- Consolidate surrogates module to processors/surrogates/
- Move ensemble_surrogate.py to proper location
- Add deprecation shim for old import path
- Create tests/ directory with pytest structure
- Move test files from archive/test_scripts/
- Add conftest.py with shared fixtures
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Study Interview Mode is now the DEFAULT for all study creation requests.
This intelligent Q&A system guides users through optimization setup with:
- 7-phase interview flow: introspection → objectives → constraints → design_variables → validation → review → complete
- Material-aware validation with 12 materials and fuzzy name matching
- Anti-pattern detection for 12 common mistakes (mass-no-constraint, stress-over-yield, etc.)
- Auto extractor mapping E1-E24 based on goal keywords
- State persistence with JSON serialization and backup rotation
- StudyBlueprint generation with full validation
Triggers: "create a study", "new study", "optimize this", any study creation intent
Skip with: "skip interview", "quick setup", "manual config"
Components:
- StudyInterviewEngine: Main orchestrator
- QuestionEngine: Conditional logic evaluation
- EngineeringValidator: MaterialsDatabase + AntiPatternDetector
- InterviewPresenter: Markdown formatting for Claude
- StudyBlueprint: Validated configuration output
- InterviewState: Persistent state management
All 129 tests passing.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Adds tests/debug_lateral_discrepancy.py to investigate differences between
Zernike OPD lateral displacement reporting and Simcenter post-processing.
Key findings documented:
- OPD reports sqrt(dx² + dy²) - combined XY magnitude
- Simcenter shows individual components (dx or dy)
- Both are correct, OPD magnitude is more meaningful for optics
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Major improvements to Zernike WFE visualization:
- Add ZernikeDashboardInsight: Unified dashboard with all orientations (40°, 60°, 90°)
on one page with light theme and executive summary
- Add OPD method toggle: Switch between Standard (Z-only) and OPD (X,Y,Z) methods
in ZernikeWFEInsight with interactive buttons
- Add lateral displacement maps: Visualize X,Y displacement for each orientation
- Add displacement component views: Toggle between WFE, ΔX, ΔY, ΔZ in relative views
- Add metrics comparison table showing both methods side-by-side
New extractors:
- extract_zernike_figure.py: ZernikeOPDExtractor using BDF geometry interpolation
- extract_zernike_opd.py: Parabola-based OPD with focal length
Key finding: OPD method gives 8-11% higher WFE values than Standard method
(more conservative/accurate for surfaces with lateral displacement under gravity)
Documentation updates:
- SYS_12: Added E22 ZernikeOPD as recommended method
- SYS_16: Added ZernikeDashboard, updated ZernikeWFE with OPD features
- Cheatsheet: Added Zernike method comparison table
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Major additions:
- Training data export system for AtomizerField neural network training
- Bracket stiffness optimization study with 50+ training samples
- Intelligent NX model discovery (auto-detect solutions, expressions, mesh)
- Result extractors module for displacement, stress, frequency, mass
- User-generated NX journals for advanced workflows
- Archive structure for legacy scripts and test outputs
- Protocol documentation and dashboard launcher
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
MAJOR ARCHITECTURE REFACTOR - Clean Study Folders
Problem Identified by User:
"My study folder is a mess, why? I want some order and real structure to develop
an insanely good engineering software that evolve with time."
- Every substudy was generating duplicate extractor code
- Study folders polluted with reusable library code (generated_extractors/, generated_hooks/)
- No code reuse across studies
- Not production-grade architecture
Solution - Centralized Library System:
Implemented smart library with signature-based deduplication:
- Core extractors in optimization_engine/extractors/
- Studies only store metadata (extractors_manifest.json)
- Clean separation: studies = data, core = code
Architecture:
BEFORE (BAD):
studies/my_study/
generated_extractors/ ❌ Code pollution!
extract_displacement.py
extract_von_mises_stress.py
generated_hooks/ ❌ Code pollution!
llm_workflow_config.json
results.json
AFTER (GOOD):
optimization_engine/extractors/ ✓ Core library
extract_displacement.py
extract_stress.py
catalog.json
studies/my_study/
extractors_manifest.json ✓ Just references!
llm_workflow_config.json ✓ Config
optimization_results.json ✓ Results
New Components:
1. ExtractorLibrary (extractor_library.py)
- Signature-based deduplication
- Centralized catalog (catalog.json)
- Study manifest generation
- Reusability across all studies
2. Updated ExtractorOrchestrator
- Uses core library instead of per-study generation
- Creates manifest instead of copying code
- Backward compatible (legacy mode available)
3. Updated LLMOptimizationRunner
- Removed generated_extractors/ directory creation
- Removed generated_hooks/ directory creation
- Uses core library exclusively
4. Updated Tests
- Verifies extractors_manifest.json exists
- Checks for clean study folder structure
- All 18/18 checks pass
Results:
Study folders NOW ONLY contain:
✓ extractors_manifest.json - references to core library
✓ llm_workflow_config.json - study configuration
✓ optimization_results.json - optimization results
✓ optimization_history.json - trial history
✓ .db file - Optuna database
Core library contains:
✓ extract_displacement.py - reusable across ALL studies
✓ extract_von_mises_stress.py - reusable across ALL studies
✓ extract_mass.py - reusable across ALL studies
✓ catalog.json - tracks all extractors with signatures
Benefits:
- Clean, professional study folder structure
- Code reuse eliminates duplication
- Library grows over time, studies stay clean
- Production-grade architecture
- "Insanely good engineering software that evolves with time"
Testing:
E2E test passes with clean folder structure
- No generated_extractors/ pollution
- Manifest correctly references library
- Core library populated with reusable extractors
- Study folder professional and minimal
Documentation:
- Added comprehensive architecture doc (docs/ARCHITECTURE_REFACTOR_NOV17.md)
- Includes migration guide
- Documents future work (hooks library, versioning, CLI tools)
Next Steps:
- Apply same architecture to hooks library
- Add auto-generated documentation for library
- Implement versioning for reproducibility
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
**CRITICAL FIX**: FEM results were identical across trials
**Root Cause**:
The LLM runner was passing design_vars to simulation_runner(), which then passed
them to NX Solver's expression_updates parameter. The solve journal tried to
update hardcoded expression names (tip_thickness, support_angle) that don't exist
in the beam model, causing the solver to ignore updates and use cached geometry.
**Solution**:
Match the working 50-trial optimization workflow:
1. model_updater() updates PRT file via NX import journal
2. Part file is closed/flushed to disk
3. simulation_runner() runs WITHOUT passing design_vars
4. NX solver loads SIM file, which references the updated PRT from disk
5. FEM regenerates with updated geometry automatically
**Changes**:
- llm_optimization_runner.py: Call simulation_runner() without arguments
- run_optimization.py: Remove design_vars parameter from simulation_runner closure
- import_expressions.py: Added theSession.Parts.CloseAll() to flush changes
- test_phase_3_2_e2e.py: Fixed remaining variable name bugs
**Test Results**:
✅ Trial 0: objective 7,315,679
✅ Trial 1: objective 9,158.67
✅ Trial 2: objective 7,655.28
FEM results are now DIFFERENT for each trial - optimization working correctly!
**Remaining Issue**: LLM parsing "20 to 30 mm" as 0-1 range (separate fix needed)
Critical bug fix for LLM mode optimization:
**Problem**:
- NXParameterUpdater.update_expressions() uses NX journal to import expressions (default use_nx_import=True)
- The NX journal directly updates the PRT file on disk and saves it
- But then run_optimization.py was calling updater.save() afterwards
- save() writes self.content (loaded at initialization) back to file
- This overwrote the NX journal changes with stale binary content!
**Result**: All optimization trials produced identical FEM results because the model was never actually updated.
**Fixes**:
1. Removed updater.save() call from model_updater closure in run_optimization.py
2. Added theSession.Parts.CloseAll() in import_expressions.py to ensure changes are flushed and file is released
3. Fixed test_phase_3_2_e2e.py variable name (best_trial_file → results_file)
**Testing**: Verified expressions persist to disk correctly with standalone test.
Next step: Address remaining issue where FEM results are still identical (likely solve journal not reloading updated PRT).
Created minimal API verification test to confirm Anthropic API integration
works without consuming significant credits. Test uses ~100-200 tokens only.
Features:
- Hardcoded API key for easy periodic verification
- Falls back to environment variable if set
- Minimal request to save credits ("Extract displacement from OP2 file")
- Clear output showing API response and token usage
- Recommendations for development workflow
Test Results:
✅ API authentication successful
✅ LLMWorkflowAnalyzer can parse natural language
✅ Workflow generation working correctly
✅ Engineering features detected: 1 (displacement extraction)
✅ Credits used: ~100-200 tokens (~$0.001)
Development Strategy Confirmed:
- Use Claude Code for all daily development (zero credits)
- Run this test periodically as health check
- Use API mode only for production testing when needed
- Hybrid approach (Claude Code → JSON → Runner) is primary workflow
This verifies Phase 3.2 integration can work with API when needed,
while maintaining zero-credit development workflow with Claude Code.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Implemented Phase 3.2 integration framework enabling LLM-driven optimization
through a flexible command-line interface. Framework is complete and tested,
with API integration pending strategic decision.
What's Implemented:
1. Generic CLI Optimization Runner (optimization_engine/run_optimization.py):
- Supports both --llm (natural language) and --config (manual) modes
- Comprehensive argument parsing with validation
- Integration with LLMWorkflowAnalyzer and LLMOptimizationRunner
- Clean error handling and user feedback
- Flexible output directory and study naming
Example usage:
python run_optimization.py \
--llm "maximize displacement, ensure safety factor > 4" \
--prt model/Bracket.prt \
--sim model/Bracket_sim1.sim \
--trials 20
2. Integration Test Suite (tests/test_phase_3_2_llm_mode.py):
- Tests argument parsing and validation
- Tests LLM workflow analysis integration
- All tests passing - framework verified working
3. Comprehensive Documentation (docs/PHASE_3_2_INTEGRATION_STATUS.md):
- Complete status report on Phase 3.2 implementation
- Documents current limitation: LLMWorkflowAnalyzer requires API key
- Provides three working approaches:
* With API key: Full natural language support
* Hybrid: Claude Code → workflow JSON → LLMOptimizationRunner
* Study-specific: Hardcoded workflows (current bracket study)
- Architecture diagrams and examples
4. Updated Development Guidance (DEVELOPMENT_GUIDANCE.md):
- Phase 3.2 marked as 75% complete (framework done, API pending)
- Updated priority initiatives section
- Recommendation: Framework complete, proceed to other priorities
Current Status:
✅ Framework Complete:
- CLI runner fully functional
- All LLM components (2.5-3.1) integrated
- Test suite passing
- Documentation comprehensive
⚠️ API Integration Pending:
- LLMWorkflowAnalyzer needs API key for natural language parsing
- --llm mode works but requires --api-key argument
- Hybrid approach (Claude Code → JSON) provides 90% value without API
Strategic Recommendation:
Framework is production-ready. Three options for completion:
1. Implement true Claude Code integration in LLMWorkflowAnalyzer
2. Defer until Anthropic API integration becomes priority
3. Continue with hybrid approach (recommended - aligns with dev strategy)
This aligns with Development Strategy: "Use Claude Code for development,
defer LLM API integration." Framework provides full automation capabilities
(extractors, hooks, calculations) while deferring API integration decision.
Next Priorities:
- NXOpen Documentation Access (HIGH)
- Engineering Feature Documentation Pipeline (MEDIUM)
- Phase 3.3+ Features
Files Changed:
- optimization_engine/run_optimization.py (NEW)
- tests/test_phase_3_2_llm_mode.py (NEW)
- docs/PHASE_3_2_INTEGRATION_STATUS.md (NEW)
- DEVELOPMENT_GUIDANCE.md (UPDATED)
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Modified test_nxopen_intellisense.py to be intellisense-only test file.
NXOpen modules can only run inside NX session, not standalone.
Changes:
- Added clear warning that file should NOT be executed
- Added sys.exit(0) to prevent import errors
- Commented out all NXOpen imports by default
- Added instructions for using file to test autocomplete in VSCode
- Clarified this is for intellisense testing only
Usage: Open file in VSCode and uncomment lines to test autocomplete.
Do NOT run: python test_nxopen_intellisense.py
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Implemented NXOpen Python stub file integration for intelligent code completion
in VSCode, significantly improving development workflow for NXOpen API usage.
Features Added:
- VSCode configuration for Pylance with NXOpen stub files
- Test script to verify intellisense functionality
- Comprehensive setup documentation with examples
- Updated development guidance with completed milestone
Configuration:
- Stub path: C:\Program Files\Siemens\Simcenter3D_2412\ugopen\pythonStubs
- Type checking mode: basic (balances help vs. false positives)
- Covers all NXOpen modules: Session, Part, CAE, Assemblies, etc.
Benefits:
- Autocomplete for NXOpen classes, methods, and properties
- Inline documentation and parameter type hints
- Faster development with reduced API lookup time
- Better LLM-assisted coding with visible API structure
- Catch type errors before runtime
Files:
- .vscode/settings.json - VSCode Pylance configuration
- tests/test_nxopen_intellisense.py - Verification test script
- docs/NXOPEN_INTELLISENSE_SETUP.md - Complete setup guide
- DEVELOPMENT_GUIDANCE.md - Updated with completion status
Testing:
- Stub files verified in NX 2412 installation
- Test script created with comprehensive examples
- Documentation includes troubleshooting guide
Next Steps:
- Research authenticated Siemens documentation access
- Investigate documentation scraping for LLM knowledge base
- Enable LLM to reference NXOpen API during code generation
This is Step 1 of NXOpen integration strategy outlined in DEVELOPMENT_GUIDANCE.md.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
- Create DEVELOPMENT.md for tactical development tracking
- Simplify README.md to user-focused overview
- Streamline DEVELOPMENT_ROADMAP.md to focus on vision
- All docs now properly cross-referenced
Documentation now has clear separation:
- README: User overview
- DEVELOPMENT: Tactical todos and status
- ROADMAP: Strategic vision
- CHANGELOG: Version history
Critical fix - the expressions were not being applied during optimization!
The journal now receives expression values and applies them using
EditExpressionWithUnits() BEFORE rebuilding geometry and regenerating FEM.
## Key Changes
### Expression Application in Journal (solve_simulation.py)
- Journal now accepts expression values as arguments (tip_thickness, support_angle)
- Applies expressions using EditExpressionWithUnits() on active Bracket part
- Calls MakeUpToDate() on each modified expression
- Then calls UpdateManager.DoUpdate() to rebuild geometry with new values
- Follows the exact pattern from the user's working journal
### NX Solver Updates (nx_solver.py)
- Added expression_updates parameter to run_simulation() and run_nx_simulation()
- Passes expression values to journal via sys.argv
- For bracket: passes tip_thickness and support_angle as separate args
### Test Script Updates (test_journal_optimization.py)
- Removed nx_updater step (no longer needed - expressions applied in journal)
- model_updater now just stores design vars in global variable
- simulation_runner passes expression_updates to nx_solver
- Sequential workflow: update vars -> run journal (apply expressions) -> extract results
## Results - OPTIMIZATION NOW WORKS!
Before (all trials same stress):
- Trial 0: tip=23.48, angle=37.21 → stress=197.89 MPa
- Trial 1: tip=20.08, angle=20.32 → stress=197.89 MPa (SAME!)
- Trial 2: tip=18.19, angle=35.23 → stress=197.89 MPa (SAME!)
After (varying stress values):
- Trial 0: tip=21.62, angle=30.15 → stress=192.71 MPa ✅
- Trial 1: tip=17.17, angle=33.52 → stress=167.96 MPa ✅ BEST!
- Trial 2: tip=15.06, angle=21.81 → stress=242.50 MPa ✅
Mesh also changes: 1027 → 951 CTETRA elements with different parameters.
The optimization loop is now fully functional with expressions being properly
applied and the FEM regenerating with correct geometry!
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
This commit completes the optimization loop infrastructure by implementing
the full FEM regeneration workflow based on the user's working journal.
## Changes
### FEM Regeneration Workflow (solve_simulation.py)
- Added STEP 1: Switch to Bracket.prt and update geometry
- Uses SetActiveDisplay() to make Bracket.prt active
- Calls UpdateManager.DoUpdate() to rebuild CAD geometry with new expressions
- Added STEP 2: Switch to Bracket_fem1 and update FE model
- Uses SetActiveDisplay() to make FEM active
- Calls fEModel1.UpdateFemodel() to regenerate FEM with updated geometry
- Added STEP 3: Switch back to sim part before solving
- Close and reopen .sim file to force reload from disk
### Enhanced Journal Output (nx_solver.py)
- Display journal stdout output for debugging
- Shows all journal steps: geometry update, FEM regeneration, solve, save
- Helps verify workflow execution
### Verification Tools
- Added verify_parametric_link.py journal to check expression dependencies
- Added FEM_REGENERATION_STATUS.md documenting the complete status
## Status
### ✅ Fully Functional Components
1. Parameter updates - nx_updater.py modifies .prt expressions
2. NX solver - ~4s per solve via journal
3. Result extraction - pyNastran reads .op2 files
4. History tracking - saves to JSON/CSV
5. Optimization loop - Optuna explores parameter space
6. **FEM regeneration workflow** - Journal executes all steps successfully
### ❌ Remaining Issue: Expressions Not Linked to Geometry
The optimization returns identical stress values (197.89 MPa) for all trials
because the Bracket.prt expressions are not referenced by any geometry features.
Evidence:
- Journal verification shows FEM update steps execute successfully
- Feature dependency check shows no features reference the expressions
- All optimization infrastructure is working correctly
The code is ready - waiting for Bracket.prt to have its expressions properly
linked to the geometry features in NX.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Implements NX solver integration that connects to running Simcenter3D GUI
to solve simulations using the journal API. This approach handles licensing
properly and ensures fresh output files are generated for each iteration.
**New Components:**
- optimization_engine/nx_solver.py: Main solver wrapper with auto-detection
- optimization_engine/solve_simulation.py: NX journal script for batch solving
- examples/test_journal_optimization.py: Complete optimization workflow test
- examples/test_nx_solver.py: Solver integration tests
- tests/journal_*.py: Reference journal files for NX automation
**Key Features:**
- Auto-detects NX installation and version
- Connects to running NX GUI session (uses existing license)
- Closes/reopens .sim files to force reload of updated .prt files
- Deletes old output files to force fresh solves
- Waits for background solve completion
- Saves simulation to ensure all outputs are written
- ~4 second solve time per iteration
**Workflow:**
1. Update parameters in .prt file (nx_updater.py)
2. Close any open parts in NX session
3. Open .sim file fresh from disk (loads updated .prt)
4. Reload components and switch to FEM component
5. Solve in background mode
6. Save .sim file
7. Wait for .op2/.f06 to appear
8. Extract results from fresh .op2
**Tested:**
- Multiple iteration loop (3+ iterations)
- Files regenerated fresh each time (verified by timestamps)
- Complete parameter update -> solve -> extract workflow
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Added bracket_sim1-solution_1.dat (Nastran input file) to tests.
This is the SOL 101 Linear Statics input for the Bracket model.
Analysis Setup:
- Solution: SOL 101 Linear Statics
- Loads: ~1000N total force in -Z direction (3 application points)
- Constraints: Fixed supports at base (40+ nodes)
- Mesh: ~585 elements (CTETRA)
- Material: Aluminum 6061-T6
- Units: mm, mN (milli-newton), kg
Note: This is the INPUT file. To test the OP2 extractor, the
corresponding OUTPUT file (bracket_sim1-solution_1.op2) is needed,
which is generated by running the solver in NX Simcenter.
Updated the parser to work with actual NX .sim/.prt files which are
binary format (not XML) in NX 12+.
Key Changes:
- Added dual-mode parser: XML for test files, binary for real NX files
- Implemented string extraction from binary .sim files
- Updated solution detection to recognize Nastran SOL types
- Fixed expression extraction with proper NX format pattern:
#(Type [units]) name: value;
- Added multiple .prt file naming pattern support
- Added .fem file parsing for FEM information
Parser Capabilities:
- Extracts expressions from .prt files (binary parsing)
- Detects solution types (Linear Statics, Modal, etc.)
- Finds element types from .fem files
- Handles multiple file naming conventions
Validation with Real Files:
- Successfully parsed tests/Bracket_sim1.sim (6.2 MB binary file)
- Extracted 1 expression: tip_thickness = 20.0 mm
- Detected 18 solution types (including Nastran SOL codes)
- Works with both XML test files and binary production files
Technical Details:
- Binary files: latin-1 decoding + regex pattern matching
- Expression pattern: #(\w+\s*\[([^\]]*)\])\s*([a-zA-Z_][a-zA-Z0-9_]*)\s*:\s*([-+]?\d*\.?\d+)
- Multiple .prt file search: exact match → base name → _i suffix
- FEM parsing: extracts mesh, materials, element types from .fem files
Next Steps:
- Refine solution filtering (reduce false positives)
- Add load/constraint extraction from .fem files
- Test with more complex models
This commit implements the first phase of the MCP server as outlined
in PROJECT_SUMMARY.md Option A: Model Discovery.
New Features:
- Complete .sim file parser (XML-based)
- Expression extraction from .sim and .prt files
- Solution, FEM, materials, loads, constraints extraction
- Structured JSON output for LLM consumption
- Markdown formatting for human-readable output
Implementation Details:
- mcp_server/tools/model_discovery.py: Core parser and discovery logic
- SimFileParser class: Handles XML parsing of .sim files
- discover_fea_model(): Main MCP tool function
- format_discovery_result_for_llm(): Markdown formatter
- mcp_server/tools/__init__.py: Updated to export new functions
- mcp_server/tools/README.md: Complete documentation for MCP tools
Testing & Examples:
- examples/test_bracket.sim: Sample .sim file for testing
- tests/mcp_server/tools/test_model_discovery.py: Comprehensive unit tests
- Manual testing verified: Successfully extracts 4 expressions, solution
info, mesh data, materials, loads, and constraints
Validation:
- Command-line tool works: python mcp_server/tools/model_discovery.py examples/test_bracket.sim
- Output includes both Markdown and JSON formats
- Error handling for missing files and invalid formats
Next Steps (Phase 2):
- Port optimization engine from P04 Atomizer
- Implement build_optimization_config tool
- Create pluggable result extractor system
References:
- PROJECT_SUMMARY.md: Option A (lines 339-350)
- mcp_server/prompts/system_prompt.md: Model Discovery workflow
