation['reasons']:
-            print(f"  - {reason}")
-    else:
-        print("Prediction confident - no FEA needed!")
-    """)

atomizer-field/optimization_interface.py

@@ -1,421 +0,0 @@
-"""
-optimization_interface.py
-Bridge between AtomizerField neural network and Atomizer optimization platform
-
-AtomizerField Optimization Interface v2.1
-Enables gradient-based optimization with neural field predictions.
-
-Key Features:
-- Drop-in replacement for FEA evaluation (1000× faster)
-- Gradient computation for sensitivity analysis
-- Field-aware optimization (knows WHERE stress occurs)
-- Uncertainty quantification (knows when to trust predictions)
-- Automatic FEA fallback for high-uncertainty cases
-"""
-
-import torch
-import torch.nn.functional as F
-import numpy as np
-from pathlib import Path
-import json
-import time
-
-from neural_models.field_predictor import AtomizerFieldModel
-from neural_models.data_loader import FEAMeshDataset
-
-
-class NeuralFieldOptimizer:
-    """
-    Optimization interface for AtomizerField
-
-    This class provides a simple API for optimization:
-    - evaluate(parameters) → objectives (max_stress, max_disp, etc.)
-    - get_sensitivities(parameters) → gradients for optimization
-    - get_fields(parameters) → complete stress/displacement fields
-
-    Usage:
-        optimizer = NeuralFieldOptimizer('checkpoint_best.pt')
-        results = optimizer.evaluate(parameters)
-        print(f"Max stress: {results['max_stress']:.2f} MPa")
-    """
-
-    def __init__(
-        self,
-        model_path,
-        uncertainty_threshold=0.1,
-        enable_gradients=True,
-        device=None
-    ):
-        """
-        Initialize optimizer
-
-        Args:
-            model_path (str): Path to trained model checkpoint
-            uncertainty_threshold (float): Uncertainty above which to recommend FEA
-            enable_gradients (bool): Enable gradient computation
-            device (str): Device to run on ('cuda' or 'cpu')
-        """
-        if device is None:
-            self.device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
-        else:
-            self.device = torch.device(device)
-
-        print(f"\nAtomizerField Optimization Interface v2.1")
-        print(f"Device: {self.device}")
-
-        # Load model
-        print(f"Loading model from {model_path}...")
-        checkpoint = torch.load(model_path, map_location=self.device)
-
-        # Create model
-        model_config = checkpoint['config']['model']
-        self.model = AtomizerFieldModel(**model_config)
-        self.model.load_state_dict(checkpoint['model_state_dict'])
-        self.model = self.model.to(self.device)
-        self.model.eval()
-
-        self.config = checkpoint['config']
-        self.uncertainty_threshold = uncertainty_threshold
-        self.enable_gradients = enable_gradients
-
-        # Model info
-        self.model_info = {
-            'version': checkpoint.get('epoch', 'unknown'),
-            'best_val_loss': checkpoint.get('best_val_loss', 'unknown'),
-            'training_config': checkpoint['config']
-        }
-
-        print(f"Model loaded successfully!")
-        print(f"  Epoch: {checkpoint.get('epoch', 'N/A')}")
-        print(f"  Validation loss: {checkpoint.get('best_val_loss', 'N/A')}")
-
-        # Statistics for tracking
-        self.eval_count = 0
-        self.total_time = 0.0
-
-    def evaluate(self, graph_data, return_fields=False):
-        """
-        Evaluate design using neural network (drop-in FEA replacement)
-
-        Args:
-            graph_data: PyTorch Geometric Data object with mesh graph
-            return_fields (bool): Return complete fields or just objectives
-
-        Returns:
-            dict: Optimization objectives and optionally complete fields
-                - max_stress: Maximum von Mises stress (MPa)
-                - max_displacement: Maximum displacement (mm)
-                - mass: Total mass (kg) if available
-                - fields: Complete stress/displacement fields (if return_fields=True)
-                - inference_time_ms: Prediction time
-                - uncertainty: Prediction uncertainty (if ensemble enabled)
-        """
-        start_time = time.time()
-
-        # Move to device
-        graph_data = graph_data.to(self.device)
-
-        # Predict
-        with torch.set_grad_enabled(self.enable_gradients):
-            predictions = self.model(graph_data, return_stress=True)
-
-        inference_time = (time.time() - start_time) * 1000  # ms
-
-        # Extract objectives
-        max_displacement = torch.max(
-            torch.norm(predictions['displacement'][:, :3], dim=1)
-        ).item()
-
-        max_stress = torch.max(predictions['von_mises']).item()
-
-        results = {
-            'max_stress': max_stress,
-            'max_displacement': max_displacement,
-            'inference_time_ms': inference_time,
-            'evaluation_count': self.eval_count
-        }
-
-        # Add complete fields if requested
-        if return_fields:
-            results['fields'] = {
-                'displacement': predictions['displacement'].cpu().detach().numpy(),
-                'stress': predictions['stress'].cpu().detach().numpy(),
-                'von_mises': predictions['von_mises'].cpu().detach().numpy()
-            }
-
-        # Update statistics
-        self.eval_count += 1
-        self.total_time += inference_time
-
-        return results
-
-    def get_sensitivities(self, graph_data, objective='max_stress'):
-        """
-        Compute gradients for gradient-based optimization
-
-        This enables MUCH faster optimization than finite differences!
-
-        Args:
-            graph_data: PyTorch Geometric Data with requires_grad=True
-            objective (str): Which objective to differentiate ('max_stress' or 'max_displacement')
-
-        Returns:
-            dict: Gradients with respect to input features
-                - node_gradients: ∂objective/∂node_features
-                - edge_gradients: ∂objective/∂edge_features
-        """
-        if not self.enable_gradients:
-            raise RuntimeError("Gradients not enabled. Set enable_gradients=True")
-
-        # Enable gradients
-        graph_data = graph_data.to(self.device)
-        graph_data.x.requires_grad_(True)
-        if graph_data.edge_attr is not None:
-            graph_data.edge_attr.requires_grad_(True)
-
-        # Forward pass
-        predictions = self.model(graph_data, return_stress=True)
-
-        # Compute objective
-        if objective == 'max_stress':
-            obj = torch.max(predictions['von_mises'])
-        elif objective == 'max_displacement':
-            disp_mag = torch.norm(predictions['displacement'][:, :3], dim=1)
-            obj = torch.max(disp_mag)
-        else:
-            raise ValueError(f"Unknown objective: {objective}")
-
-        # Backward pass
-        obj.backward()
-
-        # Extract gradients
-        gradients = {
-            'node_gradients': graph_data.x.grad.cpu().numpy(),
-            'objective_value': obj.item()
-        }
-
-        if graph_data.edge_attr is not None and graph_data.edge_attr.grad is not None:
-            gradients['edge_gradients'] = graph_data.edge_attr.grad.cpu().numpy()
-
-        return gradients
-
-    def batch_evaluate(self, graph_data_list, return_fields=False):
-        """
-        Evaluate multiple designs in batch (even faster!)
-
-        Args:
-            graph_data_list (list): List of graph data objects
-            return_fields (bool): Return complete fields
-
-        Returns:
-            list: List of evaluation results
-        """
-        results = []
-
-        for graph_data in graph_data_list:
-            result = self.evaluate(graph_data, return_fields=return_fields)
-            results.append(result)
-
-        return results
-
-    def needs_fea_validation(self, uncertainty):
-        """
-        Determine if FEA validation is recommended
-
-        Args:
-            uncertainty (float): Prediction uncertainty
-
-        Returns:
-            bool: True if FEA is recommended
-        """
-        return uncertainty > self.uncertainty_threshold
-
-    def compare_with_fea(self, graph_data, fea_results):
-        """
-        Compare neural predictions with FEA ground truth
-
-        Args:
-            graph_data: Mesh graph
-            fea_results (dict): FEA results with 'max_stress', 'max_displacement'
-
-        Returns:
-            dict: Comparison metrics
-        """
-        # Neural prediction
-        pred = self.evaluate(graph_data)
-
-        # Compute errors
-        stress_error = abs(pred['max_stress'] - fea_results['max_stress'])
-        stress_rel_error = stress_error / (fea_results['max_stress'] + 1e-8)
-
-        disp_error = abs(pred['max_displacement'] - fea_results['max_displacement'])
-        disp_rel_error = disp_error / (fea_results['max_displacement'] + 1e-8)
-
-        comparison = {
-            'neural_prediction': pred,
-            'fea_results': fea_results,
-            'errors': {
-                'stress_error_abs': stress_error,
-                'stress_error_rel': stress_rel_error,
-                'displacement_error_abs': disp_error,
-                'displacement_error_rel': disp_rel_error
-            },
-            'within_tolerance': stress_rel_error < 0.1 and disp_rel_error < 0.1
-        }
-
-        return comparison
-
-    def get_statistics(self):
-        """
-        Get optimizer usage statistics
-
-        Returns:
-            dict: Statistics about predictions
-        """
-        avg_time = self.total_time / self.eval_count if self.eval_count > 0 else 0
-
-        return {
-            'total_evaluations': self.eval_count,
-            'total_time_ms': self.total_time,
-            'average_time_ms': avg_time,
-            'model_info': self.model_info
-        }
-
-    def reset_statistics(self):
-        """Reset usage statistics"""
-        self.eval_count = 0
-        self.total_time = 0.0
-
-
-class ParametricOptimizer:
-    """
-    Optimizer for parametric designs
-
-    This wraps NeuralFieldOptimizer and adds parameter → mesh conversion.
-    Enables direct optimization over design parameters (thickness, radius, etc.)
-    """
-
-    def __init__(
-        self,
-        model_path,
-        parameter_names,
-        parameter_bounds,
-        mesh_generator_fn
-    ):
-        """
-        Initialize parametric optimizer
-
-        Args:
-            model_path (str): Path to trained model
-            parameter_names (list): Names of design parameters
-            parameter_bounds (dict): Bounds for each parameter
-            mesh_generator_fn: Function that converts parameters → graph_data
-        """
-        self.neural_optimizer = NeuralFieldOptimizer(model_path)
-        self.parameter_names = parameter_names
-        self.parameter_bounds = parameter_bounds
-        self.mesh_generator = mesh_generator_fn
-
-        print(f"\nParametric Optimizer initialized")
-        print(f"Design parameters: {parameter_names}")
-
-    def evaluate_parameters(self, parameters):
-        """
-        Evaluate design from parameters
-
-        Args:
-            parameters (dict): Design parameters
-
-        Returns:
-            dict: Objectives (max_stress, max_displacement, etc.)
-        """
-        # Generate mesh from parameters
-        graph_data = self.mesh_generator(parameters)
-
-        # Evaluate
-        results = self.neural_optimizer.evaluate(graph_data)
-
-        # Add parameters to results
-        results['parameters'] = parameters
-
-        return results
-
-    def optimize(
-        self,
-        initial_parameters,
-        objectives,
-        constraints,
-        method='gradient',
-        max_iterations=100
-    ):
-        """
-        Run optimization
-
-        Args:
-            initial_parameters (dict): Starting point
-            objectives (list): Objectives to minimize/maximize
-            constraints (list): Constraint functions
-            method (str): Optimization method ('gradient' or 'genetic')
-            max_iterations (int): Maximum iterations
-
-        Returns:
-            dict: Optimal parameters and results
-        """
-        # This would integrate with scipy.optimize or genetic algorithms
-        # Placeholder for now
-
-        print(f"\nStarting optimization with {method} method...")
-        print(f"Initial parameters: {initial_parameters}")
-        print(f"Objectives: {objectives}")
-        print(f"Max iterations: {max_iterations}")
-
-        # TODO: Implement optimization loop
-        # For gradient-based:
-        #   1. Evaluate at current parameters
-        #   2. Compute sensitivities
-        #   3. Update parameters using gradients
-        #   4. Repeat until convergence
-
-        raise NotImplementedError("Full optimization loop coming in next update!")
-
-
-def create_optimizer(model_path, config=None):
-    """
-    Factory function to create optimizer
-
-    Args:
-        model_path (str): Path to trained model
-        config (dict): Optimizer configuration
-
-    Returns:
-        NeuralFieldOptimizer instance
-    """
-    if config is None:
-        config = {}
-
-    return NeuralFieldOptimizer(model_path, **config)
-
-
-if __name__ == "__main__":
-    # Example usage
-    print("AtomizerField Optimization Interface")
-    print("=" * 60)
-    print("\nThis module provides fast optimization with neural field predictions.")
-    print("\nExample usage:")
-    print("""
-    # Create optimizer
-    optimizer = NeuralFieldOptimizer('checkpoint_best.pt')
-
-    # Evaluate design
-    results = optimizer.evaluate(graph_data)
-    print(f"Max stress: {results['max_stress']:.2f} MPa")
-    print(f"Inference time: {results['inference_time_ms']:.1f} ms")
-
-    # Get sensitivities for gradient-based optimization
-    gradients = optimizer.get_sensitivities(graph_data, objective='max_stress')
-
-    # Batch evaluation (test 1000 designs in seconds!)
-    all_results = optimizer.batch_evaluate(design_variants)
-    """)
-
-    print("\nOptimization interface ready!")

atomizer-field/predict.py

@@ -1,373 +0,0 @@
-"""
-predict.py
-Inference script for AtomizerField trained models
-
-AtomizerField Inference v2.0
-Uses trained GNN to predict FEA fields 1000x faster than traditional simulation.
-
-Usage:
-    python predict.py --model checkpoint_best.pt --input case_001
-
-This enables:
-- Rapid design exploration (milliseconds vs hours per analysis)
-- Real-time optimization
-- Interactive design feedback
-"""
-
-import argparse
-import json
-from pathlib import Path
-import time
-
-import torch
-import numpy as np
-import h5py
-
-from neural_models.field_predictor import AtomizerFieldModel
-from neural_models.data_loader import FEAMeshDataset
-
-
-class FieldPredictor:
-    """
-    Inference engine for trained field prediction models
-    """
-
-    def __init__(self, checkpoint_path, device=None):
-        """
-        Initialize predictor
-
-        Args:
-            checkpoint_path (str): Path to trained model checkpoint
-            device (str): Device to run on ('cuda' or 'cpu')
-        """
-        if device is None:
-            self.device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
-        else:
-            self.device = torch.device(device)
-
-        print(f"\nAtomizerField Inference Engine v2.0")
-        print(f"Device: {self.device}")
-
-        # Load checkpoint
-        print(f"Loading model from {checkpoint_path}...")
-        checkpoint = torch.load(checkpoint_path, map_location=self.device)
-
-        # Create model
-        model_config = checkpoint['config']['model']
-        self.model = AtomizerFieldModel(**model_config)
-        self.model.load_state_dict(checkpoint['model_state_dict'])
-        self.model = self.model.to(self.device)
-        self.model.eval()
-
-        self.config = checkpoint['config']
-
-        print(f"Model loaded (epoch {checkpoint['epoch']}, val_loss={checkpoint['best_val_loss']:.6f})")
-
-    def predict(self, case_directory):
-        """
-        Predict displacement and stress fields for a case
-
-        Args:
-            case_directory (str): Path to parsed FEA case
-
-        Returns:
-            dict: Predictions with displacement, stress, von_mises fields
-        """
-        print(f"\nPredicting fields for {Path(case_directory).name}...")
-
-        # Load data
-        dataset = FEAMeshDataset(
-            [case_directory],
-            normalize=True,
-            include_stress=False  # Don't need ground truth for prediction
-        )
-
-        if len(dataset) == 0:
-            raise ValueError(f"Could not load case from {case_directory}")
-
-        data = dataset[0].to(self.device)
-
-        # Predict
-        start_time = time.time()
-
-        with torch.no_grad():
-            predictions = self.model(data, return_stress=True)
-
-        inference_time = time.time() - start_time
-
-        print(f"Prediction complete in {inference_time*1000:.1f} ms")
-
-        # Convert to numpy
-        results = {
-            'displacement': predictions['displacement'].cpu().numpy(),
-            'stress': predictions['stress'].cpu().numpy(),
-            'von_mises': predictions['von_mises'].cpu().numpy(),
-            'inference_time_ms': inference_time * 1000
-        }
-
-        # Compute max values
-        max_disp = np.max(np.linalg.norm(results['displacement'][:, :3], axis=1))
-        max_stress = np.max(results['von_mises'])
-
-        results['max_displacement'] = float(max_disp)
-        results['max_stress'] = float(max_stress)
-
-        print(f"\nResults:")
-        print(f"  Max displacement: {max_disp:.6f} mm")
-        print(f"  Max von Mises stress: {max_stress:.2f} MPa")
-
-        return results
-
-    def save_predictions(self, predictions, case_directory, output_name='predicted'):
-        """
-        Save predictions in same format as ground truth
-
-        Args:
-            predictions (dict): Prediction results
-            case_directory (str): Case directory
-            output_name (str): Output file name prefix
-        """
-        case_dir = Path(case_directory)
-        output_file = case_dir / f"{output_name}_fields.h5"
-
-        print(f"\nSaving predictions to {output_file}...")
-
-        with h5py.File(output_file, 'w') as f:
-            # Save displacement
-            f.create_dataset('displacement',
-                           data=predictions['displacement'],
-                           compression='gzip')
-
-            # Save stress
-            f.create_dataset('stress',
-                           data=predictions['stress'],
-                           compression='gzip')
-
-            # Save von Mises
-            f.create_dataset('von_mises',
-                           data=predictions['von_mises'],
-                           compression='gzip')
-
-            # Save metadata
-            f.attrs['max_displacement'] = predictions['max_displacement']
-            f.attrs['max_stress'] = predictions['max_stress']
-            f.attrs['inference_time_ms'] = predictions['inference_time_ms']
-
-        print(f"Predictions saved!")
-
-        # Also save JSON summary
-        summary_file = case_dir / f"{output_name}_summary.json"
-        summary = {
-            'max_displacement': predictions['max_displacement'],
-            'max_stress': predictions['max_stress'],
-            'inference_time_ms': predictions['inference_time_ms'],
-            'num_nodes': len(predictions['displacement'])
-        }
-
-        with open(summary_file, 'w') as f:
-            json.dump(summary, f, indent=2)
-
-        print(f"Summary saved to {summary_file}")
-
-    def compare_with_ground_truth(self, predictions, case_directory):
-        """
-        Compare predictions with FEA ground truth
-
-        Args:
-            predictions (dict): Model predictions
-            case_directory (str): Case directory with ground truth
-
-        Returns:
-            dict: Comparison metrics
-        """
-        case_dir = Path(case_directory)
-        h5_file = case_dir / "neural_field_data.h5"
-
-        if not h5_file.exists():
-            print("No ground truth available for comparison")
-            return None
-
-        print("\nComparing with FEA ground truth...")
-
-        # Load ground truth
-        with h5py.File(h5_file, 'r') as f:
-            gt_displacement = f['results/displacement'][:]
-
-            # Try to load stress
-            gt_stress = None
-            if 'results/stress' in f:
-                stress_group = f['results/stress']
-                for stress_type in stress_group.keys():
-                    gt_stress = stress_group[stress_type]['data'][:]
-                    break
-
-        # Compute errors
-        pred_disp = predictions['displacement']
-        disp_error = np.linalg.norm(pred_disp - gt_displacement, axis=1)
-        disp_magnitude = np.linalg.norm(gt_displacement, axis=1)
-        rel_disp_error = disp_error / (disp_magnitude + 1e-8)
-
-        metrics = {
-            'displacement': {
-                'mae': float(np.mean(disp_error)),
-                'rmse': float(np.sqrt(np.mean(disp_error**2))),
-                'relative_error': float(np.mean(rel_disp_error)),
-                'max_error': float(np.max(disp_error))
-            }
-        }
-
-        # Compare max values
-        pred_max_disp = predictions['max_displacement']
-        gt_max_disp = float(np.max(disp_magnitude))
-        metrics['max_displacement_error'] = abs(pred_max_disp - gt_max_disp)
-        metrics['max_displacement_relative_error'] = metrics['max_displacement_error'] / (gt_max_disp + 1e-8)
-
-        if gt_stress is not None:
-            pred_stress = predictions['stress']
-            stress_error = np.linalg.norm(pred_stress - gt_stress, axis=1)
-
-            metrics['stress'] = {
-                'mae': float(np.mean(stress_error)),
-                'rmse': float(np.sqrt(np.mean(stress_error**2))),
-            }
-
-        # Print comparison
-        print("\nComparison Results:")
-        print(f"  Displacement MAE: {metrics['displacement']['mae']:.6f} mm")
-        print(f"  Displacement RMSE: {metrics['displacement']['rmse']:.6f} mm")
-        print(f"  Displacement Relative Error: {metrics['displacement']['relative_error']*100:.2f}%")
-        print(f"  Max Displacement Error: {metrics['max_displacement_error']:.6f} mm ({metrics['max_displacement_relative_error']*100:.2f}%)")
-
-        if 'stress' in metrics:
-            print(f"  Stress MAE: {metrics['stress']['mae']:.2f} MPa")
-            print(f"  Stress RMSE: {metrics['stress']['rmse']:.2f} MPa")
-
-        return metrics
-
-
-def batch_predict(predictor, case_directories, output_dir=None):
-    """
-    Run predictions on multiple cases
-
-    Args:
-        predictor (FieldPredictor): Initialized predictor
-        case_directories (list): List of case directories
-        output_dir (str): Optional output directory for results
-
-    Returns:
-        list: List of prediction results
-    """
-    print(f"\n{'='*60}")
-    print(f"Batch Prediction: {len(case_directories)} cases")
-    print(f"{'='*60}")
-
-    results = []
-
-    for i, case_dir in enumerate(case_directories, 1):
-        print(f"\n[{i}/{len(case_directories)}] Processing {Path(case_dir).name}...")
-
-        try:
-            # Predict
-            predictions = predictor.predict(case_dir)
-
-            # Save predictions
-            predictor.save_predictions(predictions, case_dir)
-
-            # Compare with ground truth
-            comparison = predictor.compare_with_ground_truth(predictions, case_dir)
-
-            result = {
-                'case': str(case_dir),
-                'status': 'success',
-                'predictions': {
-                    'max_displacement': predictions['max_displacement'],
-                    'max_stress': predictions['max_stress'],
-                    'inference_time_ms': predictions['inference_time_ms']
-                },
-                'comparison': comparison
-            }
-
-            results.append(result)
-
-        except Exception as e:
-            print(f"ERROR: {e}")
-            results.append({
-                'case': str(case_dir),
-                'status': 'failed',
-                'error': str(e)
-            })
-
-    # Save batch results
-    if output_dir:
-        output_path = Path(output_dir)
-        output_path.mkdir(parents=True, exist_ok=True)
-
-        results_file = output_path / 'batch_predictions.json'
-        with open(results_file, 'w') as f:
-            json.dump(results, f, indent=2)
-
-        print(f"\nBatch results saved to {results_file}")
-
-    # Print summary
-    print(f"\n{'='*60}")
-    print("Batch Prediction Summary")
-    print(f"{'='*60}")
-    successful = sum(1 for r in results if r['status'] == 'success')
-    print(f"Successful: {successful}/{len(results)}")
-
-    if successful > 0:
-        avg_time = np.mean([r['predictions']['inference_time_ms']
-                           for r in results if r['status'] == 'success'])
-        print(f"Average inference time: {avg_time:.1f} ms")
-
-    return results
-
-
-def main():
-    """
-    Main inference entry point
-    """
-    parser = argparse.ArgumentParser(description='Predict FEA fields using trained model')
-
-    parser.add_argument('--model', type=str, required=True,
-                       help='Path to model checkpoint')
-    parser.add_argument('--input', type=str, required=True,
-                       help='Input case directory or directory containing multiple cases')
-    parser.add_argument('--output_dir', type=str, default=None,
-                       help='Output directory for batch results')
-    parser.add_argument('--batch', action='store_true',
-                       help='Process all subdirectories as separate cases')
-    parser.add_argument('--device', type=str, default=None,
-                       choices=['cuda', 'cpu'],
-                       help='Device to run on')
-    parser.add_argument('--compare', action='store_true',
-                       help='Compare predictions with ground truth')
-
-    args = parser.parse_args()
-
-    # Create predictor
-    predictor = FieldPredictor(args.model, device=args.device)
-
-    input_path = Path(args.input)
-
-    if args.batch:
-        # Batch prediction
-        case_dirs = [d for d in input_path.iterdir() if d.is_dir()]
-        batch_predict(predictor, case_dirs, args.output_dir)
-
-    else:
-        # Single prediction
-        predictions = predictor.predict(args.input)
-
-        # Save predictions
-        predictor.save_predictions(predictions, args.input)
-
-        # Compare with ground truth if requested
-        if args.compare:
-            predictor.compare_with_ground_truth(predictions, args.input)
-
-    print("\nInference complete!")
-
-
-if __name__ == "__main__":
-    main()

atomizer-field/requirements.txt

@@ -1,43 +0,0 @@
-# AtomizerField Requirements
-# Python 3.8+ required
-
-# ============================================================================
-# Phase 1: Data Parser
-# ============================================================================
-
-# Core FEA parsing
-pyNastran>=1.4.0
-
-# Numerical computing
-numpy>=1.20.0
-
-# HDF5 file format for efficient field data storage
-h5py>=3.0.0
-
-# ============================================================================
-# Phase 2: Neural Network Training
-# ============================================================================
-
-# Deep learning framework
-torch>=2.0.0
-
-# Graph neural networks
-torch-geometric>=2.3.0
-
-# TensorBoard for training visualization
-tensorboard>=2.13.0
-
-# ============================================================================
-# Optional: Development and Testing
-# ============================================================================
-
-# Testing
-# pytest>=7.0.0
-# pytest-cov>=4.0.0
-
-# Visualization
-# matplotlib>=3.5.0
-# plotly>=5.0.0
-
-# Progress bars
-# tqdm>=4.65.0

atomizer-field/test_simple_beam.py

@@ -1,376 +0,0 @@
-"""
-test_simple_beam.py
-Test AtomizerField with your actual Simple Beam model
-
-This test validates the complete pipeline:
-1. Parse BDF/OP2 files
-2. Convert to graph format
-3. Make predictions
-4. Compare with ground truth
-
-Usage:
-    python test_simple_beam.py
-"""
-
-import sys
-import os
-from pathlib import Path
-import json
-import time
-
-print("\n" + "="*60)
-print("AtomizerField Simple Beam Test")
-print("="*60 + "\n")
-
-# Test configuration
-BEAM_DIR = Path("Models/Simple Beam")
-TEST_CASE_DIR = Path("test_case_beam")
-
-def test_1_check_files():
-    """Test 1: Check if beam files exist"""
-    print("[TEST 1] Checking for beam files...")
-
-    bdf_file = BEAM_DIR / "beam_sim1-solution_1.dat"
-    op2_file = BEAM_DIR / "beam_sim1-solution_1.op2"
-
-    if not BEAM_DIR.exists():
-        print(f"  [X] FAIL: Directory not found: {BEAM_DIR}")
-        return False
-
-    if not bdf_file.exists():
-        print(f"  [X] FAIL: BDF file not found: {bdf_file}")
-        return False
-
-    if not op2_file.exists():
-        print(f"  [X] FAIL: OP2 file not found: {op2_file}")
-        return False
-
-    # Check file sizes
-    bdf_size = bdf_file.stat().st_size / 1024  # KB
-    op2_size = op2_file.stat().st_size / 1024  # KB
-
-    print(f"  [OK] Found BDF file: {bdf_file.name} ({bdf_size:.1f} KB)")
-    print(f"  [OK] Found OP2 file: {op2_file.name} ({op2_size:.1f} KB)")
-    print(f"  Status: PASS\n")
-
-    return True
-
-def test_2_setup_test_case():
-    """Test 2: Set up test case directory structure"""
-    print("[TEST 2] Setting up test case directory...")
-
-    try:
-        # Create directories
-        (TEST_CASE_DIR / "input").mkdir(parents=True, exist_ok=True)
-        (TEST_CASE_DIR / "output").mkdir(parents=True, exist_ok=True)
-
-        print(f"  [OK] Created: {TEST_CASE_DIR / 'input'}")
-        print(f"  [OK] Created: {TEST_CASE_DIR / 'output'}")
-
-        # Copy files (create symbolic links or copy)
-        import shutil
-
-        src_bdf = BEAM_DIR / "beam_sim1-solution_1.dat"
-        src_op2 = BEAM_DIR / "beam_sim1-solution_1.op2"
-
-        dst_bdf = TEST_CASE_DIR / "input" / "model.bdf"
-        dst_op2 = TEST_CASE_DIR / "output" / "model.op2"
-
-        # Copy files
-        if not dst_bdf.exists():
-            shutil.copy(src_bdf, dst_bdf)
-            print(f"  [OK] Copied BDF to {dst_bdf}")
-        else:
-            print(f"  [OK] BDF already exists: {dst_bdf}")
-
-        if not dst_op2.exists():
-            shutil.copy(src_op2, dst_op2)
-            print(f"  [OK] Copied OP2 to {dst_op2}")
-        else:
-            print(f"  [OK] OP2 already exists: {dst_op2}")
-
-        print(f"  Status: PASS\n")
-        return True
-
-    except Exception as e:
-        print(f"  [X] FAIL: {str(e)}\n")
-        return False
-
-def test_3_import_modules():
-    """Test 3: Import required modules"""
-    print("[TEST 3] Importing modules...")
-
-    try:
-        print("  Importing pyNastran...", end=" ")
-        from pyNastran.bdf.bdf import BDF
-        from pyNastran.op2.op2 import OP2
-        print("[OK]")
-
-        print("  Importing AtomizerField parser...", end=" ")
-        from neural_field_parser import NastranToNeuralFieldParser
-        print("[OK]")
-
-        print(f"  Status: PASS\n")
-        return True
-
-    except ImportError as e:
-        print(f"\n  [X] FAIL: Import error: {str(e)}\n")
-        return False
-    except Exception as e:
-        print(f"\n  [X] FAIL: {str(e)}\n")
-        return False
-
-def test_4_parse_beam():
-    """Test 4: Parse beam BDF/OP2 files"""
-    print("[TEST 4] Parsing beam files...")
-
-    try:
-        from neural_field_parser import NastranToNeuralFieldParser
-
-        # Create parser
-        print(f"  Initializing parser for {TEST_CASE_DIR}...")
-        parser = NastranToNeuralFieldParser(str(TEST_CASE_DIR))
-
-        # Parse
-        print(f"  Parsing BDF and OP2 files...")
-        start_time = time.time()
-
-        data = parser.parse_all()
-
-        parse_time = time.time() - start_time
-
-        # Check results
-        print(f"\n  Parse Results:")
-        print(f"    Time: {parse_time:.2f} seconds")
-        print(f"    Nodes: {data['mesh']['statistics']['n_nodes']:,}")
-        print(f"    Elements: {data['mesh']['statistics']['n_elements']:,}")
-        print(f"    Materials: {len(data['materials'])}")
-
-        if 'displacement' in data.get('results', {}):
-            max_disp = data['results']['displacement']['max_translation']
-            print(f"    Max displacement: {max_disp:.6f} mm")
-
-        if 'stress' in data.get('results', {}):
-            for stress_type, stress_data in data['results']['stress'].items():
-                if 'max_von_mises' in stress_data:
-                    max_vm = stress_data['max_von_mises']
-                    if max_vm is not None:
-                        print(f"    Max von Mises stress: {max_vm:.2f} MPa")
-                        break
-
-        # Check output files
-        json_file = TEST_CASE_DIR / "neural_field_data.json"
-        h5_file = TEST_CASE_DIR / "neural_field_data.h5"
-
-        if json_file.exists() and h5_file.exists():
-            json_size = json_file.stat().st_size / 1024
-            h5_size = h5_file.stat().st_size / 1024
-            print(f"\n  Output Files:")
-            print(f"    JSON: {json_size:.1f} KB")
-            print(f"    HDF5: {h5_size:.1f} KB")
-
-        print(f"  Status: PASS\n")
-        return True, data
-
-    except Exception as e:
-        print(f"  [X] FAIL: {str(e)}\n")
-        import traceback
-        traceback.print_exc()
-        return False, None
-
-def test_5_validate_data():
-    """Test 5: Validate parsed data"""
-    print("[TEST 5] Validating parsed data...")
-
-    try:
-        from validate_parsed_data import NeuralFieldDataValidator
-
-        validator = NeuralFieldDataValidator(str(TEST_CASE_DIR))
-
-        print(f"  Running validation checks...")
-        success = validator.validate()
-
-        if success:
-            print(f"  Status: PASS\n")
-        else:
-            print(f"  Status: PASS (with warnings)\n")
-
-        return True
-
-    except Exception as e:
-        print(f"  [X] FAIL: {str(e)}\n")
-        return False
-
-def test_6_load_as_graph():
-    """Test 6: Load data as graph for neural network"""
-    print("[TEST 6] Converting to graph format...")
-
-    try:
-        import torch
-        from neural_models.data_loader import FEAMeshDataset
-
-        print(f"  Creating dataset...")
-        dataset = FEAMeshDataset(
-            [str(TEST_CASE_DIR)],
-            normalize=False,  # Don't normalize for single case
-            include_stress=True,
-            cache_in_memory=False
-        )
-
-        if len(dataset) == 0:
-            print(f"  [X] FAIL: No data loaded")
-            return False
-
-        print(f"  Loading graph...")
-        graph_data = dataset[0]
-
-        print(f"\n  Graph Structure:")
-        print(f"    Nodes: {graph_data.x.shape[0]:,}")
-        print(f"    Node features: {graph_data.x.shape[1]}")
-        print(f"    Edges: {graph_data.edge_index.shape[1]:,}")
-        print(f"    Edge features: {graph_data.edge_attr.shape[1]}")
-
-        if hasattr(graph_data, 'y_displacement'):
-            print(f"    Target displacement: {graph_data.y_displacement.shape}")
-
-        if hasattr(graph_data, 'y_stress'):
-            print(f"    Target stress: {graph_data.y_stress.shape}")
-
-        print(f"  Status: PASS\n")
-        return True, graph_data
-
-    except Exception as e:
-        print(f"  [X] FAIL: {str(e)}\n")
-        import traceback
-        traceback.print_exc()
-        return False, None
-
-def test_7_neural_prediction():
-    """Test 7: Make neural network prediction (untrained model)"""
-    print("[TEST 7] Testing neural network prediction...")
-
-    try:
-        import torch
-        from neural_models.field_predictor import create_model
-
-        # Load graph from previous test
-        from neural_models.data_loader import FEAMeshDataset
-        dataset = FEAMeshDataset([str(TEST_CASE_DIR)], normalize=False, include_stress=False)
-        graph_data = dataset[0]
-
-        print(f"  Creating untrained model...")
-        config = {
-            'node_feature_dim': 12,
-            'edge_feature_dim': 5,
-            'hidden_dim': 64,
-            'num_layers': 4,
-            'dropout': 0.1
-        }
-
-        model = create_model(config)
-        model.eval()
-
-        print(f"  Running inference...")
-        start_time = time.time()
-
-        with torch.no_grad():
-            predictions = model(graph_data, return_stress=True)
-
-        inference_time = (time.time() - start_time) * 1000  # ms
-
-        # Extract results
-        max_disp_pred = torch.max(torch.norm(predictions['displacement'][:, :3], dim=1)).item()
-        max_stress_pred = torch.max(predictions['von_mises']).item()
-
-        print(f"\n  Predictions (untrained model):")
-        print(f"    Inference time: {inference_time:.2f} ms")
-        print(f"    Max displacement: {max_disp_pred:.6f} (arbitrary units)")
-        print(f"    Max stress: {max_stress_pred:.2f} (arbitrary units)")
-        print(f"\n  Note: Values are from untrained model (random weights)")
-        print(f"        After training, these should match FEA results!")
-
-        print(f"  Status: PASS\n")
-        return True
-
-    except Exception as e:
-        print(f"  [X] FAIL: {str(e)}\n")
-        import traceback
-        traceback.print_exc()
-        return False
-
-def main():
-    """Run all tests"""
-    print("Testing AtomizerField with Simple Beam model\n")
-    print("This test validates:")
-    print("  1. File existence")
-    print("  2. Directory setup")
-    print("  3. Module imports")
-    print("  4. BDF/OP2 parsing")
-    print("  5. Data validation")
-    print("  6. Graph conversion")
-    print("  7. Neural prediction\n")
-
-    results = []
-
-    # Run tests
-    tests = [
-        ("Check Files", test_1_check_files),
-        ("Setup Test Case", test_2_setup_test_case),
-        ("Import Modules", test_3_import_modules),
-        ("Parse Beam", test_4_parse_beam),
-        ("Validate Data", test_5_validate_data),
-        ("Load as Graph", test_6_load_as_graph),
-        ("Neural Prediction", test_7_neural_prediction),
-    ]
-
-    for test_name, test_func in tests:
-        result = test_func()
-
-        # Handle tests that return tuple (success, data)
-        if isinstance(result, tuple):
-            success = result[0]
-        else:
-            success = result
-
-        results.append(success)
-
-        # Stop on first failure for critical tests
-        if not success and test_name in ["Check Files", "Setup Test Case", "Import Modules"]:
-            print(f"\n[X] Critical test failed: {test_name}")
-            print("Cannot continue with remaining tests.\n")
-            break
-
-    # Summary
-    print("="*60)
-    print("TEST SUMMARY")
-    print("="*60 + "\n")
-
-    passed = sum(results)
-    total = len(results)
-
-    print(f"Tests Run: {total}")
-    print(f"  [OK] Passed: {passed}")
-    print(f"  [X] Failed: {total - passed}")
-
-    if passed == total:
-        print("\n[OK] ALL TESTS PASSED!")
-        print("\nYour Simple Beam model has been:")
-        print("  [OK] Successfully parsed")
-        print("  [OK] Converted to neural format")
-        print("  [OK] Validated for quality")
-        print("  [OK] Loaded as graph")
-        print("  [OK] Processed by neural network")
-        print("\nNext steps:")
-        print("  1. Generate more training cases (50-500)")
-        print("  2. Train the model: python train.py")
-        print("  3. Make real predictions!")
-    else:
-        print(f"\n[X] {total - passed} test(s) failed")
-        print("Review errors above and fix issues.")
-
-    print("\n" + "="*60 + "\n")
-
-    return 0 if passed == total else 1
-
-if __name__ == "__main__":
-    sys.exit(main())

atomizer-field/test_suite.py

@@ -1,402 +0,0 @@
-"""
-test_suite.py
-Master test orchestrator for AtomizerField
-
-AtomizerField Testing Framework v1.0
-Comprehensive validation from basic functionality to full neural FEA predictions.
-
-Usage:
-    python test_suite.py --quick      # 5-minute smoke tests
-    python test_suite.py --physics    # Physics validation tests
-    python test_suite.py --learning   # Learning capability tests
-    python test_suite.py --full       # Complete test suite (1 hour)
-
-Testing Strategy:
-    1. Smoke Tests (5 min) → Verify basic functionality
-    2. Physics Tests (15 min) → Validate physics constraints
-    3. Learning Tests (30 min) → Confirm learning capability
-    4. Integration Tests (1 hour) → Full system validation
-"""
-
-import sys
-import os
-import argparse
-import time
-from pathlib import Path
-import json
-from datetime import datetime
-
-# Add project root to path
-sys.path.insert(0, str(Path(__file__).parent))
-
-# Test results storage
-TEST_RESULTS = {
-    'timestamp': datetime.now().isoformat(),
-    'tests': [],
-    'summary': {
-        'total': 0,
-        'passed': 0,
-        'failed': 0,
-        'skipped': 0
-    }
-}
-
-
-class TestRunner:
-    """
-    Test orchestrator that runs all tests in sequence
-    """
-
-    def __init__(self, mode='quick'):
-        """
-        Initialize test runner
-
-        Args:
-            mode (str): Testing mode ('quick', 'physics', 'learning', 'full')
-        """
-        self.mode = mode
-        self.results_dir = Path('test_results')
-        self.results_dir.mkdir(exist_ok=True)
-
-        print(f"\n{'='*60}")
-        print(f"AtomizerField Test Suite v1.0")
-        print(f"Mode: {mode.upper()}")
-        print(f"{'='*60}\n")
-
-    def run_test(self, test_name, test_func, description):
-        """
-        Run a single test and record results
-
-        Args:
-            test_name (str): Name of test
-            test_func (callable): Test function to run
-            description (str): Test description
-
-        Returns:
-            bool: True if passed
-        """
-        print(f"[TEST] {test_name}")
-        print(f"  Description: {description}")
-
-        start_time = time.time()
-        result = {
-            'name': test_name,
-            'description': description,
-            'status': 'unknown',
-            'duration': 0,
-            'message': '',
-            'metrics': {}
-        }
-
-        try:
-            test_result = test_func()
-
-            if test_result is None or test_result is True:
-                result['status'] = 'PASS'
-                result['message'] = 'Test passed successfully'
-                print(f"  Status: [PASS]")
-                TEST_RESULTS['summary']['passed'] += 1
-            elif isinstance(test_result, dict):
-                result['status'] = test_result.get('status', 'PASS')
-                result['message'] = test_result.get('message', '')
-                result['metrics'] = test_result.get('metrics', {})
-
-                if result['status'] == 'PASS':
-                    print(f"  Status: [PASS]")
-                    TEST_RESULTS['summary']['passed'] += 1
-                else:
-                    print(f"  Status: [FAIL]")
-                    print(f"  Reason: {result['message']}")
-                    TEST_RESULTS['summary']['failed'] += 1
-            else:
-                result['status'] = 'FAIL'
-                result['message'] = str(test_result)
-                print(f"  Status: [FAIL]")
-                TEST_RESULTS['summary']['failed'] += 1
-
-        except Exception as e:
-            result['status'] = 'FAIL'
-            result['message'] = f"Exception: {str(e)}"
-            print(f"  Status: [FAIL]")
-            print(f"  Error: {str(e)}")
-            TEST_RESULTS['summary']['failed'] += 1
-
-        result['duration'] = time.time() - start_time
-        print(f"  Duration: {result['duration']:.2f}s\n")
-
-        TEST_RESULTS['tests'].append(result)
-        TEST_RESULTS['summary']['total'] += 1
-
-        return result['status'] == 'PASS'
-
-    def run_smoke_tests(self):
-        """
-        Quick smoke tests (5 minutes)
-        Verify basic functionality
-        """
-        print(f"\n{'='*60}")
-        print("PHASE 1: SMOKE TESTS (5 minutes)")
-        print(f"{'='*60}\n")
-
-        from tests import test_synthetic
-
-        # Test 1: Model creation
-        self.run_test(
-            "Model Creation",
-            test_synthetic.test_model_creation,
-            "Verify GNN model can be instantiated"
-        )
-
-        # Test 2: Forward pass
-        self.run_test(
-            "Forward Pass",
-            test_synthetic.test_forward_pass,
-            "Verify model can process dummy data"
-        )
-
-        # Test 3: Loss computation
-        self.run_test(
-            "Loss Computation",
-            test_synthetic.test_loss_computation,
-            "Verify loss functions work"
-        )
-
-    def run_physics_tests(self):
-        """
-        Physics validation tests (15 minutes)
-        Ensure physics constraints work
-        """
-        print(f"\n{'='*60}")
-        print("PHASE 2: PHYSICS VALIDATION (15 minutes)")
-        print(f"{'='*60}\n")
-
-        from tests import test_physics
-
-        # Test 1: Cantilever beam
-        self.run_test(
-            "Cantilever Beam (Analytical)",
-            test_physics.test_cantilever_analytical,
-            "Compare with δ = FL³/3EI solution"
-        )
-
-        # Test 2: Equilibrium
-        self.run_test(
-            "Equilibrium Check",
-            test_physics.test_equilibrium,
-            "Verify force balance (∇·σ + f = 0)"
-        )
-
-        # Test 3: Energy conservation
-        self.run_test(
-            "Energy Conservation",
-            test_physics.test_energy_conservation,
-            "Verify strain energy = work done"
-        )
-
-    def run_learning_tests(self):
-        """
-        Learning capability tests (30 minutes)
-        Confirm network can learn
-        """
-        print(f"\n{'='*60}")
-        print("PHASE 3: LEARNING CAPABILITY (30 minutes)")
-        print(f"{'='*60}\n")
-
-        from tests import test_learning
-
-        # Test 1: Memorization
-        self.run_test(
-            "Memorization Test",
-            test_learning.test_memorization,
-            "Can network memorize small dataset?"
-        )
-
-        # Test 2: Interpolation
-        self.run_test(
-            "Interpolation Test",
-            test_learning.test_interpolation,
-            "Can network interpolate between training points?"
-        )
-
-        # Test 3: Pattern recognition
-        self.run_test(
-            "Pattern Recognition",
-            test_learning.test_pattern_recognition,
-            "Does network learn thickness → stress relationship?"
-        )
-
-    def run_integration_tests(self):
-        """
-        Full integration tests (1 hour)
-        Complete system validation
-        """
-        print(f"\n{'='*60}")
-        print("PHASE 4: INTEGRATION TESTS (1 hour)")
-        print(f"{'='*60}\n")
-
-        from tests import test_predictions
-
-        # Test 1: Parser validation
-        self.run_test(
-            "Parser Validation",
-            test_predictions.test_parser,
-            "Verify data parsing works correctly"
-        )
-
-        # Test 2: Training pipeline
-        self.run_test(
-            "Training Pipeline",
-            test_predictions.test_training,
-            "Verify complete training workflow"
-        )
-
-        # Test 3: Prediction accuracy
-        self.run_test(
-            "Prediction Accuracy",
-            test_predictions.test_prediction_accuracy,
-            "Compare neural vs FEA predictions"
-        )
-
-    def print_summary(self):
-        """Print test summary"""
-        summary = TEST_RESULTS['summary']
-
-        print(f"\n{'='*60}")
-        print("TEST SUMMARY")
-        print(f"{'='*60}\n")
-
-        total = summary['total']
-        passed = summary['passed']
-        failed = summary['failed']
-
-        pass_rate = (passed / total * 100) if total > 0 else 0
-
-        print(f"Total Tests: {total}")
-        print(f"  + Passed: {passed}")
-        print(f"  - Failed: {failed}")
-        print(f"  Pass Rate: {pass_rate:.1f}%\n")
-
-        if failed == 0:
-            print("[SUCCESS] ALL TESTS PASSED - SYSTEM READY!")
-        else:
-            print(f"[ERROR] {failed} TEST(S) FAILED - REVIEW REQUIRED")
-
-        print(f"\n{'='*60}\n")
-
-    def save_results(self):
-        """Save test results to JSON"""
-        results_file = self.results_dir / f'test_results_{self.mode}_{int(time.time())}.json'
-
-        with open(results_file, 'w') as f:
-            json.dump(TEST_RESULTS, f, indent=2)
-
-        print(f"Results saved to: {results_file}")
-
-    def run(self):
-        """
-        Run test suite based on mode
-        """
-        start_time = time.time()
-
-        if self.mode == 'quick':
-            self.run_smoke_tests()
-
-        elif self.mode == 'physics':
-            self.run_smoke_tests()
-            self.run_physics_tests()
-
-        elif self.mode == 'learning':
-            self.run_smoke_tests()
-            self.run_physics_tests()
-            self.run_learning_tests()
-
-        elif self.mode == 'full':
-            self.run_smoke_tests()
-            self.run_physics_tests()
-            self.run_learning_tests()
-            self.run_integration_tests()
-
-        total_time = time.time() - start_time
-
-        # Print summary
-        self.print_summary()
-
-        print(f"Total testing time: {total_time/60:.1f} minutes\n")
-
-        # Save results
-        self.save_results()
-
-        # Return exit code
-        return 0 if TEST_RESULTS['summary']['failed'] == 0 else 1
-
-
-def main():
-    """Main entry point"""
-    parser = argparse.ArgumentParser(
-        description='AtomizerField Test Suite',
-        formatter_class=argparse.RawDescriptionHelpFormatter,
-        epilog="""
-Examples:
-    # Quick smoke tests (5 min)
-    python test_suite.py --quick
-
-    # Physics validation (15 min)
-    python test_suite.py --physics
-
-    # Learning tests (30 min)
-    python test_suite.py --learning
-
-    # Full test suite (1 hour)
-    python test_suite.py --full
-        """
-    )
-
-    parser.add_argument(
-        '--quick',
-        action='store_true',
-        help='Run quick smoke tests (5 minutes)'
-    )
-
-    parser.add_argument(
-        '--physics',
-        action='store_true',
-        help='Run physics validation tests (15 minutes)'
-    )
-
-    parser.add_argument(
-        '--learning',
-        action='store_true',
-        help='Run learning capability tests (30 minutes)'
-    )
-
-    parser.add_argument(
-        '--full',
-        action='store_true',
-        help='Run complete test suite (1 hour)'
-    )
-
-    args = parser.parse_args()
-
-    # Determine mode
-    if args.full:
-        mode = 'full'
-    elif args.learning:
-        mode = 'learning'
-    elif args.physics:
-        mode = 'physics'
-    elif args.quick:
-        mode = 'quick'
-    else:
-        # Default to quick if no mode specified
-        mode = 'quick'
-        print("No mode specified, defaulting to --quick")
-
-    # Run tests
-    runner = TestRunner(mode=mode)
-    exit_code = runner.run()
-
-    sys.exit(exit_code)
-
-
-if __name__ == "__main__":
-    main()

atomizer-field/tests/__init__.py

@@ -1,6 +0,0 @@
-"""
-AtomizerField Test Suite
-Comprehensive testing framework for neural field learning
-"""
-
-__version__ = "1.0.0"

atomizer-field/tests/analytical_cases.py

@@ -1,446 +0,0 @@
-"""
-analytical_cases.py
-Analytical solutions for classical mechanics problems
-
-Provides known solutions for validation:
-- Cantilever beam under point load
-- Simply supported beam
-- Axial tension bar
-- Pressure vessel (thin-walled cylinder)
-- Torsion of circular shaft
-
-These serve as ground truth for testing neural predictions.
-"""
-
-import numpy as np
-from dataclasses import dataclass
-from typing import Tuple
-
-
-@dataclass
-class BeamProperties:
-    """Material and geometric properties for beam"""
-    length: float  # m
-    width: float  # m
-    height: float  # m
-    E: float  # Young's modulus (Pa)
-    nu: float  # Poisson's ratio
-    rho: float  # Density (kg/m³)
-
-    @property
-    def I(self) -> float:
-        """Second moment of area for rectangular section"""
-        return (self.width * self.height**3) / 12
-
-    @property
-    def A(self) -> float:
-        """Cross-sectional area"""
-        return self.width * self.height
-
-    @property
-    def G(self) -> float:
-        """Shear modulus"""
-        return self.E / (2 * (1 + self.nu))
-
-
-def cantilever_beam_point_load(force: float, props: BeamProperties) -> dict:
-    """
-    Cantilever beam with point load at free end
-
-    Analytical solution:
-        δ_max = FL³/3EI  (at free end)
-        σ_max = FL/Z     (at fixed end)
-
-    Args:
-        force: Applied force at tip (N)
-        props: Beam properties
-
-    Returns:
-        dict with displacement, stress, reactions
-    """
-    L = props.length
-    E = props.E
-    I = props.I
-    c = props.height / 2  # Distance to neutral axis
-
-    # Maximum displacement at free end
-    delta_max = (force * L**3) / (3 * E * I)
-
-    # Maximum stress at fixed end (bending)
-    M_max = force * L  # Maximum moment at fixed end
-    Z = I / c  # Section modulus
-    sigma_max = M_max / Z
-
-    # Deflection curve: y(x) = (F/(6EI)) * x² * (3L - x)
-    def deflection_at(x):
-        """Deflection at position x along beam"""
-        if x < 0 or x > L:
-            return 0.0
-        return (force / (6 * E * I)) * x**2 * (3 * L - x)
-
-    # Bending moment: M(x) = F * (L - x)
-    def moment_at(x):
-        """Bending moment at position x"""
-        if x < 0 or x > L:
-            return 0.0
-        return force * (L - x)
-
-    # Stress: σ(x, y) = M(x) * y / I
-    def stress_at(x, y):
-        """Bending stress at position x and distance y from neutral axis"""
-        M = moment_at(x)
-        return (M * y) / I
-
-    return {
-        'type': 'cantilever_point_load',
-        'delta_max': delta_max,
-        'sigma_max': sigma_max,
-        'deflection_function': deflection_at,
-        'moment_function': moment_at,
-        'stress_function': stress_at,
-        'load': force,
-        'properties': props
-    }
-
-
-def simply_supported_beam_point_load(force: float, props: BeamProperties) -> dict:
-    """
-    Simply supported beam with point load at center
-
-    Analytical solution:
-        δ_max = FL³/48EI  (at center)
-        σ_max = FL/4Z     (at center)
-
-    Args:
-        force: Applied force at center (N)
-        props: Beam properties
-
-    Returns:
-        dict with displacement, stress, reactions
-    """
-    L = props.length
-    E = props.E
-    I = props.I
-    c = props.height / 2
-
-    # Maximum displacement at center
-    delta_max = (force * L**3) / (48 * E * I)
-
-    # Maximum stress at center
-    M_max = force * L / 4  # Maximum moment at center
-    Z = I / c
-    sigma_max = M_max / Z
-
-    # Deflection curve (for 0 < x < L/2):
-    # y(x) = (F/(48EI)) * x * (3L² - 4x²)
-    def deflection_at(x):
-        """Deflection at position x along beam"""
-        if x < 0 or x > L:
-            return 0.0
-        if x <= L/2:
-            return (force / (48 * E * I)) * x * (3 * L**2 - 4 * x**2)
-        else:
-            # Symmetric about center
-            return deflection_at(L - x)
-
-    # Bending moment: M(x) = (F/2) * x  for x < L/2
-    def moment_at(x):
-        """Bending moment at position x"""
-        if x < 0 or x > L:
-            return 0.0
-        if x <= L/2:
-            return (force / 2) * x
-        else:
-            return (force / 2) * (L - x)
-
-    def stress_at(x, y):
-        """Bending stress at position x and distance y from neutral axis"""
-        M = moment_at(x)
-        return (M * y) / I
-
-    return {
-        'type': 'simply_supported_point_load',
-        'delta_max': delta_max,
-        'sigma_max': sigma_max,
-        'deflection_function': deflection_at,
-        'moment_function': moment_at,
-        'stress_function': stress_at,
-        'load': force,
-        'properties': props,
-        'reactions': force / 2  # Each support
-    }
-
-
-def axial_tension_bar(force: float, props: BeamProperties) -> dict:
-    """
-    Bar under axial tension
-
-    Analytical solution:
-        δ = FL/EA  (total elongation)
-        σ = F/A    (uniform stress)
-        ε = σ/E    (uniform strain)
-
-    Args:
-        force: Axial force (N)
-        props: Bar properties
-
-    Returns:
-        dict with displacement, stress, strain
-    """
-    L = props.length
-    E = props.E
-    A = props.A
-
-    # Total elongation
-    delta = (force * L) / (E * A)
-
-    # Uniform stress
-    sigma = force / A
-
-    # Uniform strain
-    epsilon = sigma / E
-
-    # Displacement is linear along length
-    def displacement_at(x):
-        """Axial displacement at position x"""
-        if x < 0 or x > L:
-            return 0.0
-        return (force * x) / (E * A)
-
-    return {
-        'type': 'axial_tension',
-        'delta_total': delta,
-        'sigma': sigma,
-        'epsilon': epsilon,
-        'displacement_function': displacement_at,
-        'load': force,
-        'properties': props
-    }
-
-
-def thin_wall_pressure_vessel(pressure: float, radius: float, thickness: float,
-                               length: float, E: float, nu: float) -> dict:
-    """
-    Thin-walled cylindrical pressure vessel
-
-    Analytical solution:
-        σ_hoop = pr/t      (circumferential stress)
-        σ_axial = pr/2t    (longitudinal stress)
-        ε_hoop = (1/E)(σ_h - ν*σ_a)
-        ε_axial = (1/E)(σ_a - ν*σ_h)
-
-    Args:
-        pressure: Internal pressure (Pa)
-        radius: Mean radius (m)
-        thickness: Wall thickness (m)
-        length: Cylinder length (m)
-        E: Young's modulus (Pa)
-        nu: Poisson's ratio
-
-    Returns:
-        dict with stresses and strains
-    """
-    # Stresses
-    sigma_hoop = (pressure * radius) / thickness
-    sigma_axial = (pressure * radius) / (2 * thickness)
-
-    # Strains
-    epsilon_hoop = (1/E) * (sigma_hoop - nu * sigma_axial)
-    epsilon_axial = (1/E) * (sigma_axial - nu * sigma_hoop)
-
-    # Radial expansion
-    delta_r = epsilon_hoop * radius
-
-    return {
-        'type': 'pressure_vessel',
-        'sigma_hoop': sigma_hoop,
-        'sigma_axial': sigma_axial,
-        'epsilon_hoop': epsilon_hoop,
-        'epsilon_axial': epsilon_axial,
-        'radial_expansion': delta_r,
-        'pressure': pressure,
-        'radius': radius,
-        'thickness': thickness
-    }
-
-
-def torsion_circular_shaft(torque: float, radius: float, length: float, G: float) -> dict:
-    """
-    Circular shaft under torsion
-
-    Analytical solution:
-        θ = TL/GJ          (angle of twist)
-        τ_max = Tr/J       (maximum shear stress at surface)
-        γ_max = τ_max/G    (maximum shear strain)
-
-    Args:
-        torque: Applied torque (N·m)
-        radius: Shaft radius (m)
-        length: Shaft length (m)
-        G: Shear modulus (Pa)
-
-    Returns:
-        dict with twist angle, stress, strain
-    """
-    # Polar moment of inertia
-    J = (np.pi * radius**4) / 2
-
-    # Angle of twist
-    theta = (torque * length) / (G * J)
-
-    # Maximum shear stress (at surface)
-    tau_max = (torque * radius) / J
-
-    # Maximum shear strain
-    gamma_max = tau_max / G
-
-    # Shear stress at radius r
-    def shear_stress_at(r):
-        """Shear stress at radial distance r from center"""
-        if r < 0 or r > radius:
-            return 0.0
-        return (torque * r) / J
-
-    return {
-        'type': 'torsion',
-        'theta': theta,
-        'tau_max': tau_max,
-        'gamma_max': gamma_max,
-        'shear_stress_function': shear_stress_at,
-        'torque': torque,
-        'radius': radius,
-        'length': length
-    }
-
-
-# Standard test cases with typical values
-def get_standard_cantilever() -> Tuple[float, BeamProperties]:
-    """Standard cantilever test case"""
-    props = BeamProperties(
-        length=1.0,      # 1 m
-        width=0.05,      # 50 mm
-        height=0.1,      # 100 mm
-        E=210e9,         # Steel: 210 GPa
-        nu=0.3,
-        rho=7850         # kg/m³
-    )
-    force = 1000.0  # 1 kN
-    return force, props
-
-
-def get_standard_simply_supported() -> Tuple[float, BeamProperties]:
-    """Standard simply supported beam test case"""
-    props = BeamProperties(
-        length=2.0,      # 2 m
-        width=0.05,      # 50 mm
-        height=0.1,      # 100 mm
-        E=210e9,         # Steel
-        nu=0.3,
-        rho=7850
-    )
-    force = 5000.0  # 5 kN
-    return force, props
-
-
-def get_standard_tension_bar() -> Tuple[float, BeamProperties]:
-    """Standard tension bar test case"""
-    props = BeamProperties(
-        length=1.0,      # 1 m
-        width=0.02,      # 20 mm
-        height=0.02,     # 20 mm (square bar)
-        E=210e9,         # Steel
-        nu=0.3,
-        rho=7850
-    )
-    force = 10000.0  # 10 kN
-    return force, props
-
-
-# Example usage and validation
-if __name__ == "__main__":
-    print("Analytical Test Cases\n")
-    print("="*60)
-
-    # Test 1: Cantilever beam
-    print("\n1. Cantilever Beam (Point Load at Tip)")
-    print("-"*60)
-    force, props = get_standard_cantilever()
-    result = cantilever_beam_point_load(force, props)
-
-    print(f"Load: {force} N")
-    print(f"Length: {props.length} m")
-    print(f"E: {props.E/1e9:.0f} GPa")
-    print(f"I: {props.I*1e12:.3f} mm⁴")
-    print(f"\nResults:")
-    print(f"  Max displacement: {result['delta_max']*1000:.3f} mm")
-    print(f"  Max stress: {result['sigma_max']/1e6:.1f} MPa")
-
-    # Verify deflection at intermediate points
-    print(f"\nDeflection profile:")
-    for x in [0.0, 0.25, 0.5, 0.75, 1.0]:
-        x_m = x * props.length
-        delta = result['deflection_function'](x_m)
-        print(f"  x = {x:.2f}L: δ = {delta*1000:.3f} mm")
-
-    # Test 2: Simply supported beam
-    print("\n2. Simply Supported Beam (Point Load at Center)")
-    print("-"*60)
-    force, props = get_standard_simply_supported()
-    result = simply_supported_beam_point_load(force, props)
-
-    print(f"Load: {force} N")
-    print(f"Length: {props.length} m")
-    print(f"\nResults:")
-    print(f"  Max displacement: {result['delta_max']*1000:.3f} mm")
-    print(f"  Max stress: {result['sigma_max']/1e6:.1f} MPa")
-    print(f"  Reactions: {result['reactions']} N each")
-
-    # Test 3: Axial tension
-    print("\n3. Axial Tension Bar")
-    print("-"*60)
-    force, props = get_standard_tension_bar()
-    result = axial_tension_bar(force, props)
-
-    print(f"Load: {force} N")
-    print(f"Length: {props.length} m")
-    print(f"Area: {props.A*1e6:.0f} mm²")
-    print(f"\nResults:")
-    print(f"  Total elongation: {result['delta_total']*1e6:.3f} μm")
-    print(f"  Stress: {result['sigma']/1e6:.1f} MPa")
-    print(f"  Strain: {result['epsilon']*1e6:.1f} με")
-
-    # Test 4: Pressure vessel
-    print("\n4. Thin-Walled Pressure Vessel")
-    print("-"*60)
-    pressure = 10e6  # 10 MPa
-    radius = 0.5     # 500 mm
-    thickness = 0.01  # 10 mm
-    result = thin_wall_pressure_vessel(pressure, radius, thickness, 2.0, 210e9, 0.3)
-
-    print(f"Pressure: {pressure/1e6:.1f} MPa")
-    print(f"Radius: {radius*1000:.0f} mm")
-    print(f"Thickness: {thickness*1000:.0f} mm")
-    print(f"\nResults:")
-    print(f"  Hoop stress: {result['sigma_hoop']/1e6:.1f} MPa")
-    print(f"  Axial stress: {result['sigma_axial']/1e6:.1f} MPa")
-    print(f"  Radial expansion: {result['radial_expansion']*1e6:.3f} μm")
-
-    # Test 5: Torsion
-    print("\n5. Circular Shaft in Torsion")
-    print("-"*60)
-    torque = 1000  # 1000 N·m
-    radius = 0.05  # 50 mm
-    length = 1.0   # 1 m
-    G = 80e9       # 80 GPa
-    result = torsion_circular_shaft(torque, radius, length, G)
-
-    print(f"Torque: {torque} N·m")
-    print(f"Radius: {radius*1000:.0f} mm")
-    print(f"Length: {length:.1f} m")
-    print(f"\nResults:")
-    print(f"  Twist angle: {result['theta']*180/np.pi:.3f}°")
-    print(f"  Max shear stress: {result['tau_max']/1e6:.1f} MPa")
-    print(f"  Max shear strain: {result['gamma_max']*1e6:.1f} με")
-
-    print("\n" + "="*60)
-    print("All analytical solutions validated!")

atomizer-field/tests/test_learning.py

@@ -1,468 +0,0 @@
-"""
-test_learning.py
-Learning capability tests
-
-Tests that the neural network can actually learn:
-- Memorization: Can it memorize 10 examples?
-- Interpolation: Can it generalize between training points?
-- Extrapolation: Can it predict beyond training range?
-- Pattern recognition: Does it learn physical relationships?
-"""
-
-import torch
-import torch.nn as nn
-import numpy as np
-import sys
-from pathlib import Path
-
-# Add parent directory to path
-sys.path.insert(0, str(Path(__file__).parent.parent))
-
-from neural_models.field_predictor import create_model
-from neural_models.physics_losses import create_loss_function
-from torch_geometric.data import Data
-
-
-def create_synthetic_dataset(n_samples=10, variation='load'):
-    """
-    Create synthetic FEA-like dataset with known patterns
-
-    Args:
-        n_samples: Number of samples
-        variation: Parameter to vary ('load', 'stiffness', 'geometry')
-
-    Returns:
-        List of (graph_data, target_displacement, target_stress) tuples
-    """
-    dataset = []
-
-    for i in range(n_samples):
-        num_nodes = 20
-        num_edges = 40
-
-        # Base features
-        x = torch.randn(num_nodes, 12) * 0.1
-
-        # Vary parameter based on type
-        if variation == 'load':
-            load_factor = 1.0 + i * 0.5  # Vary load from 1.0 to 5.5
-            x[:, 9:12] = torch.randn(num_nodes, 3) * load_factor
-
-        elif variation == 'stiffness':
-            stiffness_factor = 1.0 + i * 0.2  # Vary stiffness
-            edge_attr = torch.randn(num_edges, 5) * 0.1
-            edge_attr[:, 0] = stiffness_factor  # Young's modulus
-
-        elif variation == 'geometry':
-            geometry_factor = 1.0 + i * 0.1  # Vary geometry
-            x[:, 0:3] = torch.randn(num_nodes, 3) * geometry_factor
-
-        # Create edges
-        edge_index = torch.randint(0, num_nodes, (2, num_edges))
-
-        # Default edge attributes if not varying stiffness
-        if variation != 'stiffness':
-            edge_attr = torch.randn(num_edges, 5) * 0.1
-            edge_attr[:, 0] = 1.0  # Constant Young's modulus
-
-        batch = torch.zeros(num_nodes, dtype=torch.long)
-
-        data = Data(x=x, edge_index=edge_index, edge_attr=edge_attr, batch=batch)
-
-        # Create synthetic targets with known relationship
-        # Displacement proportional to load / stiffness
-        if variation == 'load':
-            target_displacement = torch.randn(num_nodes, 6) * load_factor
-        elif variation == 'stiffness':
-            target_displacement = torch.randn(num_nodes, 6) / stiffness_factor
-        else:
-            target_displacement = torch.randn(num_nodes, 6)
-
-        # Stress also follows known pattern
-        target_stress = target_displacement * 2.0  # Simple linear relationship
-
-        dataset.append((data, target_displacement, target_stress))
-
-    return dataset
-
-
-def test_memorization():
-    """
-    Test 1: Can network memorize small dataset?
-
-    Expected: After training on 10 examples, can achieve < 1% error
-
-    This tests basic learning capability - if it can't memorize,
-    something is fundamentally wrong.
-    """
-    print("    Creating small dataset (10 samples)...")
-
-    # Create tiny dataset
-    dataset = create_synthetic_dataset(n_samples=10, variation='load')
-
-    # Create model
-    config = {
-        'node_feature_dim': 12,
-        'edge_feature_dim': 5,
-        'hidden_dim': 64,
-        'num_layers': 4,
-        'dropout': 0.0  # No dropout for memorization
-    }
-
-    model = create_model(config)
-    loss_fn = create_loss_function('mse')
-    optimizer = torch.optim.Adam(model.parameters(), lr=0.001)
-
-    print("    Training for 100 epochs...")
-
-    model.train()
-    losses = []
-
-    for epoch in range(100):
-        epoch_loss = 0.0
-
-        for graph_data, target_disp, target_stress in dataset:
-            optimizer.zero_grad()
-
-            # Forward pass
-            predictions = model(graph_data, return_stress=True)
-
-            # Compute loss
-            targets = {
-                'displacement': target_disp,
-                'stress': target_stress
-            }
-
-            loss_dict = loss_fn(predictions, targets)
-            loss = loss_dict['total_loss']
-
-            # Backward pass
-            loss.backward()
-            optimizer.step()
-
-            epoch_loss += loss.item()
-
-        avg_loss = epoch_loss / len(dataset)
-        losses.append(avg_loss)
-
-        if (epoch + 1) % 20 == 0:
-            print(f"      Epoch {epoch+1}/100: Loss = {avg_loss:.6f}")
-
-    final_loss = losses[-1]
-    initial_loss = losses[0]
-    improvement = (initial_loss - final_loss) / initial_loss * 100
-
-    print(f"    Initial loss: {initial_loss:.6f}")
-    print(f"    Final loss: {final_loss:.6f}")
-    print(f"    Improvement: {improvement:.1f}%")
-
-    # Success if loss decreased significantly
-    success = improvement > 50.0
-
-    return {
-        'status': 'PASS' if success else 'FAIL',
-        'message': f'Memorization {"successful" if success else "failed"} ({improvement:.1f}% improvement)',
-        'metrics': {
-            'initial_loss': float(initial_loss),
-            'final_loss': float(final_loss),
-            'improvement_percent': float(improvement),
-            'converged': final_loss < 0.1
-        }
-    }
-
-
-def test_interpolation():
-    """
-    Test 2: Can network interpolate?
-
-    Expected: After training on [1, 3, 5], predict [2, 4] with < 5% error
-
-    This tests generalization capability within training range.
-    """
-    print("    Creating interpolation dataset...")
-
-    # Train on samples 0, 2, 4, 6, 8 (odd indices)
-    train_indices = [0, 2, 4, 6, 8]
-    test_indices = [1, 3, 5, 7]  # Even indices (interpolation)
-
-    full_dataset = create_synthetic_dataset(n_samples=10, variation='load')
-
-    train_dataset = [full_dataset[i] for i in train_indices]
-    test_dataset = [full_dataset[i] for i in test_indices]
-
-    # Create model
-    config = {
-        'node_feature_dim': 12,
-        'edge_feature_dim': 5,
-        'hidden_dim': 64,
-        'num_layers': 4,
-        'dropout': 0.1
-    }
-
-    model = create_model(config)
-    loss_fn = create_loss_function('mse')
-    optimizer = torch.optim.Adam(model.parameters(), lr=0.001)
-
-    print(f"    Training on {len(train_dataset)} samples...")
-
-    # Train
-    model.train()
-    for epoch in range(50):
-        for graph_data, target_disp, target_stress in train_dataset:
-            optimizer.zero_grad()
-
-            predictions = model(graph_data, return_stress=True)
-
-            targets = {
-                'displacement': target_disp,
-                'stress': target_stress
-            }
-
-            loss_dict = loss_fn(predictions, targets)
-            loss = loss_dict['total_loss']
-
-            loss.backward()
-            optimizer.step()
-
-    # Test interpolation
-    print(f"    Testing interpolation on {len(test_dataset)} samples...")
-
-    model.eval()
-    test_errors = []
-
-    with torch.no_grad():
-        for graph_data, target_disp, target_stress in test_dataset:
-            predictions = model(graph_data, return_stress=True)
-
-            # Compute relative error
-            pred_disp = predictions['displacement']
-            error = torch.mean(torch.abs(pred_disp - target_disp) / (torch.abs(target_disp) + 1e-8))
-            test_errors.append(error.item())
-
-    avg_error = np.mean(test_errors) * 100
-
-    print(f"    Average interpolation error: {avg_error:.2f}%")
-
-    # Success if error reasonable for untrained interpolation
-    success = avg_error < 100.0  # Lenient for this basic test
-
-    return {
-        'status': 'PASS' if success else 'FAIL',
-        'message': f'Interpolation test completed ({avg_error:.2f}% error)',
-        'metrics': {
-            'average_error_percent': float(avg_error),
-            'test_samples': len(test_dataset),
-            'train_samples': len(train_dataset)
-        }
-    }
-
-
-def test_extrapolation():
-    """
-    Test 3: Can network extrapolate?
-
-    Expected: After training on [1-5], predict [7-10] with < 20% error
-
-    This tests generalization beyond training range (harder than interpolation).
-    """
-    print("    Creating extrapolation dataset...")
-
-    # Train on first 5 samples
-    train_indices = list(range(5))
-    test_indices = list(range(7, 10))  # Extrapolate to higher values
-
-    full_dataset = create_synthetic_dataset(n_samples=10, variation='load')
-
-    train_dataset = [full_dataset[i] for i in train_indices]
-    test_dataset = [full_dataset[i] for i in test_indices]
-
-    # Create model
-    config = {
-        'node_feature_dim': 12,
-        'edge_feature_dim': 5,
-        'hidden_dim': 64,
-        'num_layers': 4,
-        'dropout': 0.1
-    }
-
-    model = create_model(config)
-    loss_fn = create_loss_function('mse')
-    optimizer = torch.optim.Adam(model.parameters(), lr=0.001)
-
-    print(f"    Training on samples 1-5...")
-
-    # Train
-    model.train()
-    for epoch in range(50):
-        for graph_data, target_disp, target_stress in train_dataset:
-            optimizer.zero_grad()
-
-            predictions = model(graph_data, return_stress=True)
-
-            targets = {
-                'displacement': target_disp,
-                'stress': target_stress
-            }
-
-            loss_dict = loss_fn(predictions, targets)
-            loss = loss_dict['total_loss']
-
-            loss.backward()
-            optimizer.step()
-
-    # Test extrapolation
-    print(f"    Testing extrapolation on samples 7-10...")
-
-    model.eval()
-    test_errors = []
-
-    with torch.no_grad():
-        for graph_data, target_disp, target_stress in test_dataset:
-            predictions = model(graph_data, return_stress=True)
-
-            pred_disp = predictions['displacement']
-            error = torch.mean(torch.abs(pred_disp - target_disp) / (torch.abs(target_disp) + 1e-8))
-            test_errors.append(error.item())
-
-    avg_error = np.mean(test_errors) * 100
-
-    print(f"    Average extrapolation error: {avg_error:.2f}%")
-    print(f"    Note: Extrapolation is harder than interpolation.")
-
-    # Success if error is reasonable (extrapolation is hard)
-    success = avg_error < 200.0  # Very lenient for basic test
-
-    return {
-        'status': 'PASS' if success else 'FAIL',
-        'message': f'Extrapolation test completed ({avg_error:.2f}% error)',
-        'metrics': {
-            'average_error_percent': float(avg_error),
-            'test_samples': len(test_dataset),
-            'train_samples': len(train_dataset)
-        }
-    }
-
-
-def test_pattern_recognition():
-    """
-    Test 4: Can network learn physical patterns?
-
-    Expected: Learn that thickness ↑ → stress ↓
-
-    This tests if network understands relationships, not just memorization.
-    """
-    print("    Testing pattern recognition...")
-
-    # Create dataset with clear pattern: stiffness ↑ → displacement ↓
-    dataset = create_synthetic_dataset(n_samples=20, variation='stiffness')
-
-    # Create model
-    config = {
-        'node_feature_dim': 12,
-        'edge_feature_dim': 5,
-        'hidden_dim': 64,
-        'num_layers': 4,
-        'dropout': 0.1
-    }
-
-    model = create_model(config)
-    loss_fn = create_loss_function('mse')
-    optimizer = torch.optim.Adam(model.parameters(), lr=0.001)
-
-    print("    Training on stiffness variation dataset...")
-
-    # Train
-    model.train()
-    for epoch in range(50):
-        for graph_data, target_disp, target_stress in dataset:
-            optimizer.zero_grad()
-
-            predictions = model(graph_data, return_stress=True)
-
-            targets = {
-                'displacement': target_disp,
-                'stress': target_stress
-            }
-
-            loss_dict = loss_fn(predictions, targets)
-            loss = loss_dict['total_loss']
-
-            loss.backward()
-            optimizer.step()
-
-    # Test pattern: predict two cases with different stiffness
-    print("    Testing learned pattern...")
-
-    model.eval()
-
-    # Low stiffness case
-    low_stiff_data, low_stiff_disp, _ = dataset[0]
-
-    # High stiffness case
-    high_stiff_data, high_stiff_disp, _ = dataset[-1]
-
-    with torch.no_grad():
-        low_pred = model(low_stiff_data, return_stress=False)
-        high_pred = model(high_stiff_data, return_stress=False)
-
-    # Check if pattern learned: low stiffness → high displacement
-    low_disp_mag = torch.mean(torch.abs(low_pred['displacement'])).item()
-    high_disp_mag = torch.mean(torch.abs(high_pred['displacement'])).item()
-
-    print(f"    Low stiffness displacement: {low_disp_mag:.6f}")
-    print(f"    High stiffness displacement: {high_disp_mag:.6f}")
-
-    # Pattern learned if low stiffness has higher displacement
-    # (But with random data this might not hold - this is a template)
-    pattern_ratio = low_disp_mag / (high_disp_mag + 1e-8)
-
-    print(f"    Pattern ratio (should be > 1.0): {pattern_ratio:.2f}")
-    print(f"    Note: With synthetic random data, pattern may not emerge.")
-    print(f"          Real training data should show clear physical patterns.")
-
-    # Just check predictions are reasonable magnitude
-    success = (low_disp_mag > 0.0 and high_disp_mag > 0.0)
-
-    return {
-        'status': 'PASS' if success else 'FAIL',
-        'message': f'Pattern recognition test completed',
-        'metrics': {
-            'low_stiffness_displacement': float(low_disp_mag),
-            'high_stiffness_displacement': float(high_disp_mag),
-            'pattern_ratio': float(pattern_ratio)
-        }
-    }
-
-
-if __name__ == "__main__":
-    print("\nRunning learning capability tests...\n")
-
-    tests = [
-        ("Memorization Test", test_memorization),
-        ("Interpolation Test", test_interpolation),
-        ("Extrapolation Test", test_extrapolation),
-        ("Pattern Recognition", test_pattern_recognition)
-    ]
-
-    passed = 0
-    failed = 0
-
-    for name, test_func in tests:
-        print(f"[TEST] {name}")
-        try:
-            result = test_func()
-            if result['status'] == 'PASS':
-                print(f"  ✓ PASS\n")
-                passed += 1
-            else:
-                print(f"  ✗ FAIL: {result['message']}\n")
-                failed += 1
-        except Exception as e:
-            print(f"  ✗ FAIL: {str(e)}\n")
-            import traceback
-            traceback.print_exc()
-            failed += 1
-
-    print(f"\nResults: {passed} passed, {failed} failed")
-    print(f"\nNote: These tests use SYNTHETIC data and train for limited epochs.")
-    print(f"Real training on actual FEA data will show better learning performance.")

atomizer-field/tests/test_physics.py

@@ -1,385 +0,0 @@
-"""
-test_physics.py
-Physics validation tests with analytical solutions
-
-Tests that the neural network respects fundamental physics:
-- Cantilever beam (δ = FL³/3EI)
-- Simply supported beam (δ = FL³/48EI)
-- Equilibrium (∇·σ + f = 0)
-- Energy conservation (strain energy = work done)
-"""
-
-import torch
-import numpy as np
-import sys
-from pathlib import Path
-
-# Add parent directory to path
-sys.path.insert(0, str(Path(__file__).parent.parent))
-
-from neural_models.field_predictor import create_model
-from torch_geometric.data import Data
-
-
-def create_cantilever_beam_graph(length=1.0, force=1000.0, E=210e9, I=1e-6):
-    """
-    Create synthetic cantilever beam graph with analytical solution
-
-    Analytical solution: δ_max = FL³/3EI
-
-    Args:
-        length: Beam length (m)
-        force: Applied force (N)
-        E: Young's modulus (Pa)
-        I: Second moment of area (m^4)
-
-    Returns:
-        graph_data: PyG Data object
-        analytical_displacement: Expected max displacement (m)
-    """
-    # Calculate analytical solution
-    analytical_displacement = (force * length**3) / (3 * E * I)
-
-    # Create simple beam mesh (10 nodes along length)
-    num_nodes = 10
-    x_coords = np.linspace(0, length, num_nodes)
-
-    # Node features: [x, y, z, bc_x, bc_y, bc_z, bc_rx, bc_ry, bc_rz, load_x, load_y, load_z]
-    node_features = np.zeros((num_nodes, 12))
-    node_features[:, 0] = x_coords  # x coordinates
-
-    # Boundary conditions at x=0 (fixed end)
-    node_features[0, 3:9] = 1.0  # All DOF constrained
-
-    # Applied force at x=length (free end)
-    node_features[-1, 10] = force  # Force in y direction
-
-    # Create edges (connect adjacent nodes)
-    edge_index = []
-    for i in range(num_nodes - 1):
-        edge_index.append([i, i+1])
-        edge_index.append([i+1, i])
-
-    edge_index = torch.tensor(edge_index, dtype=torch.long).t()
-
-    # Edge features: [E, nu, rho, G, alpha]
-    num_edges = edge_index.shape[1]
-    edge_features = np.zeros((num_edges, 5))
-    edge_features[:, 0] = E / 1e11  # Normalized Young's modulus
-    edge_features[:, 1] = 0.3  # Poisson's ratio
-    edge_features[:, 2] = 7850 / 10000  # Normalized density
-    edge_features[:, 3] = E / (2 * (1 + 0.3)) / 1e11  # Normalized shear modulus
-    edge_features[:, 4] = 1.2e-5  # Thermal expansion
-
-    # Convert to tensors
-    x = torch.tensor(node_features, dtype=torch.float32)
-    edge_attr = torch.tensor(edge_features, dtype=torch.float32)
-    batch = torch.zeros(num_nodes, dtype=torch.long)
-
-    data = Data(x=x, edge_index=edge_index, edge_attr=edge_attr, batch=batch)
-
-    return data, analytical_displacement
-
-
-def test_cantilever_analytical():
-    """
-    Test 1: Cantilever beam with analytical solution
-
-    Expected: Neural prediction within 5% of δ = FL³/3EI
-
-    Note: This test uses an untrained model, so it will fail until
-    the model is trained on cantilever beam data. This test serves
-    as a template for post-training validation.
-    """
-    print("    Creating cantilever beam test case...")
-
-    # Create test case
-    graph_data, analytical_disp = create_cantilever_beam_graph(
-        length=1.0,
-        force=1000.0,
-        E=210e9,
-        I=1e-6
-    )
-
-    print(f"    Analytical max displacement: {analytical_disp*1000:.6f} mm")
-
-    # Create model (untrained)
-    config = {
-        'node_feature_dim': 12,
-        'edge_feature_dim': 5,
-        'hidden_dim': 64,
-        'num_layers': 4,
-        'dropout': 0.1
-    }
-
-    model = create_model(config)
-    model.eval()
-
-    # Make prediction
-    print("    Running neural prediction...")
-    with torch.no_grad():
-        results = model(graph_data, return_stress=False)
-
-    # Extract max displacement (y-direction at free end)
-    predicted_disp = torch.max(torch.abs(results['displacement'][:, 1])).item()
-
-    print(f"    Predicted max displacement: {predicted_disp:.6f} (arbitrary units)")
-
-    # Calculate error (will be large for untrained model)
-    # After training, this should be < 5%
-    error = abs(predicted_disp - analytical_disp) / analytical_disp * 100
-
-    print(f"    Error: {error:.1f}%")
-    print(f"    Note: Model is untrained. After training, expect < 5% error.")
-
-    # For now, just check that prediction completed
-    success = results['displacement'].shape[0] == graph_data.x.shape[0]
-
-    return {
-        'status': 'PASS' if success else 'FAIL',
-        'message': f'Cantilever test completed (untrained model)',
-        'metrics': {
-            'analytical_displacement_mm': float(analytical_disp * 1000),
-            'predicted_displacement': float(predicted_disp),
-            'error_percent': float(error),
-            'trained': False
-        }
-    }
-
-
-def test_equilibrium():
-    """
-    Test 2: Force equilibrium check
-
-    Expected: ∇·σ + f = 0 (force balance)
-
-    Checks that predicted stress field satisfies equilibrium.
-    For trained model, equilibrium residual should be < 1e-6.
-    """
-    print("    Testing equilibrium constraint...")
-
-    # Create simple test case
-    num_nodes = 20
-    num_edges = 40
-
-    x = torch.randn(num_nodes, 12)
-    edge_index = torch.randint(0, num_nodes, (2, num_edges))
-    edge_attr = torch.randn(num_edges, 5)
-    batch = torch.zeros(num_nodes, dtype=torch.long)
-
-    data = Data(x=x, edge_index=edge_index, edge_attr=edge_attr, batch=batch)
-
-    # Create model
-    config = {
-        'node_feature_dim': 12,
-        'edge_feature_dim': 5,
-        'hidden_dim': 64,
-        'num_layers': 4,
-        'dropout': 0.1
-    }
-
-    model = create_model(config)
-    model.eval()
-
-    # Make prediction
-    with torch.no_grad():
-        results = model(data, return_stress=True)
-
-    # Compute equilibrium residual (simplified check)
-    # In real implementation, would compute ∇·σ numerically
-    stress = results['stress']
-    stress_gradient_norm = torch.mean(torch.abs(stress)).item()
-
-    print(f"    Stress field magnitude: {stress_gradient_norm:.6f}")
-    print(f"    Note: Full equilibrium check requires mesh connectivity.")
-    print(f"    After training with physics loss, residual should be < 1e-6.")
-
-    return {
-        'status': 'PASS',
-        'message': 'Equilibrium check completed',
-        'metrics': {
-            'stress_magnitude': float(stress_gradient_norm),
-            'trained': False
-        }
-    }
-
-
-def test_energy_conservation():
-    """
-    Test 3: Energy conservation
-
-    Expected: Strain energy = Work done by external forces
-
-    U = (1/2)∫ σ:ε dV = ∫ f·u dS
-    """
-    print("    Testing energy conservation...")
-
-    # Create test case with known loading
-    num_nodes = 30
-    num_edges = 60
-
-    x = torch.randn(num_nodes, 12)
-    # Add known external force
-    x[:, 9:12] = 0.0  # Clear loads
-    x[0, 10] = 1000.0  # 1000 N in y direction at node 0
-
-    edge_index = torch.randint(0, num_nodes, (2, num_edges))
-    edge_attr = torch.randn(num_edges, 5)
-    batch = torch.zeros(num_nodes, dtype=torch.long)
-
-    data = Data(x=x, edge_index=edge_index, edge_attr=edge_attr, batch=batch)
-
-    # Create model
-    config = {
-        'node_feature_dim': 12,
-        'edge_feature_dim': 5,
-        'hidden_dim': 64,
-        'num_layers': 4,
-        'dropout': 0.1
-    }
-
-    model = create_model(config)
-    model.eval()
-
-    # Make prediction
-    with torch.no_grad():
-        results = model(data, return_stress=True)
-
-    # Compute external work (simplified)
-    displacement = results['displacement']
-    force = x[:, 9:12]
-
-    external_work = torch.sum(force * displacement[:, :3]).item()
-
-    # Compute strain energy (simplified: U ≈ (1/2) σ:ε)
-    stress = results['stress']
-    # For small deformations: ε ≈ ∇u, approximate with displacement gradient
-    strain_energy = 0.5 * torch.sum(stress * displacement).item()
-
-    print(f"    External work: {external_work:.6f}")
-    print(f"    Strain energy: {strain_energy:.6f}")
-    print(f"    Note: Simplified calculation. Full energy check requires")
-    print(f"          proper strain computation from displacement gradients.")
-
-    return {
-        'status': 'PASS',
-        'message': 'Energy conservation check completed',
-        'metrics': {
-            'external_work': float(external_work),
-            'strain_energy': float(strain_energy),
-            'trained': False
-        }
-    }
-
-
-def test_constitutive_law():
-    """
-    Test 4: Constitutive law (Hooke's law)
-
-    Expected: σ = C:ε (stress proportional to strain)
-
-    For linear elastic materials: σ = E·ε for 1D
-    """
-    print("    Testing constitutive law...")
-
-    # Create simple uniaxial test case
-    num_nodes = 10
-
-    # Simple bar under tension
-    x = torch.zeros(num_nodes, 12)
-    x[:, 0] = torch.linspace(0, 1, num_nodes)  # x coordinates
-
-    # Fixed at x=0
-    x[0, 3:9] = 1.0
-
-    # Force at x=1
-    x[-1, 9] = 1000.0  # Axial force
-
-    # Create edges
-    edge_index = []
-    for i in range(num_nodes - 1):
-        edge_index.append([i, i+1])
-        edge_index.append([i+1, i])
-
-    edge_index = torch.tensor(edge_index, dtype=torch.long).t()
-
-    # Material properties
-    E = 210e9  # Young's modulus
-    edge_attr = torch.zeros(edge_index.shape[1], 5)
-    edge_attr[:, 0] = E / 1e11  # Normalized
-    edge_attr[:, 1] = 0.3  # Poisson's ratio
-
-    batch = torch.zeros(num_nodes, dtype=torch.long)
-
-    data = Data(x=x, edge_index=edge_index, edge_attr=edge_attr, batch=batch)
-
-    # Create model
-    config = {
-        'node_feature_dim': 12,
-        'edge_feature_dim': 5,
-        'hidden_dim': 64,
-        'num_layers': 4,
-        'dropout': 0.1
-    }
-
-    model = create_model(config)
-    model.eval()
-
-    # Make prediction
-    with torch.no_grad():
-        results = model(data, return_stress=True)
-
-    # Check stress-strain relationship
-    displacement = results['displacement']
-    stress = results['stress']
-
-    # For trained model with physics loss, stress should follow σ = E·ε
-    print(f"    Displacement range: {displacement[:, 0].min():.6f} to {displacement[:, 0].max():.6f}")
-    print(f"    Stress range: {stress[:, 0].min():.6f} to {stress[:, 0].max():.6f}")
-    print(f"    Note: After training with constitutive loss, stress should")
-    print(f"          be proportional to strain (σ = E·ε).")
-
-    return {
-        'status': 'PASS',
-        'message': 'Constitutive law check completed',
-        'metrics': {
-            'displacement_range': [float(displacement[:, 0].min()), float(displacement[:, 0].max())],
-            'stress_range': [float(stress[:, 0].min()), float(stress[:, 0].max())],
-            'trained': False
-        }
-    }
-
-
-if __name__ == "__main__":
-    print("\nRunning physics validation tests...\n")
-
-    tests = [
-        ("Cantilever Analytical", test_cantilever_analytical),
-        ("Equilibrium Check", test_equilibrium),
-        ("Energy Conservation", test_energy_conservation),
-        ("Constitutive Law", test_constitutive_law)
-    ]
-
-    passed = 0
-    failed = 0
-
-    for name, test_func in tests:
-        print(f"[TEST] {name}")
-        try:
-            result = test_func()
-            if result['status'] == 'PASS':
-                print(f"  ✓ PASS\n")
-                passed += 1
-            else:
-                print(f"  ✗ FAIL: {result['message']}\n")
-                failed += 1
-        except Exception as e:
-            print(f"  ✗ FAIL: {str(e)}\n")
-            import traceback
-            traceback.print_exc()
-            failed += 1
-
-    print(f"\nResults: {passed} passed, {failed} failed")
-    print(f"\nNote: These tests use an UNTRAINED model.")
-    print(f"After training with physics-informed losses, all tests should pass")
-    print(f"with errors < 5% for analytical solutions.")

atomizer-field/tests/test_predictions.py

@@ -1,462 +0,0 @@
-"""
-test_predictions.py
-Integration tests for complete pipeline
-
-Tests the full system from parsing to prediction:
-- Parser validation with real data
-- Training pipeline end-to-end
-- Prediction accuracy vs FEA
-- Performance benchmarks
-"""
-
-import torch
-import numpy as np
-import sys
-from pathlib import Path
-import json
-import time
-
-# Add parent directory to path
-sys.path.insert(0, str(Path(__file__).parent.parent))
-
-from neural_field_parser import NastranToNeuralFieldParser
-from neural_models.data_loader import FEAMeshDataset
-from neural_models.field_predictor import create_model
-from neural_models.physics_losses import create_loss_function
-
-
-def test_parser():
-    """
-    Test 1: Parser validation
-
-    Expected: Successfully parse BDF/OP2 files and create valid output
-
-    Uses test_case_beam if available, otherwise creates minimal test.
-    """
-    print("    Checking for test data...")
-
-    test_dir = Path("test_case_beam")
-
-    if not test_dir.exists():
-        print(f"    ⚠ Warning: {test_dir} not found")
-        print(f"    Skipping parser test - run test_simple_beam.py first")
-        return {
-            'status': 'PASS',
-            'message': 'Parser test skipped (no test data)',
-            'metrics': {'skipped': True}
-        }
-
-    print(f"    Found test directory: {test_dir}")
-
-    try:
-        # Check if already parsed
-        json_file = test_dir / "neural_field_data.json"
-        h5_file = test_dir / "neural_field_data.h5"
-
-        if json_file.exists() and h5_file.exists():
-            print(f"    Found existing parsed data")
-
-            # Load and validate
-            with open(json_file, 'r') as f:
-                data = json.load(f)
-
-            n_nodes = data['mesh']['statistics']['n_nodes']
-            n_elements = data['mesh']['statistics']['n_elements']
-
-            print(f"    Nodes: {n_nodes:,}")
-            print(f"    Elements: {n_elements:,}")
-
-            return {
-                'status': 'PASS',
-                'message': 'Parser validation successful',
-                'metrics': {
-                    'n_nodes': n_nodes,
-                    'n_elements': n_elements,
-                    'has_results': 'results' in data
-                }
-            }
-
-        else:
-            print(f"    Parsed data not found - run test_simple_beam.py first")
-            return {
-                'status': 'PASS',
-                'message': 'Parser test skipped (data not parsed yet)',
-                'metrics': {'skipped': True}
-            }
-
-    except Exception as e:
-        print(f"    Error: {str(e)}")
-        return {
-            'status': 'FAIL',
-            'message': f'Parser validation failed: {str(e)}',
-            'metrics': {}
-        }
-
-
-def test_training():
-    """
-    Test 2: Training pipeline
-
-    Expected: Complete training loop runs without errors
-
-    Trains on small synthetic dataset for speed.
-    """
-    print("    Setting up training test...")
-
-    # Create minimal synthetic dataset
-    print("    Creating synthetic training data...")
-
-    dataset = []
-    for i in range(5):  # Just 5 samples for quick test
-        num_nodes = 20
-        num_edges = 40
-
-        x = torch.randn(num_nodes, 12)
-        edge_index = torch.randint(0, num_nodes, (2, num_edges))
-        edge_attr = torch.randn(num_edges, 5)
-        batch = torch.zeros(num_nodes, dtype=torch.long)
-
-        from torch_geometric.data import Data
-        data = Data(x=x, edge_index=edge_index, edge_attr=edge_attr, batch=batch)
-
-        # Add synthetic targets
-        data.y_displacement = torch.randn(num_nodes, 6)
-        data.y_stress = torch.randn(num_nodes, 6)
-
-        dataset.append(data)
-
-    print(f"    Created {len(dataset)} training samples")
-
-    # Create model
-    print("    Creating model...")
-
-    config = {
-        'node_feature_dim': 12,
-        'edge_feature_dim': 5,
-        'hidden_dim': 64,
-        'num_layers': 4,
-        'dropout': 0.1
-    }
-
-    model = create_model(config)
-    loss_fn = create_loss_function('mse')
-    optimizer = torch.optim.Adam(model.parameters(), lr=0.001)
-
-    print("    Training for 10 epochs...")
-
-    # Training loop
-    model.train()
-    start_time = time.time()
-
-    for epoch in range(10):
-        epoch_loss = 0.0
-
-        for data in dataset:
-            optimizer.zero_grad()
-
-            # Forward pass
-            predictions = model(data, return_stress=True)
-
-            # Compute loss
-            targets = {
-                'displacement': data.y_displacement,
-                'stress': data.y_stress
-            }
-
-            loss_dict = loss_fn(predictions, targets)
-            loss = loss_dict['total_loss']
-
-            # Backward pass
-            loss.backward()
-            optimizer.step()
-
-            epoch_loss += loss.item()
-
-        avg_loss = epoch_loss / len(dataset)
-
-        if (epoch + 1) % 5 == 0:
-            print(f"      Epoch {epoch+1}/10: Loss = {avg_loss:.6f}")
-
-    training_time = time.time() - start_time
-
-    print(f"    Training completed in {training_time:.2f}s")
-
-    return {
-        'status': 'PASS',
-        'message': 'Training pipeline successful',
-        'metrics': {
-            'epochs': 10,
-            'samples': len(dataset),
-            'training_time_s': float(training_time),
-            'final_loss': float(avg_loss)
-        }
-    }
-
-
-def test_prediction_accuracy():
-    """
-    Test 3: Prediction accuracy
-
-    Expected: Predictions match targets with reasonable error
-
-    Uses trained model from test_training.
-    """
-    print("    Testing prediction accuracy...")
-
-    # Create test case
-    num_nodes = 20
-    num_edges = 40
-
-    x = torch.randn(num_nodes, 12)
-    edge_index = torch.randint(0, num_nodes, (2, num_edges))
-    edge_attr = torch.randn(num_edges, 5)
-    batch = torch.zeros(num_nodes, dtype=torch.long)
-
-    from torch_geometric.data import Data
-    data = Data(x=x, edge_index=edge_index, edge_attr=edge_attr, batch=batch)
-
-    # Synthetic ground truth
-    target_disp = torch.randn(num_nodes, 6)
-    target_stress = torch.randn(num_nodes, 6)
-
-    # Create and "train" model (minimal training for test speed)
-    print("    Creating model...")
-
-    config = {
-        'node_feature_dim': 12,
-        'edge_feature_dim': 5,
-        'hidden_dim': 64,
-        'num_layers': 4,
-        'dropout': 0.0
-    }
-
-    model = create_model(config)
-
-    # Quick training to make predictions reasonable
-    model.train()
-    optimizer = torch.optim.Adam(model.parameters(), lr=0.01)
-    loss_fn = create_loss_function('mse')
-
-    for _ in range(20):
-        optimizer.zero_grad()
-
-        predictions = model(data, return_stress=True)
-
-        targets = {
-            'displacement': target_disp,
-            'stress': target_stress
-        }
-
-        loss_dict = loss_fn(predictions, targets)
-        loss = loss_dict['total_loss']
-
-        loss.backward()
-        optimizer.step()
-
-    # Test prediction
-    print("    Running prediction...")
-
-    model.eval()
-    start_time = time.time()
-
-    with torch.no_grad():
-        predictions = model(data, return_stress=True)
-
-    inference_time = (time.time() - start_time) * 1000  # ms
-
-    # Compute errors
-    disp_error = torch.mean(torch.abs(predictions['displacement'] - target_disp)).item()
-    stress_error = torch.mean(torch.abs(predictions['stress'] - target_stress)).item()
-
-    print(f"    Inference time: {inference_time:.2f} ms")
-    print(f"    Displacement error: {disp_error:.6f}")
-    print(f"    Stress error: {stress_error:.6f}")
-
-    return {
-        'status': 'PASS',
-        'message': 'Prediction accuracy test completed',
-        'metrics': {
-            'inference_time_ms': float(inference_time),
-            'displacement_error': float(disp_error),
-            'stress_error': float(stress_error),
-            'num_nodes': num_nodes
-        }
-    }
-
-
-def test_performance_benchmark():
-    """
-    Test 4: Performance benchmark
-
-    Expected: Inference time < 100ms for typical mesh
-
-    Compares neural prediction vs expected FEA time.
-    """
-    print("    Running performance benchmark...")
-
-    # Test different mesh sizes
-    mesh_sizes = [10, 50, 100, 500]
-    results = []
-
-    config = {
-        'node_feature_dim': 12,
-        'edge_feature_dim': 5,
-        'hidden_dim': 64,
-        'num_layers': 4,
-        'dropout': 0.0
-    }
-
-    model = create_model(config)
-    model.eval()
-
-    print(f"    Testing {len(mesh_sizes)} mesh sizes...")
-
-    for num_nodes in mesh_sizes:
-        num_edges = num_nodes * 2
-
-        x = torch.randn(num_nodes, 12)
-        edge_index = torch.randint(0, num_nodes, (2, num_edges))
-        edge_attr = torch.randn(num_edges, 5)
-        batch = torch.zeros(num_nodes, dtype=torch.long)
-
-        from torch_geometric.data import Data
-        data = Data(x=x, edge_index=edge_index, edge_attr=edge_attr, batch=batch)
-
-        # Warm-up
-        with torch.no_grad():
-            _ = model(data, return_stress=True)
-
-        # Benchmark (average of 10 runs)
-        times = []
-        with torch.no_grad():
-            for _ in range(10):
-                start = time.time()
-                _ = model(data, return_stress=True)
-                times.append((time.time() - start) * 1000)
-
-        avg_time = np.mean(times)
-        std_time = np.std(times)
-
-        print(f"      {num_nodes:4d} nodes: {avg_time:6.2f} ± {std_time:4.2f} ms")
-
-        results.append({
-            'num_nodes': num_nodes,
-            'avg_time_ms': float(avg_time),
-            'std_time_ms': float(std_time)
-        })
-
-    # Check if performance is acceptable (< 100ms for 100 nodes)
-    time_100_nodes = next((r['avg_time_ms'] for r in results if r['num_nodes'] == 100), None)
-
-    success = time_100_nodes is not None and time_100_nodes < 100.0
-
-    return {
-        'status': 'PASS' if success else 'FAIL',
-        'message': f'Performance benchmark completed',
-        'metrics': {
-            'results': results,
-            'time_100_nodes_ms': float(time_100_nodes) if time_100_nodes else None,
-            'passes_threshold': success
-        }
-    }
-
-
-def test_batch_inference():
-    """
-    Test 5: Batch inference
-
-    Expected: Can process multiple designs simultaneously
-
-    Important for optimization loops.
-    """
-    print("    Testing batch inference...")
-
-    batch_size = 5
-    num_nodes_per_graph = 20
-
-    config = {
-        'node_feature_dim': 12,
-        'edge_feature_dim': 5,
-        'hidden_dim': 64,
-        'num_layers': 4,
-        'dropout': 0.0
-    }
-
-    model = create_model(config)
-    model.eval()
-
-    print(f"    Creating batch of {batch_size} graphs...")
-
-    graphs = []
-    for i in range(batch_size):
-        num_nodes = num_nodes_per_graph
-        num_edges = num_nodes * 2
-
-        x = torch.randn(num_nodes, 12)
-        edge_index = torch.randint(0, num_nodes, (2, num_edges))
-        edge_attr = torch.randn(num_edges, 5)
-        batch = torch.full((num_nodes,), i, dtype=torch.long)
-
-        from torch_geometric.data import Data
-        graphs.append(Data(x=x, edge_index=edge_index, edge_attr=edge_attr, batch=batch))
-
-    # Process batch
-    print(f"    Processing batch...")
-
-    start_time = time.time()
-
-    with torch.no_grad():
-        for graph in graphs:
-            _ = model(graph, return_stress=True)
-
-    batch_time = (time.time() - start_time) * 1000
-
-    time_per_graph = batch_time / batch_size
-
-    print(f"    Batch processing time: {batch_time:.2f} ms")
-    print(f"    Time per graph: {time_per_graph:.2f} ms")
-
-    return {
-        'status': 'PASS',
-        'message': 'Batch inference successful',
-        'metrics': {
-            'batch_size': batch_size,
-            'total_time_ms': float(batch_time),
-            'time_per_graph_ms': float(time_per_graph)
-        }
-    }
-
-
-if __name__ == "__main__":
-    print("\nRunning integration tests...\n")
-
-    tests = [
-        ("Parser Validation", test_parser),
-        ("Training Pipeline", test_training),
-        ("Prediction Accuracy", test_prediction_accuracy),
-        ("Performance Benchmark", test_performance_benchmark),
-        ("Batch Inference", test_batch_inference)
-    ]
-
-    passed = 0
-    failed = 0
-
-    for name, test_func in tests:
-        print(f"[TEST] {name}")
-        try:
-            result = test_func()
-            if result['status'] == 'PASS':
-                print(f"  ✓ PASS\n")
-                passed += 1
-            else:
-                print(f"  ✗ FAIL: {result['message']}\n")
-                failed += 1
-        except Exception as e:
-            print(f"  ✗ FAIL: {str(e)}\n")
-            import traceback
-            traceback.print_exc()
-            failed += 1
-
-    print(f"\nResults: {passed} passed, {failed} failed")
-    print(f"\nNote: Parser test requires test_case_beam directory.")
-    print(f"Run 'python test_simple_beam.py' first to create test data.")

atomizer-field/tests/test_synthetic.py

@@ -1,296 +0,0 @@
-"""
-test_synthetic.py
-Synthetic tests with known analytical solutions
-
-Tests basic functionality without real FEA data:
-- Model can be created
-- Forward pass works
-- Loss functions compute correctly
-- Predictions have correct shape
-"""
-
-import torch
-import numpy as np
-import sys
-from pathlib import Path
-
-# Add parent directory to path
-sys.path.insert(0, str(Path(__file__).parent.parent))
-
-from neural_models.field_predictor import create_model
-from neural_models.physics_losses import create_loss_function
-from torch_geometric.data import Data
-
-
-def test_model_creation():
-    """
-    Test 1: Can we create the model?
-
-    Expected: Model instantiates with correct number of parameters
-    """
-    print("    Creating GNN model...")
-
-    config = {
-        'node_feature_dim': 12,
-        'edge_feature_dim': 5,
-        'hidden_dim': 64,
-        'num_layers': 4,
-        'dropout': 0.1
-    }
-
-    model = create_model(config)
-
-    # Count parameters
-    num_params = sum(p.numel() for p in model.parameters())
-
-    print(f"    Model created: {num_params:,} parameters")
-
-    return {
-        'status': 'PASS',
-        'message': f'Model created successfully ({num_params:,} params)',
-        'metrics': {'parameters': num_params}
-    }
-
-
-def test_forward_pass():
-    """
-    Test 2: Can model process data?
-
-    Expected: Forward pass completes without errors
-    """
-    print("    Testing forward pass...")
-
-    # Create model
-    config = {
-        'node_feature_dim': 12,
-        'edge_feature_dim': 5,
-        'hidden_dim': 64,
-        'num_layers': 4,
-        'dropout': 0.1
-    }
-
-    model = create_model(config)
-    model.eval()
-
-    # Create dummy data
-    num_nodes = 100
-    num_edges = 300
-
-    x = torch.randn(num_nodes, 12)  # Node features
-    edge_index = torch.randint(0, num_nodes, (2, num_edges))  # Connectivity
-    edge_attr = torch.randn(num_edges, 5)  # Edge features
-    batch = torch.zeros(num_nodes, dtype=torch.long)  # Batch assignment
-
-    data = Data(x=x, edge_index=edge_index, edge_attr=edge_attr, batch=batch)
-
-    # Forward pass
-    with torch.no_grad():
-        results = model(data, return_stress=True)
-
-    # Check outputs
-    assert 'displacement' in results, "Missing displacement output"
-    assert 'stress' in results, "Missing stress output"
-    assert 'von_mises' in results, "Missing von Mises output"
-
-    # Check shapes
-    assert results['displacement'].shape == (num_nodes, 6), f"Wrong displacement shape: {results['displacement'].shape}"
-    assert results['stress'].shape == (num_nodes, 6), f"Wrong stress shape: {results['stress'].shape}"
-    assert results['von_mises'].shape == (num_nodes,), f"Wrong von Mises shape: {results['von_mises'].shape}"
-
-    print(f"    Displacement shape: {results['displacement'].shape} [OK]")
-    print(f"    Stress shape: {results['stress'].shape} [OK]")
-    print(f"    Von Mises shape: {results['von_mises'].shape} [OK]")
-
-    return {
-        'status': 'PASS',
-        'message': 'Forward pass successful',
-        'metrics': {
-            'num_nodes': num_nodes,
-            'displacement_shape': list(results['displacement'].shape),
-            'stress_shape': list(results['stress'].shape)
-        }
-    }
-
-
-def test_loss_computation():
-    """
-    Test 3: Do loss functions work?
-
-    Expected: All loss types compute without errors
-    """
-    print("    Testing loss functions...")
-
-    # Create dummy predictions and targets
-    num_nodes = 100
-
-    predictions = {
-        'displacement': torch.randn(num_nodes, 6),
-        'stress': torch.randn(num_nodes, 6),
-        'von_mises': torch.abs(torch.randn(num_nodes))
-    }
-
-    targets = {
-        'displacement': torch.randn(num_nodes, 6),
-        'stress': torch.randn(num_nodes, 6)
-    }
-
-    loss_types = ['mse', 'relative', 'physics', 'max']
-    loss_values = {}
-
-    for loss_type in loss_types:
-        loss_fn = create_loss_function(loss_type)
-        losses = loss_fn(predictions, targets)
-
-        assert 'total_loss' in losses, f"Missing total_loss for {loss_type}"
-        assert not torch.isnan(losses['total_loss']), f"NaN loss for {loss_type}"
-        assert not torch.isinf(losses['total_loss']), f"Inf loss for {loss_type}"
-
-        loss_values[loss_type] = losses['total_loss'].item()
-        print(f"    {loss_type.upper()} loss: {loss_values[loss_type]:.6f} [OK]")
-
-    return {
-        'status': 'PASS',
-        'message': 'All loss functions working',
-        'metrics': loss_values
-    }
-
-
-def test_batch_processing():
-    """
-    Test 4: Can model handle batches?
-
-    Expected: Batch processing works correctly
-    """
-    print("    Testing batch processing...")
-
-    config = {
-        'node_feature_dim': 12,
-        'edge_feature_dim': 5,
-        'hidden_dim': 64,
-        'num_layers': 4,
-        'dropout': 0.1
-    }
-
-    model = create_model(config)
-    model.eval()
-
-    # Create batch of 3 graphs
-    graphs = []
-    for i in range(3):
-        num_nodes = 50 + i * 10  # Different sizes
-        num_edges = 150 + i * 30
-
-        x = torch.randn(num_nodes, 12)
-        edge_index = torch.randint(0, num_nodes, (2, num_edges))
-        edge_attr = torch.randn(num_edges, 5)
-        batch = torch.full((num_nodes,), i, dtype=torch.long)
-
-        graphs.append(Data(x=x, edge_index=edge_index, edge_attr=edge_attr, batch=batch))
-
-    # Process batch
-    total_nodes = sum(g.x.shape[0] for g in graphs)
-
-    with torch.no_grad():
-        for i, graph in enumerate(graphs):
-            results = model(graph, return_stress=True)
-            print(f"    Graph {i+1}: {graph.x.shape[0]} nodes -> predictions [OK]")
-
-    return {
-        'status': 'PASS',
-        'message': 'Batch processing successful',
-        'metrics': {'num_graphs': len(graphs), 'total_nodes': total_nodes}
-    }
-
-
-def test_gradient_flow():
-    """
-    Test 5: Do gradients flow correctly?
-
-    Expected: Gradients computed without errors
-    """
-    print("    Testing gradient flow...")
-
-    config = {
-        'node_feature_dim': 12,
-        'edge_feature_dim': 5,
-        'hidden_dim': 64,
-        'num_layers': 4,
-        'dropout': 0.1
-    }
-
-    model = create_model(config)
-    model.train()
-
-    # Create dummy data
-    num_nodes = 50
-    num_edges = 150
-
-    x = torch.randn(num_nodes, 12)
-    edge_index = torch.randint(0, num_nodes, (2, num_edges))
-    edge_attr = torch.randn(num_edges, 5)
-    batch = torch.zeros(num_nodes, dtype=torch.long)
-
-    data = Data(x=x, edge_index=edge_index, edge_attr=edge_attr, batch=batch)
-
-    # Forward pass
-    results = model(data, return_stress=True)
-
-    # Compute loss
-    targets = {
-        'displacement': torch.randn(num_nodes, 6),
-        'stress': torch.randn(num_nodes, 6)
-    }
-
-    loss_fn = create_loss_function('mse')
-    losses = loss_fn(results, targets)
-
-    # Backward pass
-    losses['total_loss'].backward()
-
-    # Check gradients
-    has_grad = sum(1 for p in model.parameters() if p.grad is not None)
-    total_params = sum(1 for _ in model.parameters())
-
-    print(f"    Parameters with gradients: {has_grad}/{total_params} [OK]")
-
-    assert has_grad == total_params, f"Not all parameters have gradients"
-
-    return {
-        'status': 'PASS',
-        'message': 'Gradients computed successfully',
-        'metrics': {
-            'parameters_with_grad': has_grad,
-            'total_parameters': total_params
-        }
-    }
-
-
-if __name__ == "__main__":
-    print("\nRunning synthetic tests...\n")
-
-    tests = [
-        ("Model Creation", test_model_creation),
-        ("Forward Pass", test_forward_pass),
-        ("Loss Computation", test_loss_computation),
-        ("Batch Processing", test_batch_processing),
-        ("Gradient Flow", test_gradient_flow)
-    ]
-
-    passed = 0
-    failed = 0
-
-    for name, test_func in tests:
-        print(f"[TEST] {name}")
-        try:
-            result = test_func()
-            if result['status'] == 'PASS':
-                print(f"  [PASS]\n")
-                passed += 1
-            else:
-                print(f"  [FAIL]: {result['message']}\n")
-                failed += 1
-        except Exception as e:
-            print(f"  [FAIL]: {str(e)}\n")
-            failed += 1
-
-    print(f"\nResults: {passed} passed, {failed} failed")

atomizer-field/train.py

@@ -1,451 +0,0 @@
-"""
-train.py
-Training script for AtomizerField neural field predictor
-
-AtomizerField Training Pipeline v2.0
-Trains Graph Neural Networks to predict complete FEA field results.
-
-Usage:
-    python train.py --train_dir ./training_data --val_dir ./validation_data
-
-Key Features:
-- Multi-GPU support
-- Checkpoint saving/loading
-- TensorBoard logging
-- Early stopping
-- Learning rate scheduling
-"""
-
-import argparse
-import json
-from pathlib import Path
-import time
-from datetime import datetime
-
-import torch
-import torch.nn as nn
-import torch.optim as optim
-from torch.utils.tensorboard import SummaryWriter
-
-from neural_models.field_predictor import create_model, AtomizerFieldModel
-from neural_models.physics_losses import create_loss_function
-from neural_models.data_loader import create_dataloaders
-
-
-class Trainer:
-    """
-    Training manager for AtomizerField models
-    """
-
-    def __init__(self, config):
-        """
-        Initialize trainer
-
-        Args:
-            config (dict): Training configuration
-        """
-        self.config = config
-        self.device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
-
-        print(f"\n{'='*60}")
-        print("AtomizerField Training Pipeline v2.0")
-        print(f"{'='*60}")
-        print(f"Device: {self.device}")
-
-        # Create model
-        print("\nCreating model...")
-        self.model = create_model(config.get('model', {}))
-        self.model = self.model.to(self.device)
-
-        num_params = sum(p.numel() for p in self.model.parameters())
-        print(f"Model created: {num_params:,} parameters")
-
-        # Create loss function
-        loss_config = config.get('loss', {})
-        loss_type = loss_config.pop('type', 'mse')
-        self.criterion = create_loss_function(loss_type, loss_config)
-        print(f"Loss function: {loss_type}")
-
-        # Create optimizer
-        self.optimizer = optim.AdamW(
-            self.model.parameters(),
-            lr=config.get('learning_rate', 1e-3),
-            weight_decay=config.get('weight_decay', 1e-5)
-        )
-
-        # Learning rate scheduler
-        self.scheduler = optim.lr_scheduler.ReduceLROnPlateau(
-            self.optimizer,
-            mode='min',
-            factor=0.5,
-            patience=10,
-            verbose=True
-        )
-
-        # Training state
-        self.start_epoch = 0
-        self.best_val_loss = float('inf')
-        self.epochs_without_improvement = 0
-
-        # Create output directories
-        self.output_dir = Path(config.get('output_dir', './runs'))
-        self.output_dir.mkdir(parents=True, exist_ok=True)
-
-        # TensorBoard logging
-        self.writer = SummaryWriter(
-            log_dir=self.output_dir / 'tensorboard'
-        )
-
-        # Save config
-        with open(self.output_dir / 'config.json', 'w') as f:
-            json.dump(config, f, indent=2)
-
-    def train_epoch(self, train_loader, epoch):
-        """
-        Train for one epoch
-
-        Args:
-            train_loader: Training data loader
-            epoch (int): Current epoch number
-
-        Returns:
-            dict: Training metrics
-        """
-        self.model.train()
-
-        total_loss = 0.0
-        total_disp_loss = 0.0
-        total_stress_loss = 0.0
-        num_batches = 0
-
-        for batch_idx, batch in enumerate(train_loader):
-            # Move batch to device
-            batch = batch.to(self.device)
-
-            # Zero gradients
-            self.optimizer.zero_grad()
-
-            # Forward pass
-            predictions = self.model(batch, return_stress=True)
-
-            # Prepare targets
-            targets = {
-                'displacement': batch.y_displacement,
-            }
-            if hasattr(batch, 'y_stress'):
-                targets['stress'] = batch.y_stress
-
-            # Compute loss
-            losses = self.criterion(predictions, targets, batch)
-
-            # Backward pass
-            losses['total_loss'].backward()
-
-            # Gradient clipping (prevents exploding gradients)
-            torch.nn.utils.clip_grad_norm_(self.model.parameters(), max_norm=1.0)
-
-            # Update weights
-            self.optimizer.step()
-
-            # Accumulate metrics
-            total_loss += losses['total_loss'].item()
-            if 'displacement_loss' in losses:
-                total_disp_loss += losses['displacement_loss'].item()
-            if 'stress_loss' in losses:
-                total_stress_loss += losses['stress_loss'].item()
-            num_batches += 1
-
-            # Print progress
-            if batch_idx % 10 == 0:
-                print(f"  Batch {batch_idx}/{len(train_loader)}: "
-                      f"Loss={losses['total_loss'].item():.6f}")
-
-        # Average metrics
-        metrics = {
-            'total_loss': total_loss / num_batches,
-            'displacement_loss': total_disp_loss / num_batches,
-            'stress_loss': total_stress_loss / num_batches
-        }
-
-        return metrics
-
-    def validate(self, val_loader):
-        """
-        Validate model
-
-        Args:
-            val_loader: Validation data loader
-
-        Returns:
-            dict: Validation metrics
-        """
-        self.model.eval()
-
-        total_loss = 0.0
-        total_disp_loss = 0.0
-        total_stress_loss = 0.0
-        num_batches = 0
-
-        with torch.no_grad():
-            for batch in val_loader:
-                # Move batch to device
-                batch = batch.to(self.device)
-
-                # Forward pass
-                predictions = self.model(batch, return_stress=True)
-
-                # Prepare targets
-                targets = {
-                    'displacement': batch.y_displacement,
-                }
-                if hasattr(batch, 'y_stress'):
-                    targets['stress'] = batch.y_stress
-
-                # Compute loss
-                losses = self.criterion(predictions, targets, batch)
-
-                # Accumulate metrics
-                total_loss += losses['total_loss'].item()
-                if 'displacement_loss' in losses:
-                    total_disp_loss += losses['displacement_loss'].item()
-                if 'stress_loss' in losses:
-                    total_stress_loss += losses['stress_loss'].item()
-                num_batches += 1
-
-        # Average metrics
-        metrics = {
-            'total_loss': total_loss / num_batches,
-            'displacement_loss': total_disp_loss / num_batches,
-            'stress_loss': total_stress_loss / num_batches
-        }
-
-        return metrics
-
-    def train(self, train_loader, val_loader, num_epochs):
-        """
-        Main training loop
-
-        Args:
-            train_loader: Training data loader
-            val_loader: Validation data loader
-            num_epochs (int): Number of epochs to train
-        """
-        print(f"\n{'='*60}")
-        print(f"Starting training for {num_epochs} epochs")
-        print(f"{'='*60}\n")
-
-        for epoch in range(self.start_epoch, num_epochs):
-            epoch_start_time = time.time()
-
-            print(f"Epoch {epoch + 1}/{num_epochs}")
-            print("-" * 60)
-
-            # Train
-            train_metrics = self.train_epoch(train_loader, epoch)
-
-            # Validate
-            val_metrics = self.validate(val_loader)
-
-            epoch_time = time.time() - epoch_start_time
-
-            # Print metrics
-            print(f"\nEpoch {epoch + 1} Results:")
-            print(f"  Training Loss: {train_metrics['total_loss']:.6f}")
-            print(f"    Displacement: {train_metrics['displacement_loss']:.6f}")
-            print(f"    Stress: {train_metrics['stress_loss']:.6f}")
-            print(f"  Validation Loss: {val_metrics['total_loss']:.6f}")
-            print(f"    Displacement: {val_metrics['displacement_loss']:.6f}")
-            print(f"    Stress: {val_metrics['stress_loss']:.6f}")
-            print(f"  Time: {epoch_time:.1f}s")
-
-            # Log to TensorBoard
-            self.writer.add_scalar('Loss/train', train_metrics['total_loss'], epoch)
-            self.writer.add_scalar('Loss/val', val_metrics['total_loss'], epoch)
-            self.writer.add_scalar('DisplacementLoss/train', train_metrics['displacement_loss'], epoch)
-            self.writer.add_scalar('DisplacementLoss/val', val_metrics['displacement_loss'], epoch)
-            self.writer.add_scalar('StressLoss/train', train_metrics['stress_loss'], epoch)
-            self.writer.add_scalar('StressLoss/val', val_metrics['stress_loss'], epoch)
-            self.writer.add_scalar('LearningRate', self.optimizer.param_groups[0]['lr'], epoch)
-
-            # Learning rate scheduling
-            self.scheduler.step(val_metrics['total_loss'])
-
-            # Save checkpoint
-            is_best = val_metrics['total_loss'] < self.best_val_loss
-            if is_best:
-                self.best_val_loss = val_metrics['total_loss']
-                self.epochs_without_improvement = 0
-                print(f"  New best validation loss: {self.best_val_loss:.6f}")
-            else:
-                self.epochs_without_improvement += 1
-
-            self.save_checkpoint(epoch, val_metrics, is_best)
-
-            # Early stopping
-            patience = self.config.get('early_stopping_patience', 50)
-            if self.epochs_without_improvement >= patience:
-                print(f"\nEarly stopping after {patience} epochs without improvement")
-                break
-
-            print()
-
-        print(f"\n{'='*60}")
-        print("Training complete!")
-        print(f"Best validation loss: {self.best_val_loss:.6f}")
-        print(f"{'='*60}\n")
-
-        self.writer.close()
-
-    def save_checkpoint(self, epoch, metrics, is_best=False):
-        """
-        Save model checkpoint
-
-        Args:
-            epoch (int): Current epoch
-            metrics (dict): Validation metrics
-            is_best (bool): Whether this is the best model so far
-        """
-        checkpoint = {
-            'epoch': epoch,
-            'model_state_dict': self.model.state_dict(),
-            'optimizer_state_dict': self.optimizer.state_dict(),
-            'scheduler_state_dict': self.scheduler.state_dict(),
-            'best_val_loss': self.best_val_loss,
-            'config': self.config,
-            'metrics': metrics
-        }
-
-        # Save latest checkpoint
-        checkpoint_path = self.output_dir / 'checkpoint_latest.pt'
-        torch.save(checkpoint, checkpoint_path)
-
-        # Save best checkpoint
-        if is_best:
-            best_path = self.output_dir / 'checkpoint_best.pt'
-            torch.save(checkpoint, best_path)
-            print(f"  Saved best model to {best_path}")
-
-        # Save periodic checkpoint
-        if (epoch + 1) % 10 == 0:
-            periodic_path = self.output_dir / f'checkpoint_epoch_{epoch + 1}.pt'
-            torch.save(checkpoint, periodic_path)
-
-    def load_checkpoint(self, checkpoint_path):
-        """
-        Load model checkpoint
-
-        Args:
-            checkpoint_path (str): Path to checkpoint file
-        """
-        checkpoint = torch.load(checkpoint_path, map_location=self.device)
-
-        self.model.load_state_dict(checkpoint['model_state_dict'])
-        self.optimizer.load_state_dict(checkpoint['optimizer_state_dict'])
-        self.scheduler.load_state_dict(checkpoint['scheduler_state_dict'])
-        self.start_epoch = checkpoint['epoch'] + 1
-        self.best_val_loss = checkpoint['best_val_loss']
-
-        print(f"Loaded checkpoint from epoch {checkpoint['epoch']}")
-        print(f"Best validation loss: {self.best_val_loss:.6f}")
-
-
-def main():
-    """
-    Main training entry point
-    """
-    parser = argparse.ArgumentParser(description='Train AtomizerField neural field predictor')
-
-    # Data arguments
-    parser.add_argument('--train_dir', type=str, required=True,
-                       help='Directory containing training cases')
-    parser.add_argument('--val_dir', type=str, required=True,
-                       help='Directory containing validation cases')
-
-    # Training arguments
-    parser.add_argument('--epochs', type=int, default=100,
-                       help='Number of training epochs')
-    parser.add_argument('--batch_size', type=int, default=4,
-                       help='Batch size')
-    parser.add_argument('--lr', type=float, default=1e-3,
-                       help='Learning rate')
-    parser.add_argument('--weight_decay', type=float, default=1e-5,
-                       help='Weight decay')
-
-    # Model arguments
-    parser.add_argument('--hidden_dim', type=int, default=128,
-                       help='Hidden dimension')
-    parser.add_argument('--num_layers', type=int, default=6,
-                       help='Number of GNN layers')
-    parser.add_argument('--dropout', type=float, default=0.1,
-                       help='Dropout rate')
-
-    # Loss arguments
-    parser.add_argument('--loss_type', type=str, default='mse',
-                       choices=['mse', 'relative', 'physics', 'max'],
-                       help='Loss function type')
-
-    # Other arguments
-    parser.add_argument('--output_dir', type=str, default='./runs',
-                       help='Output directory for checkpoints and logs')
-    parser.add_argument('--resume', type=str, default=None,
-                       help='Path to checkpoint to resume from')
-    parser.add_argument('--num_workers', type=int, default=0,
-                       help='Number of data loading workers')
-
-    args = parser.parse_args()
-
-    # Build configuration
-    config = {
-        'model': {
-            'node_feature_dim': 12,  # 3 coords + 6 BCs + 3 loads
-            'edge_feature_dim': 5,   # E, nu, rho, G, alpha
-            'hidden_dim': args.hidden_dim,
-            'num_layers': args.num_layers,
-            'dropout': args.dropout
-        },
-        'loss': {
-            'type': args.loss_type
-        },
-        'learning_rate': args.lr,
-        'weight_decay': args.weight_decay,
-        'batch_size': args.batch_size,
-        'num_epochs': args.epochs,
-        'output_dir': args.output_dir,
-        'early_stopping_patience': 50
-    }
-
-    # Find all case directories
-    train_cases = list(Path(args.train_dir).glob('*/'))
-    val_cases = list(Path(args.val_dir).glob('*/'))
-
-    print(f"Found {len(train_cases)} training cases")
-    print(f"Found {len(val_cases)} validation cases")
-
-    if not train_cases or not val_cases:
-        print("ERROR: No training or validation cases found!")
-        print("Please ensure your directories contain parsed FEA data.")
-        return
-
-    # Create data loaders
-    train_loader, val_loader = create_dataloaders(
-        train_cases,
-        val_cases,
-        batch_size=args.batch_size,
-        num_workers=args.num_workers,
-        normalize=True,
-        include_stress=True
-    )
-
-    # Create trainer
-    trainer = Trainer(config)
-
-    # Resume from checkpoint if specified
-    if args.resume:
-        trainer.load_checkpoint(args.resume)
-
-    # Train
-    trainer.train(train_loader, val_loader, args.epochs)
-
-
-if __name__ == "__main__":
-    main()

atomizer-field/train_parametric.py

@@ -1,789 +0,0 @@
-"""
-train_parametric.py
-Training script for AtomizerField parametric predictor
-
-AtomizerField Parametric Training Pipeline v2.0
-Trains design-conditioned GNN to predict optimization objectives directly.
-
-Usage:
-    python train_parametric.py --train_dir ./training_data --val_dir ./validation_data
-
-Key Differences from train.py (field predictor):
-- Predicts scalar objectives (mass, frequency, displacement, stress) instead of fields
-- Uses design parameters as conditioning input
-- Multi-objective loss function for all 4 outputs
-- Faster training due to simpler output structure
-
-Output:
-    checkpoint_best.pt containing:
-    - model_state_dict: Trained weights
-    - config: Model configuration
-    - normalization: Normalization statistics for inference
-    - design_var_names: Names of design variables
-    - best_val_loss: Best validation loss achieved
-"""
-
-import argparse
-import json
-import sys
-from pathlib import Path
-import time
-from datetime import datetime
-from typing import Dict, List, Any, Optional, Tuple
-
-import numpy as np
-import torch
-import torch.nn as nn
-import torch.optim as optim
-from torch.utils.data import Dataset, DataLoader
-import h5py
-
-# Try to import tensorboard, but make it optional
-try:
-    from torch.utils.tensorboard import SummaryWriter
-    TENSORBOARD_AVAILABLE = True
-except ImportError:
-    TENSORBOARD_AVAILABLE = False
-
-from neural_models.parametric_predictor import create_parametric_model, ParametricFieldPredictor
-
-
-class ParametricDataset(Dataset):
-    """
-    PyTorch Dataset for parametric training.
-
-    Loads training data exported by Atomizer's TrainingDataExporter
-    and prepares it for the parametric predictor.
-
-    Expected directory structure:
-    training_data/
-    ├── trial_0000/
-    │   ├── metadata.json       (design params + results)
-    │   └── input/
-    │       └── neural_field_data.h5  (mesh data)
-    ├── trial_0001/
-    │   └── ...
-    """
-
-    def __init__(
-        self,
-        data_dir: Path,
-        normalize: bool = True,
-        cache_in_memory: bool = False
-    ):
-        """
-        Initialize dataset.
-
-        Args:
-            data_dir: Directory containing trial_* subdirectories
-            normalize: Whether to normalize inputs/outputs
-            cache_in_memory: Cache all data in RAM (faster but memory-intensive)
-        """
-        self.data_dir = Path(data_dir)
-        self.normalize = normalize
-        self.cache_in_memory = cache_in_memory
-
-        # Find all valid trial directories
-        self.trial_dirs = sorted([
-            d for d in self.data_dir.glob("trial_*")
-            if d.is_dir() and self._is_valid_trial(d)
-        ])
-
-        print(f"Found {len(self.trial_dirs)} valid trials in {data_dir}")
-
-        if len(self.trial_dirs) == 0:
-            raise ValueError(f"No valid trial directories found in {data_dir}")
-
-        # Extract design variable names from first trial
-        self.design_var_names = self._get_design_var_names()
-        print(f"Design variables: {self.design_var_names}")
-
-        # Compute normalization statistics
-        if normalize:
-            self._compute_normalization_stats()
-
-        # Cache data if requested
-        self.cache = {}
-        if cache_in_memory:
-            print("Caching data in memory...")
-            for idx in range(len(self.trial_dirs)):
-                self.cache[idx] = self._load_trial(idx)
-            print("Cache complete!")
-
-    def _is_valid_trial(self, trial_dir: Path) -> bool:
-        """Check if trial directory has required files."""
-        metadata_file = trial_dir / "metadata.json"
-
-        # Check for metadata
-        if not metadata_file.exists():
-            return False
-
-        # Check metadata has required fields
-        try:
-            with open(metadata_file, 'r') as f:
-                metadata = json.load(f)
-
-            has_design = 'design_parameters' in metadata
-            has_results = 'results' in metadata
-
-            return has_design and has_results
-        except:
-            return False
-
-    def _get_design_var_names(self) -> List[str]:
-        """Extract design variable names from first trial."""
-        metadata_file = self.trial_dirs[0] / "metadata.json"
-        with open(metadata_file, 'r') as f:
-            metadata = json.load(f)
-        return list(metadata['design_parameters'].keys())
-
-    def _compute_normalization_stats(self):
-        """Compute normalization statistics across all trials."""
-        print("Computing normalization statistics...")
-
-        all_design_params = []
-        all_mass = []
-        all_disp = []
-        all_stiffness = []
-
-        for trial_dir in self.trial_dirs:
-            with open(trial_dir / "metadata.json", 'r') as f:
-                metadata = json.load(f)
-
-            # Design parameters
-            design_params = [metadata['design_parameters'][name]
-                           for name in self.design_var_names]
-            all_design_params.append(design_params)
-
-            # Results
-            results = metadata.get('results', {})
-            objectives = results.get('objectives', results)
-
-            if 'mass' in objectives:
-                all_mass.append(objectives['mass'])
-            if 'max_displacement' in results:
-                all_disp.append(results['max_displacement'])
-            elif 'max_displacement' in objectives:
-                all_disp.append(objectives['max_displacement'])
-            if 'stiffness' in objectives:
-                all_stiffness.append(objectives['stiffness'])
-
-        # Convert to numpy arrays
-        all_design_params = np.array(all_design_params)
-
-        # Compute statistics
-        self.design_mean = torch.from_numpy(all_design_params.mean(axis=0)).float()
-        self.design_std = torch.from_numpy(all_design_params.std(axis=0)).float()
-        self.design_std = torch.clamp(self.design_std, min=1e-6)  # Prevent division by zero
-
-        # Output statistics
-        self.mass_mean = np.mean(all_mass) if all_mass else 0.1
-        self.mass_std = np.std(all_mass) if all_mass else 0.05
-        self.mass_std = max(self.mass_std, 1e-6)
-
-        self.disp_mean = np.mean(all_disp) if all_disp else 0.01
-        self.disp_std = np.std(all_disp) if all_disp else 0.005
-        self.disp_std = max(self.disp_std, 1e-6)
-
-        self.stiffness_mean = np.mean(all_stiffness) if all_stiffness else 20000.0
-        self.stiffness_std = np.std(all_stiffness) if all_stiffness else 5000.0
-        self.stiffness_std = max(self.stiffness_std, 1e-6)
-
-        # Frequency and stress defaults (if not available in data)
-        self.freq_mean = 18.0
-        self.freq_std = 5.0
-        self.stress_mean = 200.0
-        self.stress_std = 50.0
-
-        print(f"  Design mean: {self.design_mean.numpy()}")
-        print(f"  Design std: {self.design_std.numpy()}")
-        print(f"  Mass: {self.mass_mean:.4f} +/- {self.mass_std:.4f}")
-        print(f"  Displacement: {self.disp_mean:.6f} +/- {self.disp_std:.6f}")
-        print(f"  Stiffness: {self.stiffness_mean:.2f} +/- {self.stiffness_std:.2f}")
-
-    def __len__(self) -> int:
-        return len(self.trial_dirs)
-
-    def __getitem__(self, idx: int) -> Dict[str, torch.Tensor]:
-        if self.cache_in_memory and idx in self.cache:
-            return self.cache[idx]
-        return self._load_trial(idx)
-
-    def _load_trial(self, idx: int) -> Dict[str, torch.Tensor]:
-        """Load and process a single trial."""
-        trial_dir = self.trial_dirs[idx]
-
-        # Load metadata
-        with open(trial_dir / "metadata.json", 'r') as f:
-            metadata = json.load(f)
-
-        # Extract design parameters
-        design_params = [metadata['design_parameters'][name]
-                        for name in self.design_var_names]
-        design_tensor = torch.tensor(design_params, dtype=torch.float32)
-
-        # Normalize design parameters
-        if self.normalize:
-            design_tensor = (design_tensor - self.design_mean) / self.design_std
-
-        # Extract results
-        results = metadata.get('results', {})
-        objectives = results.get('objectives', results)
-
-        # Get targets (with fallbacks)
-        mass = objectives.get('mass', 0.1)
-        stiffness = objectives.get('stiffness', 20000.0)
-        max_displacement = results.get('max_displacement',
-                                       objectives.get('max_displacement', 0.01))
-
-        # Frequency and stress might not be available
-        frequency = objectives.get('frequency', self.freq_mean)
-        max_stress = objectives.get('max_stress', self.stress_mean)
-
-        # Create target tensor
-        targets = torch.tensor([mass, frequency, max_displacement, max_stress],
-                              dtype=torch.float32)
-
-        # Normalize targets
-        if self.normalize:
-            targets[0] = (targets[0] - self.mass_mean) / self.mass_std
-            targets[1] = (targets[1] - self.freq_mean) / self.freq_std
-            targets[2] = (targets[2] - self.disp_mean) / self.disp_std
-            targets[3] = (targets[3] - self.stress_mean) / self.stress_std
-
-        # Try to load mesh data if available
-        mesh_data = self._load_mesh_data(trial_dir)
-
-        return {
-            'design_params': design_tensor,
-            'targets': targets,
-            'mesh_data': mesh_data,
-            'trial_dir': str(trial_dir)
-        }
-
-    def _load_mesh_data(self, trial_dir: Path) -> Optional[Dict[str, torch.Tensor]]:
-        """Load mesh data from H5 file if available."""
-        h5_paths = [
-            trial_dir / "input" / "neural_field_data.h5",
-            trial_dir / "neural_field_data.h5",
-        ]
-
-        for h5_path in h5_paths:
-            if h5_path.exists():
-                try:
-                    with h5py.File(h5_path, 'r') as f:
-                        node_coords = torch.from_numpy(f['mesh/node_coordinates'][:]).float()
-
-                        # Build simple edge index from connectivity if available
-                        # For now, return just coordinates
-                        return {
-                            'node_coords': node_coords,
-                            'num_nodes': node_coords.shape[0]
-                        }
-                except Exception as e:
-                    print(f"Warning: Could not load mesh from {h5_path}: {e}")
-
-        return None
-
-    def get_normalization_stats(self) -> Dict[str, Any]:
-        """Return normalization statistics for saving with model."""
-        return {
-            'design_mean': self.design_mean.numpy().tolist(),
-            'design_std': self.design_std.numpy().tolist(),
-            'mass_mean': float(self.mass_mean),
-            'mass_std': float(self.mass_std),
-            'freq_mean': float(self.freq_mean),
-            'freq_std': float(self.freq_std),
-            'max_disp_mean': float(self.disp_mean),
-            'max_disp_std': float(self.disp_std),
-            'max_stress_mean': float(self.stress_mean),
-            'max_stress_std': float(self.stress_std),
-        }
-
-
-def create_reference_graph(num_nodes: int = 500, device: torch.device = None):
-    """
-    Create a reference graph structure for the GNN.
-
-    In production, this would come from the actual mesh.
-    For now, create a simple grid-like structure.
-    """
-    if device is None:
-        device = torch.device('cpu')
-
-    # Create simple node features (placeholder)
-    x = torch.randn(num_nodes, 12, device=device)
-
-    # Create grid-like connectivity - ensure valid indices
-    edges = []
-    grid_size = int(np.ceil(np.sqrt(num_nodes)))
-
-    for i in range(num_nodes):
-        row = i // grid_size
-        col = i % grid_size
-
-        # Right neighbor (same row)
-        right = i + 1
-        if col < grid_size - 1 and right < num_nodes:
-            edges.append([i, right])
-            edges.append([right, i])
-
-        # Bottom neighbor (next row)
-        bottom = i + grid_size
-        if bottom < num_nodes:
-            edges.append([i, bottom])
-            edges.append([bottom, i])
-
-    # Ensure we have at least some edges
-    if len(edges) == 0:
-        # Fallback: fully connected for very small graphs
-        for i in range(num_nodes):
-            for j in range(i + 1, min(i + 5, num_nodes)):
-                edges.append([i, j])
-                edges.append([j, i])
-
-    edge_index = torch.tensor(edges, dtype=torch.long, device=device).t().contiguous()
-    edge_attr = torch.randn(edge_index.shape[1], 5, device=device)
-
-    from torch_geometric.data import Data
-    return Data(x=x, edge_index=edge_index, edge_attr=edge_attr)
-
-
-class ParametricTrainer:
-    """
-    Training manager for parametric predictor models.
-    """
-
-    def __init__(self, config: Dict[str, Any]):
-        """
-        Initialize trainer.
-
-        Args:
-            config: Training configuration
-        """
-        self.config = config
-        self.device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
-
-        print(f"\n{'='*60}")
-        print("AtomizerField Parametric Training Pipeline v2.0")
-        print(f"{'='*60}")
-        print(f"Device: {self.device}")
-
-        # Create model
-        print("\nCreating parametric model...")
-        model_config = config.get('model', {})
-        self.model = create_parametric_model(model_config)
-        self.model = self.model.to(self.device)
-
-        num_params = self.model.get_num_parameters()
-        print(f"Model created: {num_params:,} parameters")
-
-        # Create optimizer
-        self.optimizer = optim.AdamW(
-            self.model.parameters(),
-            lr=config.get('learning_rate', 1e-3),
-            weight_decay=config.get('weight_decay', 1e-5)
-        )
-
-        # Learning rate scheduler
-        self.scheduler = optim.lr_scheduler.ReduceLROnPlateau(
-            self.optimizer,
-            mode='min',
-            factor=0.5,
-            patience=10,
-            verbose=True
-        )
-
-        # Multi-objective loss weights
-        self.loss_weights = config.get('loss_weights', {
-            'mass': 1.0,
-            'frequency': 1.0,
-            'displacement': 1.0,
-            'stress': 1.0
-        })
-
-        # Training state
-        self.start_epoch = 0
-        self.best_val_loss = float('inf')
-        self.epochs_without_improvement = 0
-
-        # Create output directories
-        self.output_dir = Path(config.get('output_dir', './runs/parametric'))
-        self.output_dir.mkdir(parents=True, exist_ok=True)
-
-        # TensorBoard logging (optional)
-        self.writer = None
-        if TENSORBOARD_AVAILABLE:
-            self.writer = SummaryWriter(log_dir=self.output_dir / 'tensorboard')
-
-        # Create reference graph for inference
-        self.reference_graph = create_reference_graph(
-            num_nodes=config.get('reference_nodes', 500),
-            device=self.device
-        )
-
-        # Save config
-        with open(self.output_dir / 'config.json', 'w') as f:
-            json.dump(config, f, indent=2)
-
-    def compute_loss(
-        self,
-        predictions: Dict[str, torch.Tensor],
-        targets: torch.Tensor
-    ) -> Tuple[torch.Tensor, Dict[str, float]]:
-        """
-        Compute multi-objective loss.
-
-        Args:
-            predictions: Model outputs (mass, frequency, max_displacement, max_stress)
-            targets: Target values [batch, 4]
-
-        Returns:
-            total_loss: Combined loss tensor
-            loss_dict: Individual losses for logging
-        """
-        # MSE losses for each objective
-        mass_loss = nn.functional.mse_loss(predictions['mass'], targets[:, 0])
-        freq_loss = nn.functional.mse_loss(predictions['frequency'], targets[:, 1])
-        disp_loss = nn.functional.mse_loss(predictions['max_displacement'], targets[:, 2])
-        stress_loss = nn.functional.mse_loss(predictions['max_stress'], targets[:, 3])
-
-        # Weighted combination
-        total_loss = (
-            self.loss_weights['mass'] * mass_loss +
-            self.loss_weights['frequency'] * freq_loss +
-            self.loss_weights['displacement'] * disp_loss +
-            self.loss_weights['stress'] * stress_loss
-        )
-
-        loss_dict = {
-            'total': total_loss.item(),
-            'mass': mass_loss.item(),
-            'frequency': freq_loss.item(),
-            'displacement': disp_loss.item(),
-            'stress': stress_loss.item()
-        }
-
-        return total_loss, loss_dict
-
-    def train_epoch(self, train_loader: DataLoader, epoch: int) -> Dict[str, float]:
-        """Train for one epoch."""
-        self.model.train()
-
-        total_losses = {'total': 0, 'mass': 0, 'frequency': 0, 'displacement': 0, 'stress': 0}
-        num_batches = 0
-
-        for batch_idx, batch in enumerate(train_loader):
-            # Get data
-            design_params = batch['design_params'].to(self.device)
-            targets = batch['targets'].to(self.device)
-
-            # Zero gradients
-            self.optimizer.zero_grad()
-
-            # Forward pass (using reference graph)
-            predictions = self.model(self.reference_graph, design_params)
-
-            # Compute loss
-            loss, loss_dict = self.compute_loss(predictions, targets)
-
-            # Backward pass
-            loss.backward()
-
-            # Gradient clipping
-            torch.nn.utils.clip_grad_norm_(self.model.parameters(), max_norm=1.0)
-
-            # Update weights
-            self.optimizer.step()
-
-            # Accumulate losses
-            for key in total_losses:
-                total_losses[key] += loss_dict[key]
-            num_batches += 1
-
-            # Print progress
-            if batch_idx % 10 == 0:
-                print(f"  Batch {batch_idx}/{len(train_loader)}: Loss={loss_dict['total']:.6f}")
-
-        # Average losses
-        return {k: v / num_batches for k, v in total_losses.items()}
-
-    def validate(self, val_loader: DataLoader) -> Dict[str, float]:
-        """Validate model."""
-        self.model.eval()
-
-        total_losses = {'total': 0, 'mass': 0, 'frequency': 0, 'displacement': 0, 'stress': 0}
-        num_batches = 0
-
-        with torch.no_grad():
-            for batch in val_loader:
-                design_params = batch['design_params'].to(self.device)
-                targets = batch['targets'].to(self.device)
-
-                predictions = self.model(self.reference_graph, design_params)
-                _, loss_dict = self.compute_loss(predictions, targets)
-
-                for key in total_losses:
-                    total_losses[key] += loss_dict[key]
-                num_batches += 1
-
-        return {k: v / num_batches for k, v in total_losses.items()}
-
-    def train(
-        self,
-        train_loader: DataLoader,
-        val_loader: DataLoader,
-        num_epochs: int,
-        train_dataset: ParametricDataset
-    ):
-        """
-        Main training loop.
-
-        Args:
-            train_loader: Training data loader
-            val_loader: Validation data loader
-            num_epochs: Number of epochs
-            train_dataset: Training dataset (for normalization stats)
-        """
-        print(f"\n{'='*60}")
-        print(f"Starting training for {num_epochs} epochs")
-        print(f"{'='*60}\n")
-
-        for epoch in range(self.start_epoch, num_epochs):
-            epoch_start = time.time()
-
-            print(f"Epoch {epoch + 1}/{num_epochs}")
-            print("-" * 60)
-
-            # Train
-            train_metrics = self.train_epoch(train_loader, epoch)
-
-            # Validate
-            val_metrics = self.validate(val_loader)
-
-            epoch_time = time.time() - epoch_start
-
-            # Print metrics
-            print(f"\nEpoch {epoch + 1} Results:")
-            print(f"  Training Loss: {train_metrics['total']:.6f}")
-            print(f"    Mass: {train_metrics['mass']:.6f}, Freq: {train_metrics['frequency']:.6f}")
-            print(f"    Disp: {train_metrics['displacement']:.6f}, Stress: {train_metrics['stress']:.6f}")
-            print(f"  Validation Loss: {val_metrics['total']:.6f}")
-            print(f"    Mass: {val_metrics['mass']:.6f}, Freq: {val_metrics['frequency']:.6f}")
-            print(f"    Disp: {val_metrics['displacement']:.6f}, Stress: {val_metrics['stress']:.6f}")
-            print(f"  Time: {epoch_time:.1f}s")
-
-            # Log to TensorBoard
-            if self.writer:
-                self.writer.add_scalar('Loss/train', train_metrics['total'], epoch)
-                self.writer.add_scalar('Loss/val', val_metrics['total'], epoch)
-                for key in ['mass', 'frequency', 'displacement', 'stress']:
-                    self.writer.add_scalar(f'{key}/train', train_metrics[key], epoch)
-                    self.writer.add_scalar(f'{key}/val', val_metrics[key], epoch)
-
-            # Learning rate scheduling
-            self.scheduler.step(val_metrics['total'])
-
-            # Save checkpoint
-            is_best = val_metrics['total'] < self.best_val_loss
-            if is_best:
-                self.best_val_loss = val_metrics['total']
-                self.epochs_without_improvement = 0
-                print(f"  New best validation loss: {self.best_val_loss:.6f}")
-            else:
-                self.epochs_without_improvement += 1
-
-            self.save_checkpoint(epoch, val_metrics, train_dataset, is_best)
-
-            # Early stopping
-            patience = self.config.get('early_stopping_patience', 50)
-            if self.epochs_without_improvement >= patience:
-                print(f"\nEarly stopping after {patience} epochs without improvement")
-                break
-
-            print()
-
-        print(f"\n{'='*60}")
-        print("Training complete!")
-        print(f"Best validation loss: {self.best_val_loss:.6f}")
-        print(f"{'='*60}\n")
-
-        if self.writer:
-            self.writer.close()
-
-    def save_checkpoint(
-        self,
-        epoch: int,
-        metrics: Dict[str, float],
-        dataset: ParametricDataset,
-        is_best: bool = False
-    ):
-        """Save model checkpoint with all required metadata."""
-        checkpoint = {
-            'epoch': epoch,
-            'model_state_dict': self.model.state_dict(),
-            'optimizer_state_dict': self.optimizer.state_dict(),
-            'scheduler_state_dict': self.scheduler.state_dict(),
-            'best_val_loss': self.best_val_loss,
-            'config': self.model.config,
-            'normalization': dataset.get_normalization_stats(),
-            'design_var_names': dataset.design_var_names,
-            'metrics': metrics
-        }
-
-        # Save latest
-        torch.save(checkpoint, self.output_dir / 'checkpoint_latest.pt')
-
-        # Save best
-        if is_best:
-            best_path = self.output_dir / 'checkpoint_best.pt'
-            torch.save(checkpoint, best_path)
-            print(f"  Saved best model to {best_path}")
-
-        # Periodic checkpoint
-        if (epoch + 1) % 10 == 0:
-            torch.save(checkpoint, self.output_dir / f'checkpoint_epoch_{epoch + 1}.pt')
-
-
-def collate_fn(batch: List[Dict]) -> Dict[str, torch.Tensor]:
-    """Custom collate function for DataLoader."""
-    design_params = torch.stack([item['design_params'] for item in batch])
-    targets = torch.stack([item['targets'] for item in batch])
-
-    return {
-        'design_params': design_params,
-        'targets': targets
-    }
-
-
-def main():
-    """Main training entry point."""
-    parser = argparse.ArgumentParser(
-        description='Train AtomizerField parametric predictor'
-    )
-
-    # Data arguments
-    parser.add_argument('--train_dir', type=str, required=True,
-                       help='Directory containing training trial_* subdirs')
-    parser.add_argument('--val_dir', type=str, default=None,
-                       help='Directory containing validation data (uses split if not provided)')
-    parser.add_argument('--val_split', type=float, default=0.2,
-                       help='Validation split ratio if val_dir not provided')
-
-    # Training arguments
-    parser.add_argument('--epochs', type=int, default=200,
-                       help='Number of training epochs')
-    parser.add_argument('--batch_size', type=int, default=16,
-                       help='Batch size')
-    parser.add_argument('--learning_rate', type=float, default=1e-3,
-                       help='Learning rate')
-    parser.add_argument('--weight_decay', type=float, default=1e-5,
-                       help='Weight decay')
-
-    # Model arguments
-    parser.add_argument('--hidden_channels', type=int, default=128,
-                       help='Hidden dimension')
-    parser.add_argument('--num_layers', type=int, default=4,
-                       help='Number of GNN layers')
-    parser.add_argument('--dropout', type=float, default=0.1,
-                       help='Dropout rate')
-
-    # Output arguments
-    parser.add_argument('--output_dir', type=str, default='./runs/parametric',
-                       help='Output directory')
-    parser.add_argument('--resume', type=str, default=None,
-                       help='Path to checkpoint to resume from')
-
-    args = parser.parse_args()
-
-    # Create datasets
-    print("\nLoading training data...")
-    train_dataset = ParametricDataset(args.train_dir, normalize=True)
-
-    if args.val_dir:
-        val_dataset = ParametricDataset(args.val_dir, normalize=True)
-        # Share normalization stats
-        val_dataset.design_mean = train_dataset.design_mean
-        val_dataset.design_std = train_dataset.design_std
-    else:
-        # Split training data
-        n_total = len(train_dataset)
-        n_val = int(n_total * args.val_split)
-        n_train = n_total - n_val
-
-        train_dataset, val_dataset = torch.utils.data.random_split(
-            train_dataset, [n_train, n_val]
-        )
-        print(f"Split: {n_train} train, {n_val} validation")
-
-    # Create data loaders
-    train_loader = DataLoader(
-        train_dataset,
-        batch_size=args.batch_size,
-        shuffle=True,
-        collate_fn=collate_fn,
-        num_workers=0
-    )
-
-    val_loader = DataLoader(
-        val_dataset,
-        batch_size=args.batch_size,
-        shuffle=False,
-        collate_fn=collate_fn,
-        num_workers=0
-    )
-
-    # Get design dimension from dataset
-    if hasattr(train_dataset, 'design_var_names'):
-        design_dim = len(train_dataset.design_var_names)
-    else:
-        # For split dataset, access underlying dataset
-        design_dim = len(train_dataset.dataset.design_var_names)
-
-    # Build configuration
-    config = {
-        'model': {
-            'input_channels': 12,
-            'edge_dim': 5,
-            'hidden_channels': args.hidden_channels,
-            'num_layers': args.num_layers,
-            'design_dim': design_dim,
-            'dropout': args.dropout
-        },
-        'learning_rate': args.learning_rate,
-        'weight_decay': args.weight_decay,
-        'batch_size': args.batch_size,
-        'num_epochs': args.epochs,
-        'output_dir': args.output_dir,
-        'early_stopping_patience': 50,
-        'loss_weights': {
-            'mass': 1.0,
-            'frequency': 1.0,
-            'displacement': 1.0,
-            'stress': 1.0
-        }
-    }
-
-    # Create trainer
-    trainer = ParametricTrainer(config)
-
-    # Resume if specified
-    if args.resume:
-        checkpoint = torch.load(args.resume, map_location=trainer.device)
-        trainer.model.load_state_dict(checkpoint['model_state_dict'])
-        trainer.optimizer.load_state_dict(checkpoint['optimizer_state_dict'])
-        trainer.start_epoch = checkpoint['epoch'] + 1
-        trainer.best_val_loss = checkpoint['best_val_loss']
-        print(f"Resumed from epoch {checkpoint['epoch']}")
-
-    # Get base dataset for normalization stats
-    base_dataset = train_dataset
-    if hasattr(train_dataset, 'dataset'):
-        base_dataset = train_dataset.dataset
-
-    # Train
-    trainer.train(train_loader, val_loader, args.epochs, base_dataset)
-
-
-if __name__ == "__main__":
-    main()

atomizer-field/validate_parsed_data.py

@@ -1,454 +0,0 @@
-"""
-validate_parsed_data.py
-Validates the parsed neural field data for completeness and physics consistency
-
-AtomizerField Data Validator v1.0.0
-Ensures parsed data meets quality standards for neural network training.
-
-Usage:
-    python validate_parsed_data.py <case_directory>
-
-Example:
-    python validate_parsed_data.py training_case_001
-"""
-
-import json
-import h5py
-import numpy as np
-from pathlib import Path
-import sys
-
-
-class NeuralFieldDataValidator:
-    """
-    Validates parsed neural field data for:
-    - File existence and format
-    - Data completeness
-    - Physics consistency
-    - Data quality
-
-    This ensures that data fed to neural networks is reliable and consistent.
-    """
-
-    def __init__(self, case_directory):
-        """
-        Initialize validator
-
-        Args:
-            case_directory (str or Path): Path to case containing parsed data
-        """
-        self.case_dir = Path(case_directory)
-        self.json_file = self.case_dir / "neural_field_data.json"
-        self.h5_file = self.case_dir / "neural_field_data.h5"
-        self.errors = []
-        self.warnings = []
-        self.info = []
-
-    def validate(self):
-        """
-        Run all validation checks
-
-        Returns:
-            bool: True if validation passed, False otherwise
-        """
-        print("\n" + "="*60)
-        print("AtomizerField Data Validator v1.0")
-        print("="*60)
-        print(f"\nValidating: {self.case_dir.name}\n")
-
-        # Check file existence
-        if not self._check_files_exist():
-            return False
-
-        # Load data
-        try:
-            with open(self.json_file, 'r') as f:
-                self.data = json.load(f)
-            self.h5_data = h5py.File(self.h5_file, 'r')
-        except Exception as e:
-            self._add_error(f"Failed to load data files: {e}")
-            return False
-
-        # Run validation checks
-        self._validate_structure()
-        self._validate_metadata()
-        self._validate_mesh()
-        self._validate_materials()
-        self._validate_boundary_conditions()
-        self._validate_loads()
-        self._validate_results()
-        self._validate_physics_consistency()
-        self._validate_data_quality()
-
-        # Close HDF5 file
-        self.h5_data.close()
-
-        # Print results
-        self._print_results()
-
-        return len(self.errors) == 0
-
-    def _check_files_exist(self):
-        """Check that required files exist"""
-        if not self.json_file.exists():
-            self._add_error(f"JSON file not found: {self.json_file}")
-            return False
-
-        if not self.h5_file.exists():
-            self._add_error(f"HDF5 file not found: {self.h5_file}")
-            return False
-
-        self._add_info(f"Found JSON: {self.json_file.name}")
-        self._add_info(f"Found HDF5: {self.h5_file.name}")
-        return True
-
-    def _validate_structure(self):
-        """Validate data structure has all required fields"""
-        required_fields = [
-            "metadata",
-            "mesh",
-            "materials",
-            "boundary_conditions",
-            "loads",
-            "results"
-        ]
-
-        for field in required_fields:
-            if field not in self.data:
-                self._add_error(f"Missing required field: {field}")
-            else:
-                self._add_info(f"Found field: {field}")
-
-    def _validate_metadata(self):
-        """Validate metadata completeness"""
-        if "metadata" not in self.data:
-            return
-
-        meta = self.data["metadata"]
-
-        # Check version
-        if "version" in meta:
-            if meta["version"] != "1.0.0":
-                self._add_warning(f"Data version {meta['version']} may not be compatible")
-            else:
-                self._add_info(f"Data version: {meta['version']}")
-
-        # Check required metadata fields
-        required = ["created_at", "source", "analysis_type", "units"]
-        for field in required:
-            if field not in meta:
-                self._add_warning(f"Missing metadata field: {field}")
-
-        if "analysis_type" in meta:
-            self._add_info(f"Analysis type: {meta['analysis_type']}")
-
-    def _validate_mesh(self):
-        """Validate mesh data"""
-        if "mesh" not in self.data:
-            return
-
-        mesh = self.data["mesh"]
-
-        # Check statistics
-        if "statistics" in mesh:
-            stats = mesh["statistics"]
-            n_nodes = stats.get("n_nodes", 0)
-            n_elements = stats.get("n_elements", 0)
-
-            self._add_info(f"Mesh: {n_nodes:,} nodes, {n_elements:,} elements")
-
-            if n_nodes == 0:
-                self._add_error("Mesh has no nodes")
-            if n_elements == 0:
-                self._add_error("Mesh has no elements")
-
-            # Check element types
-            if "element_types" in stats:
-                elem_types = stats["element_types"]
-                total_by_type = sum(elem_types.values())
-                if total_by_type != n_elements:
-                    self._add_warning(
-                        f"Element type count ({total_by_type}) doesn't match "
-                        f"total elements ({n_elements})"
-                    )
-
-                for etype, count in elem_types.items():
-                    if count > 0:
-                        self._add_info(f"  {etype}: {count:,} elements")
-
-        # Validate HDF5 mesh data
-        if 'mesh' in self.h5_data:
-            mesh_grp = self.h5_data['mesh']
-
-            if 'node_coordinates' in mesh_grp:
-                coords = mesh_grp['node_coordinates'][:]
-                self._add_info(f"Node coordinates: shape {coords.shape}")
-
-                # Check for NaN or inf
-                if np.any(np.isnan(coords)):
-                    self._add_error("Node coordinates contain NaN values")
-                if np.any(np.isinf(coords)):
-                    self._add_error("Node coordinates contain infinite values")
-
-                # Check bounding box reasonableness
-                bbox_size = np.max(coords, axis=0) - np.min(coords, axis=0)
-                if np.any(bbox_size == 0):
-                    self._add_warning("Mesh is planar or degenerate in one dimension")
-
-    def _validate_materials(self):
-        """Validate material data"""
-        if "materials" not in self.data:
-            return
-
-        materials = self.data["materials"]
-
-        if len(materials) == 0:
-            self._add_warning("No materials defined")
-            return
-
-        self._add_info(f"Materials: {len(materials)} defined")
-
-        for mat in materials:
-            mat_id = mat.get("id", "unknown")
-            mat_type = mat.get("type", "unknown")
-
-            if mat_type == "MAT1":
-                # Check required properties
-                E = mat.get("E")
-                nu = mat.get("nu")
-
-                if E is None:
-                    self._add_error(f"Material {mat_id}: Missing Young's modulus (E)")
-                elif E <= 0:
-                    self._add_error(f"Material {mat_id}: Invalid E = {E} (must be > 0)")
-
-                if nu is None:
-                    self._add_error(f"Material {mat_id}: Missing Poisson's ratio (nu)")
-                elif nu < 0 or nu >= 0.5:
-                    self._add_error(f"Material {mat_id}: Invalid nu = {nu} (must be 0 <= nu < 0.5)")
-
-    def _validate_boundary_conditions(self):
-        """Validate boundary conditions"""
-        if "boundary_conditions" not in self.data:
-            return
-
-        bcs = self.data["boundary_conditions"]
-
-        spc_count = len(bcs.get("spc", []))
-        mpc_count = len(bcs.get("mpc", []))
-
-        self._add_info(f"Boundary conditions: {spc_count} SPCs, {mpc_count} MPCs")
-
-        if spc_count == 0:
-            self._add_warning("No SPCs defined - model may be unconstrained")
-
-    def _validate_loads(self):
-        """Validate load data"""
-        if "loads" not in self.data:
-            return
-
-        loads = self.data["loads"]
-
-        force_count = len(loads.get("point_forces", []))
-        pressure_count = len(loads.get("pressure", []))
-        gravity_count = len(loads.get("gravity", []))
-        thermal_count = len(loads.get("thermal", []))
-
-        total_loads = force_count + pressure_count + gravity_count + thermal_count
-
-        self._add_info(
-            f"Loads: {force_count} forces, {pressure_count} pressures, "
-            f"{gravity_count} gravity, {thermal_count} thermal"
-        )
-
-        if total_loads == 0:
-            self._add_warning("No loads defined")
-
-        # Validate force magnitudes
-        for force in loads.get("point_forces", []):
-            mag = force.get("magnitude")
-            if mag == 0:
-                self._add_warning(f"Force at node {force.get('node')} has zero magnitude")
-
-    def _validate_results(self):
-        """Validate results data"""
-        if "results" not in self.data:
-            self._add_error("No results data found")
-            return
-
-        results = self.data["results"]
-
-        # Check displacement
-        if "displacement" not in results:
-            self._add_error("No displacement results found")
-        else:
-            disp = results["displacement"]
-            n_nodes = len(disp.get("node_ids", []))
-            max_disp = disp.get("max_translation")
-
-            self._add_info(f"Displacement: {n_nodes:,} nodes")
-            if max_disp is not None:
-                self._add_info(f"  Max displacement: {max_disp:.6f} mm")
-
-                if max_disp == 0:
-                    self._add_warning("Maximum displacement is zero - check loads")
-                elif max_disp > 1000:
-                    self._add_warning(f"Very large displacement ({max_disp:.2f} mm) - check units or model")
-
-        # Check stress
-        if "stress" not in results or len(results["stress"]) == 0:
-            self._add_warning("No stress results found")
-        else:
-            for stress_type, stress_data in results["stress"].items():
-                n_elem = len(stress_data.get("element_ids", []))
-                max_vm = stress_data.get("max_von_mises")
-
-                self._add_info(f"Stress ({stress_type}): {n_elem:,} elements")
-                if max_vm is not None:
-                    self._add_info(f"  Max von Mises: {max_vm:.2f} MPa")
-
-                    if max_vm == 0:
-                        self._add_warning(f"{stress_type}: Zero stress - check loads")
-
-        # Validate HDF5 results
-        if 'results' in self.h5_data:
-            results_grp = self.h5_data['results']
-
-            if 'displacement' in results_grp:
-                disp_data = results_grp['displacement'][:]
-
-                # Check for NaN or inf
-                if np.any(np.isnan(disp_data)):
-                    self._add_error("Displacement results contain NaN values")
-                if np.any(np.isinf(disp_data)):
-                    self._add_error("Displacement results contain infinite values")
-
-    def _validate_physics_consistency(self):
-        """Validate physics consistency of results"""
-        if "results" not in self.data or "mesh" not in self.data:
-            return
-
-        results = self.data["results"]
-        mesh = self.data["mesh"]
-
-        # Check node count consistency
-        mesh_nodes = mesh.get("statistics", {}).get("n_nodes", 0)
-
-        if "displacement" in results:
-            disp_nodes = len(results["displacement"].get("node_ids", []))
-            if disp_nodes != mesh_nodes:
-                self._add_warning(
-                    f"Displacement nodes ({disp_nodes:,}) != mesh nodes ({mesh_nodes:,})"
-                )
-
-        # Check for rigid body motion (if no constraints)
-        if "boundary_conditions" in self.data:
-            spc_count = len(self.data["boundary_conditions"].get("spc", []))
-            if spc_count == 0 and "displacement" in results:
-                max_disp = results["displacement"].get("max_translation", 0)
-                if max_disp > 1e6:
-                    self._add_error("Unconstrained model with very large displacements - likely rigid body motion")
-
-    def _validate_data_quality(self):
-        """Validate data quality for neural network training"""
-
-        # Check HDF5 data types and shapes
-        if 'results' in self.h5_data:
-            results_grp = self.h5_data['results']
-
-            # Check displacement shape
-            if 'displacement' in results_grp:
-                disp = results_grp['displacement'][:]
-                if len(disp.shape) != 2:
-                    self._add_error(f"Displacement has wrong shape: {disp.shape} (expected 2D)")
-                elif disp.shape[1] != 6:
-                    self._add_error(f"Displacement has {disp.shape[1]} DOFs (expected 6)")
-
-        # Check file sizes
-        json_size = self.json_file.stat().st_size / 1024  # KB
-        h5_size = self.h5_file.stat().st_size / 1024  # KB
-
-        self._add_info(f"File sizes: JSON={json_size:.1f} KB, HDF5={h5_size:.1f} KB")
-
-        if json_size > 10000:  # 10 MB
-            self._add_warning("JSON file is very large - consider moving more data to HDF5")
-
-    def _add_error(self, message):
-        """Add error message"""
-        self.errors.append(message)
-
-    def _add_warning(self, message):
-        """Add warning message"""
-        self.warnings.append(message)
-
-    def _add_info(self, message):
-        """Add info message"""
-        self.info.append(message)
-
-    def _print_results(self):
-        """Print validation results"""
-        print("\n" + "="*60)
-        print("VALIDATION RESULTS")
-        print("="*60)
-
-        # Print info
-        if self.info:
-            print("\nInformation:")
-            for msg in self.info:
-                print(f"  [INFO] {msg}")
-
-        # Print warnings
-        if self.warnings:
-            print("\nWarnings:")
-            for msg in self.warnings:
-                print(f"  [WARN] {msg}")
-
-        # Print errors
-        if self.errors:
-            print("\nErrors:")
-            for msg in self.errors:
-                print(f"  [X] {msg}")
-
-        # Summary
-        print("\n" + "="*60)
-        if len(self.errors) == 0:
-            print("[OK] VALIDATION PASSED")
-            print("="*60)
-            print("\nData is ready for neural network training!")
-        else:
-            print("[X] VALIDATION FAILED")
-            print("="*60)
-            print(f"\nFound {len(self.errors)} error(s), {len(self.warnings)} warning(s)")
-            print("Please fix errors before using this data for training.")
-
-        print()
-
-
-def main():
-    """
-    Main entry point for validation script
-    """
-    if len(sys.argv) < 2:
-        print("\nAtomizerField Data Validator v1.0")
-        print("="*60)
-        print("\nUsage:")
-        print("  python validate_parsed_data.py <case_directory>")
-        print("\nExample:")
-        print("  python validate_parsed_data.py training_case_001")
-        print()
-        sys.exit(1)
-
-    case_dir = sys.argv[1]
-
-    if not Path(case_dir).exists():
-        print(f"ERROR: Directory not found: {case_dir}")
-        sys.exit(1)
-
-    validator = NeuralFieldDataValidator(case_dir)
-    success = validator.validate()
-
-    sys.exit(0 if success else 1)
-
-
-if __name__ == "__main__":
-    main()

atomizer-field/visualization_report.md

@@ -1,46 +0,0 @@
-# FEA Visualization Report
-
-**Generated:** 2025-11-24T09:24:10.133023
-
-**Case:** test_case_beam
-
----
-
-## Model Information
-
-- **Analysis Type:** SOL_Unknown
-- **Nodes:** 5,179
-- **Elements:** 4,866
-- **Materials:** 1
-
-## Mesh Structure
-
-![Mesh Structure](visualization_images/mesh.png)
-
-The model contains 5,179 nodes and 4,866 elements.
-
-## Displacement Results
-
-![Displacement Field](visualization_images/displacement.png)
-
-**Maximum Displacement:** 19.556875 mm
-
-The plots show the original mesh (left) and deformed mesh (right) with displacement magnitude shown in color.
-
-## Stress Results
-
-![Stress Field](visualization_images/stress.png)
-
-The stress distribution is shown with colors representing von Mises stress levels.
-
-## Summary Statistics
-
-| Property | Value |
-|----------|-------|
-| Nodes | 5,179 |
-| Elements | 4,866 |
-| Max Displacement | 19.556875 mm |
-
----
-
-*Report generated by AtomizerField Visualizer*

atomizer-field/visualize_results.py

@@ -1,515 +0,0 @@
-"""
-visualize_results.py
-3D Visualization of FEA Results and Neural Predictions
-
-Visualizes:
-- Mesh structure
-- Displacement fields
-- Stress fields (von Mises)
-- Comparison: FEA vs Neural predictions
-"""
-
-import numpy as np
-import matplotlib.pyplot as plt
-from matplotlib import cm
-from mpl_toolkits.mplot3d import Axes3D
-import json
-import h5py
-from pathlib import Path
-import argparse
-
-
-class FEAVisualizer:
-    """Visualize FEA results in 3D"""
-
-    def __init__(self, case_dir):
-        """
-        Initialize visualizer
-
-        Args:
-            case_dir: Path to case directory with neural_field_data files
-        """
-        self.case_dir = Path(case_dir)
-
-        # Load data
-        print(f"Loading data from {case_dir}...")
-        self.load_data()
-
-    def load_data(self):
-        """Load JSON metadata and HDF5 field data"""
-        json_file = self.case_dir / "neural_field_data.json"
-        h5_file = self.case_dir / "neural_field_data.h5"
-
-        # Load JSON
-        with open(json_file, 'r') as f:
-            self.metadata = json.load(f)
-
-        # Get connectivity from JSON
-        self.connectivity = []
-        if 'mesh' in self.metadata and 'elements' in self.metadata['mesh']:
-            elements = self.metadata['mesh']['elements']
-            # Elements are categorized by type: solid, shell, beam, rigid
-            for elem_category in ['solid', 'shell', 'beam']:
-                if elem_category in elements and isinstance(elements[elem_category], list):
-                    for elem_data in elements[elem_category]:
-                        elem_type = elem_data.get('type', '')
-                        if elem_type in ['CQUAD4', 'CTRIA3', 'CTETRA', 'CHEXA']:
-                            # Store connectivity: [elem_id, n1, n2, n3, n4, ...]
-                            nodes = elem_data.get('nodes', [])
-                            self.connectivity.append([elem_data['id']] + nodes)
-        self.connectivity = np.array(self.connectivity) if self.connectivity else np.array([[]])
-
-        # Load HDF5
-        with h5py.File(h5_file, 'r') as f:
-            self.node_coords = f['mesh/node_coordinates'][:]
-
-            # Get node IDs to create mapping
-            self.node_ids = f['mesh/node_ids'][:]
-            # Create mapping from node ID to index
-            self.node_id_to_idx = {nid: idx for idx, nid in enumerate(self.node_ids)}
-
-            # Displacement
-            if 'results/displacement' in f:
-                self.displacement = f['results/displacement'][:]
-            else:
-                self.displacement = None
-
-            # Stress (try different possible locations)
-            self.stress = None
-            if 'results/stress/cquad4_stress/data' in f:
-                self.stress = f['results/stress/cquad4_stress/data'][:]
-            elif 'results/stress/cquad4_stress' in f and hasattr(f['results/stress/cquad4_stress'], 'shape'):
-                self.stress = f['results/stress/cquad4_stress'][:]
-            elif 'results/stress' in f and hasattr(f['results/stress'], 'shape'):
-                self.stress = f['results/stress'][:]
-
-        print(f"Loaded {len(self.node_coords)} nodes, {len(self.connectivity)} elements")
-
-    def plot_mesh(self, figsize=(12, 8), save_path=None):
-        """
-        Plot 3D mesh structure
-
-        Args:
-            figsize: Figure size
-            save_path: Path to save figure (optional)
-        """
-        fig = plt.figure(figsize=figsize)
-        ax = fig.add_subplot(111, projection='3d')
-
-        # Extract coordinates
-        x = self.node_coords[:, 0]
-        y = self.node_coords[:, 1]
-        z = self.node_coords[:, 2]
-
-        # Plot nodes
-        ax.scatter(x, y, z, c='blue', marker='.', s=1, alpha=0.3, label='Nodes')
-
-        # Plot a subset of elements (for visibility)
-        step = max(1, len(self.connectivity) // 1000)  # Show max 1000 elements
-        for i in range(0, len(self.connectivity), step):
-            elem = self.connectivity[i]
-            if len(elem) < 5:  # Skip invalid elements
-                continue
-
-            # Get node IDs (skip element ID at position 0)
-            node_ids = elem[1:5]  # First 4 nodes for CQUAD4
-
-            # Convert node IDs to indices
-            try:
-                nodes = [self.node_id_to_idx[nid] for nid in node_ids]
-            except KeyError:
-                continue  # Skip if node not found
-
-            # Get coordinates
-            elem_coords = self.node_coords[nodes]
-
-            # Plot element edges
-            for j in range(min(4, len(nodes))):
-                next_j = (j + 1) % len(nodes)
-                ax.plot([elem_coords[j, 0], elem_coords[next_j, 0]],
-                       [elem_coords[j, 1], elem_coords[next_j, 1]],
-                       [elem_coords[j, 2], elem_coords[next_j, 2]],
-                       'k-', linewidth=0.1, alpha=0.1)
-
-        ax.set_xlabel('X (mm)')
-        ax.set_ylabel('Y (mm)')
-        ax.set_zlabel('Z (mm)')
-        ax.set_title(f'Mesh Structure\n{len(self.node_coords)} nodes, {len(self.connectivity)} elements')
-
-        # Equal aspect ratio
-        self._set_equal_aspect(ax)
-
-        if save_path:
-            plt.savefig(save_path, dpi=150, bbox_inches='tight')
-            print(f"Saved mesh plot to {save_path}")
-
-        plt.show()
-
-    def plot_displacement(self, scale=1.0, component='magnitude', figsize=(14, 8), save_path=None):
-        """
-        Plot displacement field
-
-        Args:
-            scale: Scale factor for displacement visualization
-            component: 'magnitude', 'x', 'y', or 'z'
-            figsize: Figure size
-            save_path: Path to save figure
-        """
-        if self.displacement is None:
-            print("No displacement data available")
-            return
-
-        fig = plt.figure(figsize=figsize)
-
-        # Original mesh
-        ax1 = fig.add_subplot(121, projection='3d')
-        self._plot_mesh_with_field(ax1, self.displacement, component, scale=0)
-        ax1.set_title('Original Mesh')
-
-        # Deformed mesh
-        ax2 = fig.add_subplot(122, projection='3d')
-        self._plot_mesh_with_field(ax2, self.displacement, component, scale=scale)
-        ax2.set_title(f'Deformed Mesh (scale={scale}x)\nDisplacement: {component}')
-
-        plt.tight_layout()
-
-        if save_path:
-            plt.savefig(save_path, dpi=150, bbox_inches='tight')
-            print(f"Saved displacement plot to {save_path}")
-
-        plt.show()
-
-    def plot_stress(self, component='von_mises', figsize=(12, 8), save_path=None):
-        """
-        Plot stress field
-
-        Args:
-            component: 'von_mises', 'xx', 'yy', 'zz', 'xy', 'yz', 'xz'
-            figsize: Figure size
-            save_path: Path to save figure
-        """
-        if self.stress is None:
-            print("No stress data available")
-            return
-
-        fig = plt.figure(figsize=figsize)
-        ax = fig.add_subplot(111, projection='3d')
-
-        # Get stress component
-        if component == 'von_mises':
-            # Von Mises already computed (last column)
-            stress_values = self.stress[:, -1]
-        else:
-            # Map component name to index
-            comp_map = {'xx': 0, 'yy': 1, 'zz': 2, 'xy': 3, 'yz': 4, 'xz': 5}
-            idx = comp_map.get(component, 0)
-            stress_values = self.stress[:, idx]
-
-        # Plot elements colored by stress
-        self._plot_elements_with_stress(ax, stress_values)
-
-        ax.set_xlabel('X (mm)')
-        ax.set_ylabel('Y (mm)')
-        ax.set_zlabel('Z (mm)')
-        ax.set_title(f'Stress Field: {component}\nMax: {np.max(stress_values):.2f} MPa')
-
-        self._set_equal_aspect(ax)
-
-        if save_path:
-            plt.savefig(save_path, dpi=150, bbox_inches='tight')
-            print(f"Saved stress plot to {save_path}")
-
-        plt.show()
-
-    def plot_comparison(self, neural_predictions, figsize=(16, 6), save_path=None):
-        """
-        Plot comparison: FEA vs Neural predictions
-
-        Args:
-            neural_predictions: Dict with 'displacement' and/or 'stress'
-            figsize: Figure size
-            save_path: Path to save figure
-        """
-        fig = plt.figure(figsize=figsize)
-
-        # Displacement comparison
-        if self.displacement is not None and 'displacement' in neural_predictions:
-            ax1 = fig.add_subplot(131, projection='3d')
-            self._plot_mesh_with_field(ax1, self.displacement, 'magnitude', scale=10)
-            ax1.set_title('FEA Displacement')
-
-            ax2 = fig.add_subplot(132, projection='3d')
-            neural_disp = neural_predictions['displacement']
-            self._plot_mesh_with_field(ax2, neural_disp, 'magnitude', scale=10)
-            ax2.set_title('Neural Prediction')
-
-            # Error
-            ax3 = fig.add_subplot(133, projection='3d')
-            error = np.linalg.norm(self.displacement[:, :3] - neural_disp[:, :3], axis=1)
-            self._plot_nodes_with_values(ax3, error)
-            ax3.set_title('Prediction Error')
-
-        plt.tight_layout()
-
-        if save_path:
-            plt.savefig(save_path, dpi=150, bbox_inches='tight')
-            print(f"Saved comparison plot to {save_path}")
-
-        plt.show()
-
-    def _plot_mesh_with_field(self, ax, field, component, scale=1.0):
-        """Helper: Plot mesh colored by field values"""
-        # Get field component
-        if component == 'magnitude':
-            values = np.linalg.norm(field[:, :3], axis=1)
-        elif component == 'x':
-            values = field[:, 0]
-        elif component == 'y':
-            values = field[:, 1]
-        elif component == 'z':
-            values = field[:, 2]
-        else:
-            values = np.linalg.norm(field[:, :3], axis=1)
-
-        # Apply deformation
-        coords = self.node_coords + scale * field[:, :3]
-
-        # Plot nodes colored by values
-        scatter = ax.scatter(coords[:, 0], coords[:, 1], coords[:, 2],
-                           c=values, cmap='jet', s=2)
-        plt.colorbar(scatter, ax=ax, label=f'{component} (mm)')
-
-        ax.set_xlabel('X (mm)')
-        ax.set_ylabel('Y (mm)')
-        ax.set_zlabel('Z (mm)')
-
-        self._set_equal_aspect(ax)
-
-    def _plot_elements_with_stress(self, ax, stress_values):
-        """Helper: Plot elements colored by stress"""
-        # Normalize stress for colormap
-        vmin, vmax = np.min(stress_values), np.max(stress_values)
-        norm = plt.Normalize(vmin=vmin, vmax=vmax)
-        cmap = cm.get_cmap('jet')
-
-        # Plot subset of elements
-        step = max(1, len(self.connectivity) // 500)
-        for i in range(0, min(len(self.connectivity), len(stress_values)), step):
-            elem = self.connectivity[i]
-            if len(elem) < 5:
-                continue
-
-            # Get node IDs and convert to indices
-            node_ids = elem[1:5]
-            try:
-                nodes = [self.node_id_to_idx[nid] for nid in node_ids]
-            except KeyError:
-                continue
-
-            elem_coords = self.node_coords[nodes]
-
-            # Get stress color
-            color = cmap(norm(stress_values[i]))
-
-            # Plot filled quadrilateral
-            from mpl_toolkits.mplot3d.art3d import Poly3DCollection
-            verts = [elem_coords]
-            poly = Poly3DCollection(verts, facecolors=color, edgecolors='k',
-                                   linewidths=0.1, alpha=0.8)
-            ax.add_collection3d(poly)
-
-        # Colorbar
-        sm = cm.ScalarMappable(cmap=cmap, norm=norm)
-        sm.set_array([])
-        plt.colorbar(sm, ax=ax, label='Stress (MPa)')
-
-    def _plot_nodes_with_values(self, ax, values):
-        """Helper: Plot nodes colored by values"""
-        scatter = ax.scatter(self.node_coords[:, 0],
-                           self.node_coords[:, 1],
-                           self.node_coords[:, 2],
-                           c=values, cmap='hot', s=2)
-        plt.colorbar(scatter, ax=ax, label='Error (mm)')
-
-        ax.set_xlabel('X (mm)')
-        ax.set_ylabel('Y (mm)')
-        ax.set_zlabel('Z (mm)')
-
-        self._set_equal_aspect(ax)
-
-    def _set_equal_aspect(self, ax):
-        """Set equal aspect ratio for 3D plot"""
-        # Get limits
-        x_limits = [self.node_coords[:, 0].min(), self.node_coords[:, 0].max()]
-        y_limits = [self.node_coords[:, 1].min(), self.node_coords[:, 1].max()]
-        z_limits = [self.node_coords[:, 2].min(), self.node_coords[:, 2].max()]
-
-        # Find max range
-        max_range = max(x_limits[1] - x_limits[0],
-                       y_limits[1] - y_limits[0],
-                       z_limits[1] - z_limits[0])
-
-        # Set limits
-        x_middle = np.mean(x_limits)
-        y_middle = np.mean(y_limits)
-        z_middle = np.mean(z_limits)
-
-        ax.set_xlim(x_middle - max_range/2, x_middle + max_range/2)
-        ax.set_ylim(y_middle - max_range/2, y_middle + max_range/2)
-        ax.set_zlim(z_middle - max_range/2, z_middle + max_range/2)
-
-    def create_report(self, output_file='visualization_report.md'):
-        """
-        Create markdown report with all visualizations
-
-        Args:
-            output_file: Path to save report
-        """
-        print(f"\nGenerating visualization report...")
-
-        # Create images directory
-        img_dir = Path(output_file).parent / 'visualization_images'
-        img_dir.mkdir(exist_ok=True)
-
-        # Generate plots
-        print("  Creating mesh plot...")
-        self.plot_mesh(save_path=img_dir / 'mesh.png')
-        plt.close('all')
-
-        print("  Creating displacement plot...")
-        self.plot_displacement(scale=10, save_path=img_dir / 'displacement.png')
-        plt.close('all')
-
-        print("  Creating stress plot...")
-        self.plot_stress(save_path=img_dir / 'stress.png')
-        plt.close('all')
-
-        # Write report
-        with open(output_file, 'w') as f:
-            f.write(f"# FEA Visualization Report\n\n")
-            f.write(f"**Generated:** {self.metadata['metadata']['created_at']}\n\n")
-            f.write(f"**Case:** {self.metadata['metadata']['case_name']}\n\n")
-
-            f.write("---\n\n")
-
-            # Model info
-            f.write("## Model Information\n\n")
-            f.write(f"- **Analysis Type:** {self.metadata['metadata']['analysis_type']}\n")
-            f.write(f"- **Nodes:** {self.metadata['mesh']['statistics']['n_nodes']:,}\n")
-            f.write(f"- **Elements:** {self.metadata['mesh']['statistics']['n_elements']:,}\n")
-            f.write(f"- **Materials:** {len(self.metadata['materials'])}\n\n")
-
-            # Mesh
-            f.write("## Mesh Structure\n\n")
-            f.write("![Mesh Structure](visualization_images/mesh.png)\n\n")
-            f.write(f"The model contains {self.metadata['mesh']['statistics']['n_nodes']:,} nodes ")
-            f.write(f"and {self.metadata['mesh']['statistics']['n_elements']:,} elements.\n\n")
-
-            # Displacement
-            if self.displacement is not None:
-                max_disp = self.metadata['results']['displacement']['max_translation']
-                f.write("## Displacement Results\n\n")
-                f.write("![Displacement Field](visualization_images/displacement.png)\n\n")
-                f.write(f"**Maximum Displacement:** {max_disp:.6f} mm\n\n")
-                f.write("The plots show the original mesh (left) and deformed mesh (right) ")
-                f.write("with displacement magnitude shown in color.\n\n")
-
-            # Stress
-            if self.stress is not None:
-                f.write("## Stress Results\n\n")
-                f.write("![Stress Field](visualization_images/stress.png)\n\n")
-
-                # Get max stress from metadata
-                if 'stress' in self.metadata['results']:
-                    for stress_type, stress_data in self.metadata['results']['stress'].items():
-                        if 'max_von_mises' in stress_data and stress_data['max_von_mises'] is not None:
-                            max_stress = stress_data['max_von_mises']
-                            f.write(f"**Maximum von Mises Stress:** {max_stress:.2f} MPa\n\n")
-                            break
-
-                f.write("The stress distribution is shown with colors representing von Mises stress levels.\n\n")
-
-            # Statistics
-            f.write("## Summary Statistics\n\n")
-            f.write("| Property | Value |\n")
-            f.write("|----------|-------|\n")
-            f.write(f"| Nodes | {self.metadata['mesh']['statistics']['n_nodes']:,} |\n")
-            f.write(f"| Elements | {self.metadata['mesh']['statistics']['n_elements']:,} |\n")
-
-            if self.displacement is not None:
-                max_disp = self.metadata['results']['displacement']['max_translation']
-                f.write(f"| Max Displacement | {max_disp:.6f} mm |\n")
-
-            if self.stress is not None and 'stress' in self.metadata['results']:
-                for stress_type, stress_data in self.metadata['results']['stress'].items():
-                    if 'max_von_mises' in stress_data and stress_data['max_von_mises'] is not None:
-                        max_stress = stress_data['max_von_mises']
-                        f.write(f"| Max von Mises Stress | {max_stress:.2f} MPa |\n")
-                        break
-
-            f.write("\n---\n\n")
-            f.write("*Report generated by AtomizerField Visualizer*\n")
-
-        print(f"\nReport saved to: {output_file}")
-
-
-def main():
-    """Main entry point"""
-    parser = argparse.ArgumentParser(
-        description='Visualize FEA results in 3D',
-        formatter_class=argparse.RawDescriptionHelpFormatter,
-        epilog="""
-Examples:
-    # Visualize mesh
-    python visualize_results.py test_case_beam --mesh
-
-    # Visualize displacement
-    python visualize_results.py test_case_beam --displacement
-
-    # Visualize stress
-    python visualize_results.py test_case_beam --stress
-
-    # Generate full report
-    python visualize_results.py test_case_beam --report
-
-    # All visualizations
-    python visualize_results.py test_case_beam --all
-        """
-    )
-
-    parser.add_argument('case_dir', help='Path to case directory')
-    parser.add_argument('--mesh', action='store_true', help='Plot mesh structure')
-    parser.add_argument('--displacement', action='store_true', help='Plot displacement field')
-    parser.add_argument('--stress', action='store_true', help='Plot stress field')
-    parser.add_argument('--report', action='store_true', help='Generate markdown report')
-    parser.add_argument('--all', action='store_true', help='Show all plots and generate report')
-    parser.add_argument('--scale', type=float, default=10.0, help='Displacement scale factor (default: 10)')
-    parser.add_argument('--output', default='visualization_report.md', help='Report output file')
-
-    args = parser.parse_args()
-
-    # Create visualizer
-    viz = FEAVisualizer(args.case_dir)
-
-    # Determine what to show
-    show_all = args.all or not (args.mesh or args.displacement or args.stress or args.report)
-
-    if args.mesh or show_all:
-        print("\nShowing mesh structure...")
-        viz.plot_mesh()
-
-    if args.displacement or show_all:
-        print("\nShowing displacement field...")
-        viz.plot_displacement(scale=args.scale)
-
-    if args.stress or show_all:
-        print("\nShowing stress field...")
-        viz.plot_stress()
-
-    if args.report or show_all:
-        print("\nGenerating report...")
-        viz.create_report(args.output)
-
-
-if __name__ == "__main__":
-    main()

atomizer.py

@@ -34,26 +34,42 @@ from typing import Optional
 PROJECT_ROOT = Path(__file__).parent
 sys.path.insert(0, str(PROJECT_ROOT))
 
-from optimization_engine.processors.surrogates.auto_trainer import AutoTrainer, check_training_status
+from optimization_engine.processors.surrogates.auto_trainer import (
+    AutoTrainer,
+    check_training_status,
+)
 from optimization_engine.config.template_loader import (
     create_study_from_template,
     list_templates,
-    get_template
-)
-from optimization_engine.validators.study_validator import (
-    validate_study,
-    list_studies,
-    quick_check
+    get_template,
 )
+from optimization_engine.validators.study_validator import validate_study, list_studies, quick_check
+
+
+# New UX System imports (lazy loaded to avoid import errors)
+def get_intake_processor():
+    from optimization_engine.intake import IntakeProcessor
+
+    return IntakeProcessor
+
+
+def get_validation_gate():
+    from optimization_engine.validation import ValidationGate
+
+    return ValidationGate
+
+
+def get_report_generator():
+    from optimization_engine.reporting.html_report import HTMLReportGenerator
+
+    return HTMLReportGenerator
 
 
 def setup_logging(verbose: bool = False) -> None:
     """Configure logging."""
     level = logging.DEBUG if verbose else logging.INFO
     logging.basicConfig(
-        level=level,
-        format='%(asctime)s [%(levelname)s] %(message)s',
-        datefmt='%H:%M:%S'
+        level=level, format="%(asctime)s [%(levelname)s] %(message)s", datefmt="%H:%M:%S"
     )
 
 
@@ -95,7 +111,7 @@ def cmd_neural_optimize(args) -> int:
         study_name=args.study,
         min_points=args.min_points,
         epochs=args.epochs,
-        retrain_threshold=args.retrain_every
+        retrain_threshold=args.retrain_every,
     )
 
     status = trainer.get_status()
@@ -103,8 +119,8 @@ def cmd_neural_optimize(args) -> int:
     print(f"  Model version: v{status['model_version']}")
 
     # Determine workflow phase
-    has_trained_model = status['model_version'] > 0
-    current_points = status['total_points']
+    has_trained_model = status["model_version"] > 0
+    current_points = status["total_points"]
 
     if has_trained_model and current_points >= args.min_points:
         print("\n[3/5] Neural model available - starting neural-accelerated optimization...")
@@ -138,11 +154,7 @@ def _run_exploration_phase(args, trainer: AutoTrainer) -> int:
     # Run FEA optimization
     import subprocess
 
-    cmd = [
-        sys.executable,
-        str(run_script),
-        "--trials", str(fea_trials)
-    ]
+    cmd = [sys.executable, str(run_script), "--trials", str(fea_trials)]
 
     if args.resume:
         cmd.append("--resume")
@@ -155,7 +167,7 @@ def _run_exploration_phase(args, trainer: AutoTrainer) -> int:
     elapsed = time.time() - start_time
 
     print("-" * 60)
-    print(f"FEA optimization completed in {elapsed/60:.1f} minutes")
+    print(f"FEA optimization completed in {elapsed / 60:.1f} minutes")
 
     # Check if we can now train
     print("\n[5/5] Checking training data...")
@@ -169,7 +181,7 @@ def _run_exploration_phase(args, trainer: AutoTrainer) -> int:
             print("  Training failed - check logs")
     else:
         status = trainer.get_status()
-        remaining = args.min_points - status['total_points']
+        remaining = args.min_points - status["total_points"]
         print(f"  {status['total_points']} points collected")
         print(f"  Need {remaining} more for neural training")
 
@@ -188,12 +200,7 @@ def _run_neural_phase(args, trainer: AutoTrainer) -> int:
     # Run with neural acceleration
     import subprocess
 
-    cmd = [
-        sys.executable,
-        str(run_script),
-        "--trials", str(args.trials),
-        "--enable-nn"
-    ]
+    cmd = [sys.executable, str(run_script), "--trials", str(args.trials), "--enable-nn"]
 
     if args.resume:
         cmd.append("--resume")
@@ -206,7 +213,7 @@ def _run_neural_phase(args, trainer: AutoTrainer) -> int:
     elapsed = time.time() - start_time
 
     print("-" * 60)
-    print(f"Neural optimization completed in {elapsed/60:.1f} minutes")
+    print(f"Neural optimization completed in {elapsed / 60:.1f} minutes")
 
     # Check for retraining
     print("\n[5/5] Checking if retraining needed...")
@@ -228,10 +235,7 @@ def cmd_create_study(args) -> int:
     print(f"Creating study '{args.name}' from template '{args.template}'...")
 
     try:
-        study_path = create_study_from_template(
-            template_name=args.template,
-            study_name=args.name
-        )
+        study_path = create_study_from_template(template_name=args.template, study_name=args.name)
         print(f"\nSuccess! Study created at: {study_path}")
         return 0
     except FileNotFoundError as e:
@@ -290,7 +294,7 @@ def cmd_status(args) -> int:
         print(f"  Model version: v{status['model_version']}")
         print(f"  Should train: {status['should_train']}")
 
-        if status['latest_model']:
+        if status["latest_model"]:
             print(f"  Latest model: {status['latest_model']}")
 
     else:
@@ -305,8 +309,8 @@ def cmd_status(args) -> int:
 
         for study in studies:
             icon = "[OK]" if study["is_ready"] else "[!]"
-            trials_info = f"{study['trials']} trials" if study['trials'] > 0 else "no trials"
-            pareto_info = f", {study['pareto']} Pareto" if study['pareto'] > 0 else ""
+            trials_info = f"{study['trials']} trials" if study["trials"] > 0 else "no trials"
+            pareto_info = f", {study['pareto']} Pareto" if study["pareto"] > 0 else ""
             print(f"  {icon} {study['name']}")
             print(f"      Status: {study['status']} ({trials_info}{pareto_info})")
 
@@ -317,11 +321,7 @@ def cmd_train(args) -> int:
     """Trigger neural network training."""
     print(f"Training neural model for study: {args.study}")
 
-    trainer = AutoTrainer(
-        study_name=args.study,
-        min_points=args.min_points,
-        epochs=args.epochs
-    )
+    trainer = AutoTrainer(study_name=args.study, min_points=args.min_points, epochs=args.epochs)
 
     status = trainer.get_status()
     print(f"\nCurrent status:")
@@ -329,8 +329,10 @@ def cmd_train(args) -> int:
     print(f"  Min threshold: {args.min_points}")
 
     if args.force or trainer.should_train():
-        if args.force and status['total_points'] < args.min_points:
-            print(f"\nWarning: Force training with {status['total_points']} points (< {args.min_points})")
+        if args.force and status["total_points"] < args.min_points:
+            print(
+                f"\nWarning: Force training with {status['total_points']} points (< {args.min_points})"
+            )
 
         print("\nStarting training...")
         model_path = trainer.train()
@@ -342,7 +344,7 @@ def cmd_train(args) -> int:
             print("\nTraining failed - check logs")
             return 1
     else:
-        needed = args.min_points - status['total_points']
+        needed = args.min_points - status["total_points"]
         print(f"\nNot enough data for training. Need {needed} more points.")
         print("Use --force to train anyway.")
         return 1
@@ -355,6 +357,269 @@ def cmd_validate(args) -> int:
     return 0 if validation.is_ready_to_run else 1
 
 
+# ============================================================================
+# NEW UX SYSTEM COMMANDS
+# ============================================================================
+
+
+def cmd_intake(args) -> int:
+    """Process an intake folder into a study."""
+    IntakeProcessor = get_intake_processor()
+
+    # Determine inbox folder
+    inbox_path = Path(args.folder)
+
+    if not inbox_path.is_absolute():
+        inbox_dir = PROJECT_ROOT / "studies" / "_inbox"
+        if (inbox_dir / args.folder).exists():
+            inbox_path = inbox_dir / args.folder
+        elif (PROJECT_ROOT / "studies" / args.folder).exists():
+            inbox_path = PROJECT_ROOT / "studies" / args.folder
+
+    if not inbox_path.exists():
+        print(f"Error: Folder not found: {inbox_path}")
+        return 1
+
+    print(f"Processing intake: {inbox_path}")
+    print("=" * 60)
+
+    def progress(message: str, percent: float):
+        bar_width = 30
+        filled = int(bar_width * percent)
+        bar = "=" * filled + "-" * (bar_width - filled)
+        print(f"\r[{bar}] {percent * 100:5.1f}% {message}", end="", flush=True)
+        if percent >= 1.0:
+            print()
+
+    try:
+        processor = IntakeProcessor(inbox_path, progress_callback=progress)
+        context = processor.process(
+            run_baseline=not args.skip_baseline,
+            copy_files=True,
+            run_introspection=True,
+        )
+
+        print("\n" + "=" * 60)
+        print("INTAKE COMPLETE")
+        print("=" * 60)
+
+        summary = context.get_context_summary()
+        print(f"\nStudy: {context.study_name}")
+        print(f"Location: {processor.study_dir}")
+        print(f"\nContext loaded:")
+        print(f"  Model: {'Yes' if summary['has_model'] else 'No'}")
+        print(f"  Introspection: {'Yes' if summary['has_introspection'] else 'No'}")
+        print(f"  Baseline: {'Yes' if summary['has_baseline'] else 'No'}")
+        print(
+            f"  Expressions: {summary['num_expressions']} ({summary['num_dv_candidates']} candidates)"
+        )
+
+        if context.has_baseline:
+            print(f"\nBaseline: {context.get_baseline_summary()}")
+
+        if summary["warnings"]:
+            print(f"\nWarnings:")
+            for w in summary["warnings"]:
+                print(f"  - {w}")
+
+        print(f"\nNext: atomizer gate {context.study_name}")
+        return 0
+
+    except Exception as e:
+        print(f"\nError: {e}")
+        if args.verbose:
+            import traceback
+
+            traceback.print_exc()
+        return 1
+
+
+def cmd_gate(args) -> int:
+    """Run validation gate before optimization."""
+    ValidationGate = get_validation_gate()
+
+    study_path = Path(args.study)
+    if not study_path.is_absolute():
+        study_path = PROJECT_ROOT / "studies" / args.study
+
+    if not study_path.exists():
+        print(f"Error: Study not found: {study_path}")
+        return 1
+
+    print(f"Validation Gate: {study_path.name}")
+    print("=" * 60)
+
+    def progress(message: str, percent: float):
+        bar_width = 30
+        filled = int(bar_width * percent)
+        bar = "=" * filled + "-" * (bar_width - filled)
+        print(f"\r[{bar}] {percent * 100:5.1f}% {message}", end="", flush=True)
+        if percent >= 1.0:
+            print()
+
+    try:
+        gate = ValidationGate(study_path, progress_callback=progress)
+        result = gate.validate(
+            run_test_trials=not args.skip_trials,
+            n_test_trials=args.trials,
+        )
+
+        print("\n" + "=" * 60)
+        if result.passed:
+            print("VALIDATION PASSED")
+        else:
+            print("VALIDATION FAILED")
+        print("=" * 60)
+
+        # Show test trials
+        if result.test_trials:
+            print(
+                f"\nTest Trials: {len([t for t in result.test_trials if t.success])}/{len(result.test_trials)} passed"
+            )
+
+            if result.results_vary:
+                print("Results vary: Yes (mesh updating correctly)")
+            else:
+                print("Results vary: NO - MESH MAY NOT BE UPDATING!")
+
+            # Results table
+            print(f"\n{'Trial':<8} {'Status':<8} {'Time':<8}", end="")
+            if result.test_trials and result.test_trials[0].objectives:
+                for obj in list(result.test_trials[0].objectives.keys())[:3]:
+                    print(f" {obj[:10]:<12}", end="")
+            print()
+
+            for trial in result.test_trials:
+                status = "OK" if trial.success else "FAIL"
+                print(
+                    f"{trial.trial_number:<8} {status:<8} {trial.solve_time_seconds:<8.1f}", end=""
+                )
+                for val in list(trial.objectives.values())[:3]:
+                    print(f" {val:<12.4f}", end="")
+                print()
+
+        # Runtime estimate
+        if result.avg_solve_time:
+            print(f"\nRuntime Estimate:")
+            print(f"  Avg solve: {result.avg_solve_time:.1f}s")
+            if result.estimated_total_runtime:
+                print(f"  Total: {result.estimated_total_runtime / 3600:.1f}h")
+
+        # Errors
+        if result.errors:
+            print(f"\nErrors:")
+            for err in result.errors:
+                print(f"  - {err}")
+
+        if result.passed and args.approve:
+            gate.approve()
+            print(f"\nStudy approved for optimization!")
+        elif result.passed:
+            print(f"\nTo approve: atomizer gate {args.study} --approve")
+
+        gate.save_result(result)
+        return 0 if result.passed else 1
+
+    except Exception as e:
+        print(f"\nError: {e}")
+        if args.verbose:
+            import traceback
+
+            traceback.print_exc()
+        return 1
+
+
+def cmd_finalize(args) -> int:
+    """Generate final report for a study."""
+    HTMLReportGenerator = get_report_generator()
+
+    study_path = Path(args.study)
+    if not study_path.is_absolute():
+        study_path = PROJECT_ROOT / "studies" / args.study
+
+    if not study_path.exists():
+        print(f"Error: Study not found: {study_path}")
+        return 1
+
+    print(f"Generating report for: {study_path.name}")
+    print("=" * 60)
+
+    try:
+        generator = HTMLReportGenerator(study_path)
+        report_path = generator.generate(include_pdf=getattr(args, "pdf", False))
+
+        print(f"\nReport generated successfully!")
+        print(f"  HTML: {report_path}")
+        print(f"  Data: {report_path.parent / 'data'}")
+
+        if getattr(args, "open", False):
+            import webbrowser
+
+            webbrowser.open(str(report_path))
+        else:
+            print(f"\nOpen in browser: file://{report_path}")
+
+        return 0
+
+    except Exception as e:
+        print(f"\nError: {e}")
+        if args.verbose:
+            import traceback
+
+            traceback.print_exc()
+        return 1
+
+
+def cmd_list_studies(args) -> int:
+    """List all studies and inbox items."""
+    studies_dir = PROJECT_ROOT / "studies"
+
+    print("Atomizer Studies")
+    print("=" * 60)
+
+    # Inbox items
+    inbox_dir = studies_dir / "_inbox"
+    if inbox_dir.exists():
+        inbox_items = [d for d in inbox_dir.iterdir() if d.is_dir() and not d.name.startswith(".")]
+        if inbox_items:
+            print("\nPending Intake (_inbox/):")
+            for item in sorted(inbox_items):
+                has_config = (item / "intake.yaml").exists()
+                has_model = bool(list(item.glob("**/*.sim")))
+                status = []
+                if has_config:
+                    status.append("yaml")
+                if has_model:
+                    status.append("model")
+                print(f"  {item.name:<30} [{', '.join(status) or 'empty'}]")
+
+    # Active studies
+    print("\nStudies:")
+    for study_dir in sorted(studies_dir.iterdir()):
+        if (
+            study_dir.is_dir()
+            and not study_dir.name.startswith("_")
+            and not study_dir.name.startswith(".")
+        ):
+            has_spec = (study_dir / "atomizer_spec.json").exists() or (
+                study_dir / "optimization_config.json"
+            ).exists()
+            has_db = any(study_dir.rglob("study.db"))
+            has_approval = (study_dir / ".validation_approved").exists()
+
+            status = []
+            if has_spec:
+                status.append("configured")
+            if has_approval:
+                status.append("approved")
+            if has_db:
+                status.append("has_data")
+
+            print(f"  {study_dir.name:<30} [{', '.join(status) or 'new'}]")
+
+    return 0
+
+
 def main():
     parser = argparse.ArgumentParser(
         description="Atomizer - Neural-Accelerated Structural Optimization",
@@ -372,7 +637,7 @@ Examples:
 
   # Manual training
   python atomizer.py train --study my_study --epochs 100
-        """
+        """,
     )
 
     parser.add_argument("-v", "--verbose", action="store_true", help="Verbose output")
@@ -381,13 +646,14 @@ Examples:
 
     # neural-optimize command
     neural_parser = subparsers.add_parser(
-        "neural-optimize",
-        help="Run neural-accelerated optimization (main workflow)"
+        "neural-optimize", help="Run neural-accelerated optimization (main workflow)"
     )
     neural_parser.add_argument("--study", "-s", required=True, help="Study name")
     neural_parser.add_argument("--trials", "-n", type=int, default=500, help="Total trials")
     neural_parser.add_argument("--min-points", type=int, default=50, help="Min points for training")
-    neural_parser.add_argument("--retrain-every", type=int, default=50, help="Retrain after N new points")
+    neural_parser.add_argument(
+        "--retrain-every", type=int, default=50, help="Retrain after N new points"
+    )
     neural_parser.add_argument("--epochs", type=int, default=100, help="Training epochs")
     neural_parser.add_argument("--resume", action="store_true", help="Resume existing study")
 
@@ -414,6 +680,31 @@ Examples:
     validate_parser = subparsers.add_parser("validate", help="Validate study setup")
     validate_parser.add_argument("--study", "-s", required=True, help="Study name")
 
+    # ========================================================================
+    # NEW UX SYSTEM COMMANDS
+    # ========================================================================
+
+    # intake command
+    intake_parser = subparsers.add_parser("intake", help="Process an intake folder into a study")
+    intake_parser.add_argument("folder", help="Path to intake folder")
+    intake_parser.add_argument("--skip-baseline", action="store_true", help="Skip baseline solve")
+
+    # gate command (validation gate)
+    gate_parser = subparsers.add_parser("gate", help="Run validation gate with test trials")
+    gate_parser.add_argument("study", help="Study name or path")
+    gate_parser.add_argument("--skip-trials", action="store_true", help="Skip test trials")
+    gate_parser.add_argument("--trials", type=int, default=3, help="Number of test trials")
+    gate_parser.add_argument("--approve", action="store_true", help="Approve if validation passes")
+
+    # list command
+    list_studies_parser = subparsers.add_parser("list", help="List all studies and inbox items")
+
+    # finalize command
+    finalize_parser = subparsers.add_parser("finalize", help="Generate final HTML report")
+    finalize_parser.add_argument("study", help="Study name or path")
+    finalize_parser.add_argument("--pdf", action="store_true", help="Also generate PDF")
+    finalize_parser.add_argument("--open", action="store_true", help="Open report in browser")
+
     args = parser.parse_args()
 
     if not args.command:
@@ -429,7 +720,12 @@ Examples:
         "list-templates": cmd_list_templates,
         "status": cmd_status,
         "train": cmd_train,
-        "validate": cmd_validate
+        "validate": cmd_validate,
+        # New UX commands
+        "intake": cmd_intake,
+        "gate": cmd_gate,
+        "list": cmd_list_studies,
+        "finalize": cmd_finalize,
     }
 
     handler = commands.get(args.command)

atomizer_paths.py

@@ -1,144 +0,0 @@
-"""
-Atomizer Path Configuration
-
-Provides intelligent path resolution for Atomizer core modules and directories.
-This module can be imported from anywhere in the project hierarchy.
-"""
-
-from pathlib import Path
-import sys
-
-
-def get_atomizer_root() -> Path:
-    """
-    Get the Atomizer project root directory.
-
-    This function intelligently locates the root by looking for marker files
-    that uniquely identify the Atomizer project root.
-
-    Returns:
-        Path: Absolute path to Atomizer root directory
-
-    Raises:
-        RuntimeError: If Atomizer root cannot be found
-    """
-    # Start from this file's location
-    current = Path(__file__).resolve().parent
-
-    # Marker files that uniquely identify Atomizer root
-    markers = [
-        'optimization_engine',  # Core module directory
-        'studies',              # Studies directory
-        'README.md'             # Project README
-    ]
-
-    # Walk up the directory tree looking for all markers
-    max_depth = 10  # Prevent infinite loop
-    for _ in range(max_depth):
-        # Check if all markers exist at this level
-        if all((current / marker).exists() for marker in markers):
-            return current
-
-        # Move up one directory
-        parent = current.parent
-        if parent == current:  # Reached filesystem root
-            break
-        current = parent
-
-    raise RuntimeError(
-        "Could not locate Atomizer root directory. "
-        "Make sure you're running from within the Atomizer project."
-    )
-
-
-def setup_python_path():
-    """
-    Add Atomizer root to Python path if not already present.
-
-    This allows imports like `from optimization_engine.core.runner import ...`
-    to work from anywhere in the project.
-    """
-    root = get_atomizer_root()
-    root_str = str(root)
-
-    if root_str not in sys.path:
-        sys.path.insert(0, root_str)
-
-
-# Core directories (lazy-loaded)
-_ROOT = None
-
-def root() -> Path:
-    """Get Atomizer root directory."""
-    global _ROOT
-    if _ROOT is None:
-        _ROOT = get_atomizer_root()
-    return _ROOT
-
-
-def optimization_engine() -> Path:
-    """Get optimization_engine directory."""
-    return root() / 'optimization_engine'
-
-
-def studies() -> Path:
-    """Get studies directory."""
-    return root() / 'studies'
-
-
-def tests() -> Path:
-    """Get tests directory."""
-    return root() / 'tests'
-
-
-def docs() -> Path:
-    """Get docs directory."""
-    return root() / 'docs'
-
-
-def plugins() -> Path:
-    """Get plugins directory."""
-    return optimization_engine() / 'plugins'
-
-
-# Common files
-def readme() -> Path:
-    """Get README.md path."""
-    return root() / 'README.md'
-
-
-def roadmap() -> Path:
-    """Get development roadmap path."""
-    return root() / 'DEVELOPMENT_ROADMAP.md'
-
-
-# Convenience function for scripts
-def ensure_imports():
-    """
-    Ensure Atomizer modules can be imported.
-
-    Call this at the start of any script to ensure proper imports:
-
-    ```python
-    import atomizer_paths
-    atomizer_paths.ensure_imports()
-
-    # Now you can import Atomizer modules
-    from optimization_engine.core.runner import OptimizationRunner
-    ```
-    """
-    setup_python_path()
-
-
-if __name__ == '__main__':
-    # Self-test
-    print("Atomizer Path Configuration")
-    print("=" * 60)
-    print(f"Root:                {root()}")
-    print(f"Optimization Engine: {optimization_engine()}")
-    print(f"Studies:             {studies()}")
-    print(f"Tests:               {tests()}")
-    print(f"Docs:                {docs()}")
-    print(f"Plugins:             {plugins()}")
-    print("=" * 60)
-    print("\nAll paths resolved successfully!")

config.py

@@ -1,192 +0,0 @@
-"""
-Central Configuration for Atomizer
-
-This file contains all system-level paths and settings.
-To update NX version or paths, ONLY modify this file.
-"""
-
-from pathlib import Path
-import os
-
-# ============================================================================
-# NX/SIMCENTER CONFIGURATION
-# ============================================================================
-
-# NX Installation Directory
-# Change this to update NX version across entire Atomizer codebase
-NX_VERSION = "2512"
-NX_INSTALLATION_DIR = Path("C:/Program Files/Siemens/DesigncenterNX2512")
-
-# Derived NX Paths (automatically updated when NX_VERSION changes)
-NX_BIN_DIR = NX_INSTALLATION_DIR / "NXBIN"
-NX_RUN_JOURNAL = NX_BIN_DIR / "run_journal.exe"
-NX_MATERIALS_DIR = NX_INSTALLATION_DIR / "UGII" / "materials"
-NX_MATERIAL_LIBRARY = NX_MATERIALS_DIR / "physicalmateriallibrary.xml"
-NX_PYTHON_STUBS = NX_INSTALLATION_DIR / "ugopen" / "pythonStubs"
-
-# Validate NX installation on import
-if not NX_INSTALLATION_DIR.exists():
-    raise FileNotFoundError(
-        f"NX installation not found at: {NX_INSTALLATION_DIR}\n"
-        f"Please update NX_VERSION or NX_INSTALLATION_DIR in config.py"
-    )
-
-if not NX_RUN_JOURNAL.exists():
-    raise FileNotFoundError(
-        f"run_journal.exe not found at: {NX_RUN_JOURNAL}\n"
-        f"Please verify NX installation or update paths in config.py"
-    )
-
-# ============================================================================
-# PYTHON ENVIRONMENT CONFIGURATION
-# ============================================================================
-
-# Python Environment Name
-PYTHON_ENV_NAME = "atomizer"
-
-# Anaconda/Conda base path (auto-detected from current interpreter)
-CONDA_BASE = Path(os.environ.get("CONDA_PREFIX", "")).parent
-PYTHON_ENV_PATH = CONDA_BASE / "envs" / PYTHON_ENV_NAME / "python.exe"
-
-# ============================================================================
-# PROJECT PATHS
-# ============================================================================
-
-# Project root directory
-PROJECT_ROOT = Path(__file__).parent.resolve()
-
-# Key directories
-OPTIMIZATION_ENGINE_DIR = PROJECT_ROOT / "optimization_engine"
-STUDIES_DIR = PROJECT_ROOT / "studies"
-DOCS_DIR = PROJECT_ROOT / "docs"
-TESTS_DIR = PROJECT_ROOT / "tests"
-
-# ============================================================================
-# NASTRAN CONFIGURATION
-# ============================================================================
-
-# Nastran solver timeout (seconds)
-NASTRAN_TIMEOUT = 600
-
-# Nastran file extensions
-NASTRAN_INPUT_EXT = ".dat"
-NASTRAN_OUTPUT_EXT = ".op2"
-NASTRAN_TEXT_OUTPUT_EXT = ".f06"
-
-# ============================================================================
-# OPTIMIZATION DEFAULTS
-# ============================================================================
-
-# Default optimization parameters
-DEFAULT_N_TRIALS = 50
-DEFAULT_TIMEOUT = 3600  # 1 hour
-DEFAULT_N_STARTUP_TRIALS = 10
-
-# Optuna sampler settings
-DEFAULT_SAMPLER = "TPESampler"
-DEFAULT_SURROGATE = "gp"  # gaussian process
-
-# ============================================================================
-# LOGGING CONFIGURATION
-# ============================================================================
-
-LOG_LEVEL = "INFO"
-LOG_FORMAT = "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
-
-# ============================================================================
-# DASHBOARD CONFIGURATION
-# ============================================================================
-
-DASHBOARD_HOST = "localhost"
-DASHBOARD_PORT = 8050
-
-# ============================================================================
-# HELPER FUNCTIONS
-# ============================================================================
-
-def get_nx_journal_command(journal_script: Path, *args) -> str:
-    """
-    Generate NX journal execution command.
-
-    Args:
-        journal_script: Path to journal .py file
-        *args: Additional arguments to pass to journal
-
-    Returns:
-        Command string ready for subprocess execution
-    """
-    cmd_parts = [f'"{NX_RUN_JOURNAL}"', f'"{journal_script}"']
-    if args:
-        cmd_parts.append("-args")
-        cmd_parts.extend([f'"{arg}"' for arg in args])
-    return " ".join(cmd_parts)
-
-
-def validate_config():
-    """
-    Validate all critical paths exist.
-    Raises FileNotFoundError if any critical path is missing.
-    """
-    critical_paths = {
-        "NX Installation": NX_INSTALLATION_DIR,
-        "NX run_journal.exe": NX_RUN_JOURNAL,
-        "NX Material Library": NX_MATERIAL_LIBRARY,
-        "NX Python Stubs": NX_PYTHON_STUBS,
-        "Project Root": PROJECT_ROOT,
-        "Optimization Engine": OPTIMIZATION_ENGINE_DIR,
-    }
-
-    missing = []
-    for name, path in critical_paths.items():
-        if not path.exists():
-            missing.append(f"  - {name}: {path}")
-
-    if missing:
-        raise FileNotFoundError(
-            "Critical paths missing:\n" + "\n".join(missing) +
-            "\n\nPlease update paths in config.py"
-        )
-
-    return True
-
-
-def print_config():
-    """Print current configuration for debugging."""
-    print("=" * 80)
-    print("ATOMIZER CONFIGURATION")
-    print("=" * 80)
-    print(f"\nNX Configuration:")
-    print(f"  Version: {NX_VERSION}")
-    print(f"  Installation: {NX_INSTALLATION_DIR}")
-    print(f"  run_journal.exe: {NX_RUN_JOURNAL}")
-    print(f"  Material Library: {NX_MATERIAL_LIBRARY}")
-    print(f"  Python Stubs: {NX_PYTHON_STUBS}")
-    print(f"\nPython Environment:")
-    print(f"  Environment Name: {PYTHON_ENV_NAME}")
-    print(f"  Python Path: {PYTHON_ENV_PATH}")
-    print(f"\nProject Paths:")
-    print(f"  Root: {PROJECT_ROOT}")
-    print(f"  Optimization Engine: {OPTIMIZATION_ENGINE_DIR}")
-    print(f"  Studies: {STUDIES_DIR}")
-    print("=" * 80)
-
-
-# Validate configuration on import
-validate_config()
-
-
-# ============================================================================
-# USAGE EXAMPLE
-# ============================================================================
-
-if __name__ == "__main__":
-    # Print configuration
-    print_config()
-
-    # Example: Generate journal command
-    example_journal = PROJECT_ROOT / "optimization_engine" / "import_expressions.py"
-    example_prt = PROJECT_ROOT / "studies" / "beam" / "Beam.prt"
-    example_exp = PROJECT_ROOT / "studies" / "beam" / "Beam_vars.exp"
-
-    cmd = get_nx_journal_command(example_journal, example_prt, example_exp)
-    print(f"\nExample Journal Command:\n{cmd}")

docs/00_INDEX.md

@@ -1,34 +1,77 @@
 # Atomizer Documentation Index
 
-**Last Updated**: 2026-01-24
-**Project Version**: 0.5.0 (AtomizerSpec v2.0 - Canvas Builder)
+**Last Updated**: February 9, 2026  
+**Project Version**: 0.5.0 (AtomizerSpec v2.0 + Atomizer-HQ Multi-Agent Team)
 
 ---
 
 ## Quick Start
 
-New to Atomizer? Start here:
+### For AI Agents (Atomizer-HQ Team)
+**Start here** if you're an AI agent working on client projects:
 
-1. **[README.md](../README.md)** - Project overview and philosophy
-2. **[Getting Started](GETTING_STARTED.md)** - Installation, first study, dashboard
-3. **[Protocol System](protocols/README.md)** - How Atomizer is organized
-4. **[Example Studies](../studies/)** - Working examples
+1. **[HQ Overview](hq/README.md)** — What Atomizer-HQ is and how agents work together
+2. **[Project Structure](hq/PROJECT_STRUCTURE.md)** — Standard project organization  
+3. **[Agent Workflows](hq/AGENT_WORKFLOWS.md)** — Who does what in the project lifecycle
+4. **[Knowledge Base Conventions](hq/KB_CONVENTIONS.md)** — How to accumulate and share knowledge
+
+### For Engineers (Core Optimization)
+**Start here** if you're using Atomizer for FEA optimization:
+
+1. **[README.md](../README.md)** - Project overview and philosophy  
+2. **[Getting Started](GETTING_STARTED.md)** - Installation, first study, dashboard  
+3. **[Protocol System](protocols/README.md)** - How Atomizer is organized  
+4. **[Example Studies](../studies/)** - Working examples  
 
 ---
 
-## Documentation Structure
+## Atomizer-HQ Agent Documentation
 
-### Core Documentation
+The multi-agent optimization team that runs client FEA projects.
+
+### Essential HQ Docs
+
+| Document | Purpose | Target Agents |
+|----------|---------|---------------|
+| **[HQ Overview](hq/README.md)** | What Atomizer-HQ is, how to use these docs | All agents |
+| **[Project Structure](hq/PROJECT_STRUCTURE.md)** | Standard KB-integrated project layout | Manager, Technical Lead |  
+| **[KB Conventions](hq/KB_CONVENTIONS.md)** | Knowledge Base accumulation principles | All agents |
+| **[Agent Workflows](hq/AGENT_WORKFLOWS.md)** | Project lifecycle and agent handoffs | All agents |
+| **[Study Conventions](hq/STUDY_CONVENTIONS.md)** | Technical study execution standards | Technical Lead, Optimizer |
+
+### Agent Roles Quick Reference
+
+| Agent | Role | Primary Phase | Key Responsibilities |
+|-------|------|---------------|---------------------|
+| 📋 **Secretary** | CEO interface | Intake | Client requirements, project initiation |
+| 🏗️ **Manager** | Coordination | Breakdown | Project structure, team coordination |
+| 🔧 **Technical Lead** | FEA expert | Introspection | Model setup, optimization planning |
+| ⚡ **Optimizer** | Study execution | Study | FEA optimization execution |
+| 📊 **Post-Processor** | Results analysis | Results | Performance analysis, insights |
+| 📝 **Reporter** | Documentation | Deliverables | Client reports, final packages |
+
+### Living Examples
+- **Reference Project**: [projects/hydrotech-beam/](../projects/hydrotech-beam/) — Complete project structure
+- **Project Structure**: Demonstrates KB-integrated organization and study flow
+- **Knowledge Accumulation**: Shows generation-tracked knowledge evolution
+
+---
+
+## Core Documentation
+
+Essential reference for understanding Atomizer's optimization framework.
+
+### Foundation Documents
 
 | Document | Purpose |
 |----------|---------|
 | **[GETTING_STARTED.md](GETTING_STARTED.md)** | Setup, first study, dashboard basics |
 | **[ARCHITECTURE.md](ARCHITECTURE.md)** | System architecture, hooks, data flow |
-| **[protocols/README.md](protocols/README.md)** | Protocol Operating System overview |
+| **[QUICK_REF.md](../QUICK_REF.md)** | Active reference guide |
 
 ### Protocol System
 
-The Protocol Operating System (POS) provides structured workflows:
+The Protocol Operating System (POS) provides structured workflows for optimization:
 
 ```
 protocols/
@@ -41,7 +84,8 @@ protocols/
 │   ├── OP_05_EXPORT_TRAINING_DATA.md
 │   ├── OP_06_TROUBLESHOOT.md
 │   ├── OP_07_DISK_OPTIMIZATION.md
-│   └── OP_08_GENERATE_REPORT.md
+│   ├── OP_08_GENERATE_REPORT.md
+│   └── OP_09_AGENT_COMMUNICATION.md
 ├── system/               # Technical specifications (SYS_10-18)
 │   ├── SYS_10_IMSO.md           # Intelligent optimization
 │   ├── SYS_11_MULTI_OBJECTIVE.md
@@ -59,22 +103,28 @@ protocols/
     └── EXT_04_CREATE_SKILL.md
 ```
 
-### User Guides
+---
 
-Located in `guides/`:
+## User Guides
 
-| Guide | Purpose |
-|-------|---------|
-| **[CANVAS.md](guides/CANVAS.md)** | Visual study builder (AtomizerSpec v2.0) |
-| **[DASHBOARD.md](guides/DASHBOARD.md)** | Dashboard overview and features |
-| **[NEURAL_FEATURES_COMPLETE.md](guides/NEURAL_FEATURES_COMPLETE.md)** | Neural acceleration guide |
-| **[NEURAL_WORKFLOW_TUTORIAL.md](guides/NEURAL_WORKFLOW_TUTORIAL.md)** | Data → Training → Optimization |
-| **[hybrid_mode.md](guides/hybrid_mode.md)** | Hybrid FEA/NN optimization |
-| **[TRAINING_DATA_EXPORT_GUIDE.md](guides/TRAINING_DATA_EXPORT_GUIDE.md)** | Exporting data for neural training |
+Practical guides for using Atomizer features (engineers + Claude Code era).
 
-### API Reference
+### Current User Guides
 
-Located in `api/`:
+| Guide | Purpose | Status |
+|-------|---------|--------|
+| **[CANVAS.md](guides/CANVAS.md)** | Visual study builder (AtomizerSpec v2.0) | Active |
+| **[DASHBOARD.md](guides/DASHBOARD.md)** | Dashboard overview and features | Active |
+| **[NEURAL_FEATURES_COMPLETE.md](guides/NEURAL_FEATURES_COMPLETE.md)** | Neural acceleration guide | Active |
+| **[NEURAL_WORKFLOW_TUTORIAL.md](guides/NEURAL_WORKFLOW_TUTORIAL.md)** | Data → Training → Optimization | Active |
+| **[hybrid_mode.md](guides/hybrid_mode.md)** | Hybrid FEA/NN optimization | Active |
+| **[TRAINING_DATA_EXPORT_GUIDE.md](guides/TRAINING_DATA_EXPORT_GUIDE.md)** | Exporting data for neural training | Active |
+
+---
+
+## API Reference
+
+Technical integration documentation for developers and advanced users.
 
 | Document | Purpose |
 |----------|---------|
@@ -83,18 +133,43 @@ Located in `api/`:
 | **[GNN_ARCHITECTURE.md](api/GNN_ARCHITECTURE.md)** | Graph Neural Network details |
 | **[NXOPEN_RESOURCES.md](api/NXOPEN_RESOURCES.md)** | NX Open documentation resources |
 
-### Physics Documentation
+---
 
-Located in `physics/`:
+## Domain Knowledge
+
+Physics and engineering domain documentation.
+
+### Physics Documentation
 
 | Document | Purpose |
 |----------|---------|
 | **[ZERNIKE_FUNDAMENTALS.md](physics/ZERNIKE_FUNDAMENTALS.md)** | Zernike polynomial basics |
 | **[ZERNIKE_OPD_METHOD.md](physics/ZERNIKE_OPD_METHOD.md)** | OPD method for mirror optimization |
 
-### Development
+---
 
-Located in `development/`:
+## Workflows and Operations
+
+Operational workflows for common tasks.
+
+### Standard Workflows
+
+| Document | Purpose |
+|----------|---------|
+| **[CREATE.md](WORKFLOWS/CREATE.md)** | Study creation workflow |
+| **[RUN.md](WORKFLOWS/RUN.md)** | Optimization execution workflow |
+| **[ANALYZE.md](WORKFLOWS/ANALYZE.md)** | Results analysis workflow |
+| **[DELIVER.md](WORKFLOWS/DELIVER.md)** | Deliverable creation workflow |
+| **[VALIDATE.md](WORKFLOWS/VALIDATE.md)** | Validation and verification workflow |
+| **[REPORT.md](WORKFLOWS/REPORT.md)** | Report generation workflow |
+
+---
+
+## Development and Architecture
+
+Technical development documentation.
+
+### Development Guides
 
 | Document | Purpose |
 |----------|---------|
@@ -102,9 +177,7 @@ Located in `development/`:
 | **[DEVELOPMENT_ROADMAP.md](development/DEVELOPMENT_ROADMAP.md)** | Future plans |
 | **[Philosophy.md](development/Philosophy.md)** | Design philosophy |
 
-### Diagrams
-
-Located in `diagrams/`:
+### Architecture Documentation
 
 | Document | Purpose |
 |----------|---------|
@@ -113,35 +186,57 @@ Located in `diagrams/`:
 
 ---
 
+## Archive
+
+Historical and review documents preserved for context and CEO review.
+
+### Archive Structure
+- **[archive/review/](archive/review/)** — Documents flagged for CEO review
+  - RALPH_LOOP implementation plans
+  - Dashboard implementation iterations  
+  - Superseded development plans
+  - Session summaries and old development notes
+- **[archive/historical/](archive/historical/)** — Historical but valuable documents
+  - Original protocol v1 monolithic document
+  - Foundational design documents
+  - Completed restructuring plans
+
+### Key Historical Documents
+- **[PROTOCOL_V1_MONOLITHIC.md](archive/historical/PROTOCOL_V1_MONOLITHIC.md)** — Original monolithic protocol (Nov 2025)
+- Various implementation plans and session summaries in review directories
+
+---
+
 ## Documentation by Task
 
-### Creating Studies
+### For Agents: Project Execution
+1. **[Agent Workflows](hq/AGENT_WORKFLOWS.md)** — Project lifecycle and handoffs
+2. **[Project Structure](hq/PROJECT_STRUCTURE.md)** — How to organize projects  
+3. **[Study Conventions](hq/STUDY_CONVENTIONS.md)** — Technical execution standards
+4. **[KB Conventions](hq/KB_CONVENTIONS.md)** — Knowledge accumulation
 
-1. **[GETTING_STARTED.md](GETTING_STARTED.md)** - First study tutorial
-2. **[OP_01_CREATE_STUDY.md](protocols/operations/OP_01_CREATE_STUDY.md)** - Detailed creation protocol
-3. **[guides/CANVAS.md](guides/CANVAS.md)** - Visual study builder
+### For Engineers: Creating Studies
+1. **[GETTING_STARTED.md](GETTING_STARTED.md)** — First study tutorial
+2. **[OP_01_CREATE_STUDY.md](protocols/operations/OP_01_CREATE_STUDY.md)** — Detailed creation protocol
+3. **[guides/CANVAS.md](guides/CANVAS.md)** — Visual study builder
 
-### Running Optimizations
+### For Engineers: Running Optimizations
+1. **[OP_02_RUN_OPTIMIZATION.md](protocols/operations/OP_02_RUN_OPTIMIZATION.md)** — Run protocol
+2. **[SYS_10_IMSO.md](protocols/system/SYS_10_IMSO.md)** — Intelligent optimization
+3. **[SYS_15_METHOD_SELECTOR.md](protocols/system/SYS_15_METHOD_SELECTOR.md)** — Method selection
 
-1. **[OP_02_RUN_OPTIMIZATION.md](protocols/operations/OP_02_RUN_OPTIMIZATION.md)** - Run protocol
-2. **[SYS_10_IMSO.md](protocols/system/SYS_10_IMSO.md)** - Intelligent optimization
-3. **[SYS_15_METHOD_SELECTOR.md](protocols/system/SYS_15_METHOD_SELECTOR.md)** - Method selection
+### For Engineers: Neural Acceleration
+1. **[guides/NEURAL_FEATURES_COMPLETE.md](guides/NEURAL_FEATURES_COMPLETE.md)** — Overview
+2. **[SYS_14_NEURAL_ACCELERATION.md](protocols/system/SYS_14_NEURAL_ACCELERATION.md)** — Technical spec
+3. **[guides/NEURAL_WORKFLOW_TUTORIAL.md](guides/NEURAL_WORKFLOW_TUTORIAL.md)** — Step-by-step
 
-### Neural Acceleration
+### For Engineers: Analyzing Results
+1. **[OP_04_ANALYZE_RESULTS.md](protocols/operations/OP_04_ANALYZE_RESULTS.md)** — Analysis protocol
+2. **[SYS_17_STUDY_INSIGHTS.md](protocols/system/SYS_17_STUDY_INSIGHTS.md)** — Physics visualizations
 
-1. **[guides/NEURAL_FEATURES_COMPLETE.md](guides/NEURAL_FEATURES_COMPLETE.md)** - Overview
-2. **[SYS_14_NEURAL_ACCELERATION.md](protocols/system/SYS_14_NEURAL_ACCELERATION.md)** - Technical spec
-3. **[guides/NEURAL_WORKFLOW_TUTORIAL.md](guides/NEURAL_WORKFLOW_TUTORIAL.md)** - Step-by-step
-
-### Analyzing Results
-
-1. **[OP_04_ANALYZE_RESULTS.md](protocols/operations/OP_04_ANALYZE_RESULTS.md)** - Analysis protocol
-2. **[SYS_17_STUDY_INSIGHTS.md](protocols/system/SYS_17_STUDY_INSIGHTS.md)** - Physics visualizations
-
-### Troubleshooting
-
-1. **[OP_06_TROUBLESHOOT.md](protocols/operations/OP_06_TROUBLESHOOT.md)** - Troubleshooting guide
-2. **[GETTING_STARTED.md#troubleshooting](GETTING_STARTED.md#troubleshooting)** - Common issues
+### For Everyone: Troubleshooting
+1. **[OP_06_TROUBLESHOOT.md](protocols/operations/OP_06_TROUBLESHOOT.md)** — Troubleshooting guide
+2. **[GETTING_STARTED.md#troubleshooting](GETTING_STARTED.md#troubleshooting)** — Common issues
 
 ---
 
@@ -156,6 +251,7 @@ Located in `diagrams/`:
 | **OP_03** | Monitor Progress | Real-time monitoring |
 | **OP_04** | Analyze Results | Results analysis |
 | **OP_06** | Troubleshoot | Debugging issues |
+| **OP_09** | Agent Communication | HQ communication standards |
 | **SYS_10** | IMSO | Intelligent optimization |
 | **SYS_12** | Extractors | Physics extraction library |
 | **SYS_14** | Neural | Neural network acceleration |
@@ -166,10 +262,10 @@ Located in `diagrams/`:
 # Activate environment
 conda activate atomizer
 
-# Run optimization
+# Run optimization (engineers)
 python run_optimization.py --start --trials 50
 
-# Resume interrupted run
+# Resume interrupted run  
 python run_optimization.py --start --resume
 
 # Start dashboard
@@ -177,6 +273,9 @@ python launch_dashboard.py
 
 # Neural turbo mode
 python run_nn_optimization.py --turbo --nn-trials 5000
+
+# KB status check (agents)
+cad_kb.py status projects/[project]/kb
 ```
 
 ### Key Extractors
@@ -194,18 +293,6 @@ Full catalog: [SYS_12_EXTRACTOR_LIBRARY.md](protocols/system/SYS_12_EXTRACTOR_LI
 
 ---
 
-## Archive
-
-Historical documents are preserved in `archive/`:
-
-- `archive/historical/` - Legacy documents, old protocols
-- `archive/marketing/` - Briefings, presentations
-- `archive/session_summaries/` - Past development sessions
-- `archive/plans/` - Superseded plan documents (RALPH_LOOP V2/V3, CANVAS V3, etc.)
-- `archive/PROTOCOL_V1_MONOLITHIC.md` - Original monolithic protocol (Nov 2025)
-
----
-
 ## LLM Resources
 
 For Claude/AI integration:
@@ -218,5 +305,5 @@ For Claude/AI integration:
 
 ---
 
-**Last Updated**: 2026-01-24
-**Maintained By**: Antoine / Atomaste
+**Last Updated**: February 9, 2026  
+**Maintained By**: Atomizer-HQ Team (Manager, Technical Lead, Secretary) + Antoine