Atomizer/CHANGELOG.md

# Changelog

All notable changes to Atomizer will be documented in this file.

The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).

## [Unreleased]

## [0.5.0] - 2025-01-24

### Project Cleanup & Organization
- Deleted 102+ orphaned MCP session temp files
- Removed build artifacts (htmlcov, dist, __pycache__)
- Archived superseded plan documents (RALPH_LOOP V2/V3, CANVAS V3, etc.)
- Moved debug/analysis scripts from tests/ to tools/analysis/
- Updated .gitignore with missing patterns
- Cleaned empty directories

## [0.4.0] - 2025-01-22

### Canvas UX Improvements (Phases 7-9)
- **Resizable Panels**: Left sidebar (200-400px) and right panel (280-600px) with localStorage persistence
- **All Palette Items Enabled**: All 8 node types now draggable (model, solver, designVar, extractor, objective, constraint, algorithm, surrogate)
- **Solver Configuration**: Engine selection (NX Nastran, MSC Nastran, Python Script) with solution type dropdowns (SOL101-SOL200)

### AtomizerSpec v2.0
- Unified JSON configuration schema for all studies
- Added SolverEngine and NastranSolutionType types
- Canvas position persistence for all nodes
- Migration support from legacy optimization_config.json

## [0.3.0] - 2025-01-18

### Dashboard V3.1 - Canvas Builder
- Visual workflow builder with 9 node types
- Spec ↔ ReactFlow bidirectional converter
- WebSocket real-time synchronization
- Claude chat integration
- Custom extractors with in-canvas code editor
- Model introspection panel

### Learning Atomizer Core (LAC)
- Persistent memory system for accumulated knowledge
- Session insights recording (failures, workarounds, patterns)
- Optimization outcome tracking

## [0.2.5] - 2025-01-16

### GNN Surrogate for Zernike Optimization
- PolarMirrorGraph with fixed 3000-node polar grid
- ZernikeGNN model with design-conditioned convolutions
- Differentiable GPU-accelerated Zernike fitting
- Training pipeline with multi-task loss

### DevLoop Automation
- Closed-loop development system with AI agents
- Gemini planning, Claude implementation
- Playwright browser testing for dashboard UI

## [0.2.1] - 2025-01-07

### Optimization Engine v2.0 Restructure
- Reorganized into modular subpackages (core/, nx/, study/, config/)
- SpecManager for AtomizerSpec handling
- Deprecation warnings for old import paths

### Phase 3.3 - Dashboard & Multi-Solution Support (November 23, 2025)

#### Added
- **React Dashboard** with comprehensive multi-objective visualization
  - Parallel Coordinates Plot with research-based design
    - Light theme with high-visibility colors (white background, dark text)
    - Interactive trial selection and highlighting
    - Color-coded axes: Design Variables (blue) → Objectives (green) → Constraints (yellow)
    - Automatic constraint extraction from trial user_attrs
    - Support for units display (mm, MPa, Hz, g, etc.)
  - Pareto Front scatter plot for multi-objective optimization
  - Real-time WebSocket updates for live monitoring
  - FastAPI backend (port 8000) with Vite frontend (port 3003)
  - Optimizer Strategy Panel showing algorithm info and metrics
  - Comprehensive dashboard documentation: [DASHBOARD.md](docs/DASHBOARD.md)

- **NX Multi-Solution Protocol** documentation
  - Critical fix for multi-solution workflows documented
  - Best practices for static + modal, thermal + structural simulations
  - [NX_MULTI_SOLUTION_PROTOCOL.md](docs/NX_MULTI_SOLUTION_PROTOCOL.md)

- **Centralized Extractor Library**
  - `optimization_engine/extractors/` with base classes
  - Eliminates code duplication across studies
  - Unified error handling and OP2 file processing

#### Changed
- **CRITICAL FIX**: Multi-solution NX workflows now use `SolveAllSolutions()` API
  - Ensures all solutions (static + modal, etc.) complete before returning
  - Uses Foreground mode for reliable multi-solution solves
  - Prevents stale OP2 files and identical results across trials
  - Implementation in `optimization_engine/solve_simulation.py` lines 271-295

#### Fixed
- Multi-solution NX simulations only solving first solution
- Parallel coordinates plot crashes due to undefined axis labels
- Dashboard page crashes from missing data validation
- Identical frequency values across trials in multi-solution studies
- NaN values in constraint visualization

### Phase 3.2 - Integration & NX Enhancements (In Progress)

#### Added
- **NX Expression Import System** (2025-11-17)
  - Robust .exp file-based expression updates via NX journal scripts
  - Supports ALL NX expression types including binary-stored ones
  - Automatic unit detection and formatting
  - Fixes issue with `hole_count` and other feature-linked expressions
  - Documentation: [NX_EXPRESSION_IMPORT_SYSTEM.md](docs/NX_EXPRESSION_IMPORT_SYSTEM.md)
  - New journal: `import_expressions.py` for .exp file import
  - Enhanced `nx_updater.py` with `update_expressions_via_import()` method

- **4D Design Space Validation** (2025-11-17)
  - Validated full 4-variable optimization (beam_half_core_thickness, beam_face_thickness, holes_diameter, hole_count)
  - All variables now updating correctly in optimization loop
  - Mesh adaptation verified across different hole_count values

### Phase 2 - LLM Integration (Completed 85%)
- Natural language interface for optimization configuration
- Feature registry with capability catalog
- Claude skill for Atomizer navigation
- LLM workflow analyzer and extractor orchestration
- Dynamic code generation for hooks and extractors

---

## [0.2.0] - 2025-01-16

### Phase 1 - Plugin System & Infrastructure ✅

#### Added
- **Plugin Architecture**
  - Hook manager with lifecycle execution at `pre_solve`, `post_solve`, and `post_extraction` points
  - Plugin auto-discovery from `optimization_engine/plugins/` directory
  - Priority-based hook execution
  - Context passing system for hooks (output_dir, trial_number, design_variables, results)

- **Logging Infrastructure**
  - Detailed per-trial logs in `optimization_results/trial_logs/`
    - Complete iteration trace with timestamps
    - Design variables, configuration, execution timeline
    - Extracted results and constraint evaluations
  - High-level optimization progress log (`optimization.log`)
    - Configuration summary header
    - Trial START and COMPLETE entries (one line per trial)
    - Compact format for easy progress monitoring

- **Logging Plugins**
  - `detailed_logger.py` - Creates detailed trial logs
  - `optimization_logger.py` - Creates high-level optimization.log
  - `log_solve_complete.py` - Appends solve completion to trial logs
  - `log_results.py` - Appends extracted results to trial logs
  - `optimization_logger_results.py` - Appends results to optimization.log

- **Project Organization**
  - Studies folder structure with standardized layout
  - Comprehensive studies documentation ([studies/README.md](studies/README.md))
  - Model files organized in `model/` subdirectory (`.prt`, `.sim`, `.fem`)
  - Intelligent path resolution system (`atomizer_paths.py`)
  - Marker-based project root detection

- **Test Suite**
  - `test_hooks_with_bracket.py` - Hook validation test (3 trials)
  - `run_5trial_test.py` - Quick integration test (5 trials)
  - `test_journal_optimization.py` - Full optimization test

#### Changed
- Renamed `examples/` folder to `studies/`
- Moved bracket example to `studies/bracket_stress_minimization/`
- Consolidated FEA files into `model/` subfolder
- Updated all test scripts to use `atomizer_paths` for imports
- Runner now passes `output_dir` to all hook contexts

#### Removed
- Obsolete test scripts from examples/ (14 files deleted)
- `optimization_logs/` and `optimization_results/` from root directory

#### Fixed
- Log files now correctly generated in study-specific `optimization_results/` folder
- Path resolution works regardless of script location
- Hooks properly registered with `register_hooks()` function

---

## [0.1.0] - 2025-01-10

### Initial Release

#### Core Features
- Optuna integration with TPE sampler
- NX journal integration for expression updates and simulation execution
- OP2 result extraction (stress, displacement)
- Study management with folder-based isolation
- Web dashboard for real-time monitoring
- Precision control (4-decimal rounding for mm/degrees/MPa)
- Crash recovery and optimization resumption

---

## Development Timeline

- **Phase 1** (✅ Completed 2025-01-16): Plugin system & hooks
- **Phase 2** (🟡 Starting): LLM interface with natural language configuration
- **Phase 3** (Planned): Dynamic code generation for custom objectives
- **Phase 4** (Planned): Intelligent analysis and surrogate quality assessment
- **Phase 5** (Planned): Automated HTML/PDF report generation
- **Phase 6** (Planned): NX MCP server with full API documentation
- **Phase 7** (Planned): Self-improving feature registry

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**Maintainer**: Antoine Polvé (antoine@atomaste.com)
**License**: Proprietary - Atomaste © 2025