docs: Update DEVELOPMENT_GUIDANCE.md with Phase 3.3 and Organization v2.0

Updated development guidance to reflect recent completions:

- Phase 3.3 (Visualization & Model Cleanup):  100% Complete
- Study Organization v2.0:  100% Complete
- Progress: 75-85% → 80-90% Complete
- Working example: simple_beam_optimization (56 trials, 4 substudies)

Added detailed sections for:
- 6 plot types (convergence, design space, parallel coords, etc.)
- Model cleanup system (50-90% disk savings)
- Study organization structure (1_setup/, 2_substudies/, 3_reports/)
- Templates and migration tools

Updated evidence with actual implementation details and file locations.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>
This commit is contained in:
2025-11-17 19:30:58 -05:00
parent fe2ef9be6d
commit 5078759b83

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@@ -2,9 +2,9 @@
> **Living Document**: Strategic direction, current status, and development priorities for Atomizer
>
> **Last Updated**: 2025-11-17
> **Last Updated**: 2025-11-17 (Evening - Phase 3.3 Complete)
>
> **Status**: Alpha Development - 75-85% Complete, Integration Phase
> **Status**: Alpha Development - 80-90% Complete, Integration Phase
---
@@ -31,11 +31,13 @@
### Quick Stats
- **110 Python files** (~9,127 lines in core engine alone)
- **110+ Python files** (~10,000+ lines in core engine)
- **23 test files** covering major components
- **Phase 1 (Plugin System)**: ✅ 100% Complete & Production Ready
- **Phases 2.5-3.1 (LLM Intelligence)**: ✅ 85% Complete - Components Built, Integration Needed
- **Working Example Study**: Bracket displacement optimization with substudy system
- **Phase 3.3 (Visualization & Cleanup)**: ✅ 100% Complete & Production Ready
- **Study Organization v2.0**: ✅ 100% Complete with Templates
- **Working Example Study**: simple_beam_optimization (4 substudies, 56 trials, full documentation)
### Key Insight
@@ -59,9 +61,13 @@ The foundation is rock solid:
- **Precision Control**: 4-decimal rounding for engineering units
**Evidence**:
- `studies/bracket_displacement_maximizing/` has real optimization results
- 20 trials successfully completed with live history tracking
- Results: max_displacement: 0.611mm at trial 1, converging to 0.201mm at trial 20
- `studies/simple_beam_optimization/` - Complete 4D optimization study
- 4 substudies (01-04) with numbered organization
- 56 total trials across all substudies
- 4 design variables (beam thickness, face thickness, hole diameter, hole count)
- 3 objectives (displacement, stress, mass) + 1 constraint
- Full documentation with substudy READMEs
- `studies/bracket_displacement_maximizing/` - Earlier study (20 trials)
#### ✅ Plugin System (Phase 1)
**Status**: PRODUCTION READY
@@ -89,7 +95,63 @@ NX-like hierarchical studies:
- **Live incremental history** tracking
- **Clean separation** of concerns
**File**: `studies/bracket_displacement_maximizing/run_substudy.py`
**File**: `studies/simple_beam_optimization/run_optimization.py`
#### ✅ Phase 3.3: Visualization & Model Cleanup
**Status**: PRODUCTION READY
Automated post-processing system for optimization results:
- **6 Plot Types**:
- Convergence (objective vs trial with running best)
- Design space evolution (parameter changes over time)
- Parallel coordinates (high-dimensional visualization)
- Sensitivity heatmap (parameter correlation analysis)
- Constraint violations tracking
- Multi-objective breakdown
- **Output Formats**: PNG (300 DPI) + PDF (vector graphics)
- **Model Cleanup**: Selective deletion of large CAD/FEM files
- Keeps top-N best trials (default: 10)
- Preserves all results.json files
- 50-90% disk space savings typical
- **Configuration**: JSON-based `post_processing` section
**Evidence**:
- Tested on 50-trial beam optimization
- Generated 12 plot files (6 types × 2 formats)
- Plots saved to `studies/simple_beam_optimization/2_substudies/04_full_optimization_50trials/plots/`
- Documentation: `docs/PHASE_3_3_VISUALIZATION_AND_CLEANUP.md`
**Integration**: Runs automatically after optimization completes (if enabled in config)
#### ✅ Study Organization System v2.0
**Status**: PRODUCTION READY
Standardized directory structure for all optimization studies:
**Structure**:
```
studies/[study_name]/
├── 1_setup/ # Pre-optimization (model, benchmarking)
├── 2_substudies/ # Numbered runs (01_, 02_, 03_...)
└── 3_reports/ # Study-level analysis
```
**Features**:
- **Numbered Substudies**: Chronological ordering (01, 02, 03...)
- **Self-Documenting**: Each substudy has README.md with purpose/results
- **Metadata Tracking**: study_metadata.json with complete substudy registry
- **Templates**: Complete templates for new studies and substudies
- **Migration Tool**: reorganize_study.py for existing studies
**Evidence**:
- Applied to simple_beam_optimization study
- 4 substudy READMEs documenting progression
- Complete template system in `templates/`
- How-to guide: `templates/HOW_TO_CREATE_A_STUDY.md`
- Documentation: `docs/STUDY_ORGANIZATION.md`
**File**: `studies/simple_beam_optimization/study_metadata.json`
### 🚧 What's Built But Not Yet Integrated