feat: Add Protocol 13 adaptive optimization, Plotly charts, and dashboard improvements
## Protocol 13: Adaptive Multi-Objective Optimization - Iterative FEA + Neural Network surrogate workflow - Initial FEA sampling, NN training, NN-accelerated search - FEA validation of top NN predictions, retraining loop - adaptive_state.json tracks iteration history and best values - M1 mirror study (V11) with 103 FEA, 3000 NN trials ## Dashboard Visualization Enhancements - Added Plotly.js interactive charts (parallel coords, Pareto, convergence) - Lazy loading with React.lazy() for performance - Code splitting: plotly.js-basic-dist (~1MB vs 3.5MB) - Chart library toggle (Recharts default, Plotly on-demand) - ExpandableChart component for full-screen modal views - ConsoleOutput component for real-time log viewing ## Documentation - Protocol 13 detailed documentation - Dashboard visualization guide - Plotly components README - Updated run-optimization skill with Mode 5 (adaptive) ## Bug Fixes - Fixed TypeScript errors in dashboard components - Fixed Card component to accept ReactNode title - Removed unused imports across components 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
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Antoine
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This document describes the multi-part assembly FEM workflow used when optimizing complex assemblies with `.afm` (Assembly FEM) files.
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## CRITICAL: Working Copy Requirement
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**NEVER run optimization directly on user's master model files.**
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Before any optimization run, ALL model files must be copied to the study's working directory:
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```
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Source (NEVER MODIFY) Working Copy (optimization runs here)
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────────────────────────────────────────────────────────────────────────────
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C:/Users/.../M1-Gigabit/Latest/ studies/{study}/1_setup/model/
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├── M1_Blank.prt → ├── M1_Blank.prt
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├── M1_Blank_fem1.fem → ├── M1_Blank_fem1.fem
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├── M1_Blank_fem1_i.prt → ├── M1_Blank_fem1_i.prt
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├── M1_Vertical_Support_Skeleton.prt → ├── M1_Vertical_Support_Skeleton.prt
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├── ASSY_M1_assyfem1.afm → ├── ASSY_M1_assyfem1.afm
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└── ASSY_M1_assyfem1_sim1.sim → └── ASSY_M1_assyfem1_sim1.sim
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```
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**Why**: Optimization iteratively modifies expressions, meshes, and saves files. If corruption occurs during iteration (solver crash, bad parameter combo), the working copy can be deleted and re-copied. Master files remain safe.
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**Files to Copy**:
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- `*.prt` - All part files (geometry + idealized)
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- `*.fem` - All FEM files
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- `*.afm` - Assembly FEM files
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- `*.sim` - Simulation files
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- `*.exp` - Expression files (if any)
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## Overview
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Assembly FEMs have a more complex dependency chain than single-part simulations:
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@@ -40,6 +67,29 @@ Open M1_Blank.prt
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The `.prt` file contains the parametric CAD model with expressions that drive dimensions. These expressions are updated with new design parameter values, then the geometry is rebuilt.
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### Step 1b: Update ALL Linked Geometry Parts (CRITICAL!)
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**⚠️ THIS STEP IS CRITICAL - SKIPPING IT CAUSES CORRUPT RESULTS ⚠️**
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```
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For each geometry part with linked expressions:
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├── Open M1_Vertical_Support_Skeleton.prt
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├── DoUpdate() - propagate linked expression changes
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├── Geometry rebuilds to match M1_Blank
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└── Save part
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```
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**Why this is critical:**
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- M1_Vertical_Support_Skeleton has expressions linked to M1_Blank
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- When M1_Blank geometry changes, the support skeleton MUST also update
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- If not updated, FEM nodes will be at OLD positions → nodes not coincident → merge fails
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- Result: "billion nm" RMS values (corrupt displacement data)
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**Rule: YOU MUST UPDATE ALL GEOMETRY PARTS UNDER THE .sim FILE!**
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- If there are 5 geometry parts, update all 5
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- If there are 10 geometry parts, update all 10
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- Unless explicitly told otherwise in the study config
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### Step 2: Update Component FEM Files (.fem)
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```
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@@ -180,9 +230,100 @@ See `optimization_engine/solve_simulation.py` for the full implementation:
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- `update_assembly_fem()` - Step 3 implementation
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- `solve_simulation_file()` - Step 4 implementation
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## HEEDS-Style Iteration Folder Management (V9+)
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For complex assemblies, each optimization trial uses a fresh copy of the master model:
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```
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study_name/
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├── 1_setup/
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│ └── model/ # Master model files (NEVER MODIFY)
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│ ├── ASSY_M1.prt
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│ ├── ASSY_M1_assyfem1.afm
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│ ├── ASSY_M1_assyfem1_sim1.sim
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│ ├── M1_Blank.prt
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│ ├── M1_Blank_fem1.fem
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│ └── ...
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├── 2_iterations/
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│ ├── iter0/ # Trial 0 working copy
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│ │ ├── [all model files]
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│ │ ├── params.exp # Expression values for this trial
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│ │ └── results/ # OP2, Zernike CSV, etc.
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│ ├── iter1/ # Trial 1 working copy
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│ └── ...
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└── 3_results/
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└── study.db # Optuna database
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```
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### Why Fresh Copies Per Iteration?
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1. **Corruption isolation**: If mesh regeneration fails mid-trial, only that iteration is affected
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2. **Reproducibility**: Can re-run any trial by using its params.exp
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3. **Debugging**: All intermediate files preserved for post-mortem analysis
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4. **Parallelization**: Multiple NX sessions could run different iterations (future)
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### Iteration Folder Contents
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| File | Purpose |
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|------|---------|
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| `*.prt, *.fem, *.afm, *.sim` | Fresh copy of all NX model files |
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| `params.exp` | Expression file with trial parameter values |
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| `*-solution_1.op2` | Nastran results (after solve) |
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| `results/zernike_trial_N.csv` | Extracted Zernike metrics |
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### 0-Based Iteration Numbering
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Iterations are numbered starting from 0 to match Optuna trial numbers:
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- `iter0` = Optuna trial 0 = Dashboard shows trial 0
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- `iter1` = Optuna trial 1 = Dashboard shows trial 1
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This ensures cross-referencing between dashboard, database, and file system is straightforward.
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## Multi-Subcase Solutions
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For gravity analysis at multiple orientations, use subcases:
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```
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Simulation Setup in NX:
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├── Subcase 1: 90 deg elevation (zenith/polishing)
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├── Subcase 2: 20 deg elevation (low angle reference)
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├── Subcase 3: 40 deg elevation
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└── Subcase 4: 60 deg elevation
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```
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### Solving All Subcases
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Use `solution_name=None` or `solve_all_subcases=True` to ensure all subcases are solved:
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```json
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"nx_settings": {
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"solution_name": "Solution 1",
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"solve_all_subcases": true
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}
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```
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### Subcase ID Mapping
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NX subcase IDs (1, 2, 3, 4) may not match the angle labels. Always define explicit mapping:
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```json
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"zernike_settings": {
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"subcases": ["1", "2", "3", "4"],
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"subcase_labels": {
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"1": "90deg",
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"2": "20deg",
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"3": "40deg",
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"4": "60deg"
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},
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"reference_subcase": "2"
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}
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```
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## Tips
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1. **Start with baseline solve**: Before optimization, manually verify the full workflow completes in NX
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2. **Check mesh quality**: Poor mesh quality after updates can cause solve failures
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3. **Monitor memory**: Assembly FEMs with many components use significant memory
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4. **Use Foreground mode**: For multi-subcase solutions, Foreground mode ensures all subcases complete
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5. **Validate OP2 data**: Check for corrupt results (all zeros, unrealistic magnitudes) before processing
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6. **Preserve user NX sessions**: NXSessionManager tracks PIDs to avoid closing user's NX instances
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