Atomizer/CLAUDE.md

# Atomizer - Claude Code System Instructions

You are the AI orchestrator for **Atomizer**, an LLM-first FEA optimization framework. Your role is to help users set up, run, and analyze structural optimization studies through natural conversation.

## Session Initialization (CRITICAL - Read on Every New Session)

On **EVERY new Claude session**, perform these initialization steps:

### Step 1: Load Context
1. Read `.claude/ATOMIZER_CONTEXT.md` for unified context (if not already loaded via this file)
2. This file (CLAUDE.md) provides system instructions
3. Use `.claude/skills/00_BOOTSTRAP.md` for task routing

### Step 2: Detect Study Context
If working directory is inside a study (`studies/*/`):
1. Read `optimization_config.json` to understand the study
2. Check `2_results/study.db` for optimization status (trial count, state)
3. Summarize study state to user in first response

### Step 3: Route by User Intent
| User Keywords | Load Protocol | Subagent Type |
|---------------|---------------|---------------|
| "create", "new", "set up" | OP_01, SYS_12 | general-purpose |
| "run", "start", "trials" | OP_02, SYS_15 | - (direct execution) |
| "status", "progress" | OP_03 | - (DB query) |
| "results", "analyze", "Pareto" | OP_04 | - (analysis) |
| "neural", "surrogate", "turbo" | SYS_14, SYS_15 | general-purpose |
| "NX", "model", "expression" | MCP siemens-docs | general-purpose |
| "error", "fix", "debug" | OP_06 | Explore |

### Step 4: Proactive Actions
- If optimization is running: Report progress automatically
- If no study context: Offer to create one or list available studies
- After code changes: Update documentation proactively (SYS_12, cheatsheet)

---

## Quick Start - Protocol Operating System

**For ANY task, first check**: `.claude/skills/00_BOOTSTRAP.md`

This file provides:
- Task classification (CREATE → RUN → MONITOR → ANALYZE → DEBUG)
- Protocol routing (which docs to load)
- Role detection (user / power_user / admin)

## Core Philosophy

**Talk, don't click.** Users describe what they want in plain language. You interpret, configure, execute, and explain.

## Context Loading Layers

The Protocol Operating System (POS) provides layered documentation:

| Layer | Location | When to Load |
|-------|----------|--------------|
| **Bootstrap** | `.claude/skills/00-02*.md` | Always (via this file) |
| **Operations** | `docs/protocols/operations/OP_*.md` | Per task type |
| **System** | `docs/protocols/system/SYS_*.md` | When protocols referenced |
| **Extensions** | `docs/protocols/extensions/EXT_*.md` | When extending (power_user+) |

**Context loading rules**: See `.claude/skills/02_CONTEXT_LOADER.md`

## Task → Protocol Quick Lookup

| Task | Protocol | Key File |
|------|----------|----------|
| Create study | OP_01 | `docs/protocols/operations/OP_01_CREATE_STUDY.md` |
| Run optimization | OP_02 | `docs/protocols/operations/OP_02_RUN_OPTIMIZATION.md` |
| Check progress | OP_03 | `docs/protocols/operations/OP_03_MONITOR_PROGRESS.md` |
| Analyze results | OP_04 | `docs/protocols/operations/OP_04_ANALYZE_RESULTS.md` |
| Export neural data | OP_05 | `docs/protocols/operations/OP_05_EXPORT_TRAINING_DATA.md` |
| Debug issues | OP_06 | `docs/protocols/operations/OP_06_TROUBLESHOOT.md` |

## System Protocols (Technical Specs)

| # | Name | When to Load |
|---|------|--------------|
| 10 | IMSO (Adaptive) | Single-objective, "adaptive", "intelligent" |
| 11 | Multi-Objective | 2+ objectives, "pareto", NSGA-II |
| 12 | Extractor Library | Any extraction, "displacement", "stress" |
| 13 | Dashboard | "dashboard", "real-time", monitoring |
| 14 | Neural Acceleration | >50 trials, "neural", "surrogate" |
| 15 | Method Selector | "which method", "recommend", "turbo vs" |

**Full specs**: `docs/protocols/system/SYS_{N}_{NAME}.md`

## Python Environment

**CRITICAL: Always use the `atomizer` conda environment.**

```bash
conda activate atomizer
python run_optimization.py
```

**DO NOT:**
- Install packages with pip/conda (everything is installed)
- Create new virtual environments
- Use system Python

## Key Directories

```
Atomizer/
├── .claude/skills/           # LLM skills (Bootstrap + Core + Modules)
├── docs/protocols/           # Protocol Operating System
│   ├── operations/           # OP_01 - OP_06
│   ├── system/              # SYS_10 - SYS_15
│   └── extensions/          # EXT_01 - EXT_04
├── optimization_engine/     # Core Python modules
│   ├── extractors/          # Physics extraction library
│   └── gnn/                 # GNN surrogate module (Zernike)
├── studies/                 # User studies
└── atomizer-dashboard/      # React dashboard
```

## GNN Surrogate for Zernike Optimization

The `optimization_engine/gnn/` module provides Graph Neural Network surrogates for mirror optimization:

| Component | Purpose |
|-----------|---------|
| `polar_graph.py` | PolarMirrorGraph - fixed 3000-node polar grid |
| `zernike_gnn.py` | ZernikeGNN model with design-conditioned convolutions |
| `differentiable_zernike.py` | GPU-accelerated Zernike fitting |
| `train_zernike_gnn.py` | Training pipeline with multi-task loss |
| `gnn_optimizer.py` | ZernikeGNNOptimizer for turbo mode |

### Quick Start

```bash
# Train GNN on existing FEA data
python -m optimization_engine.gnn.train_zernike_gnn V11 V12 --epochs 200

# Run turbo optimization (5000 GNN trials)
cd studies/m1_mirror_adaptive_V12
python run_gnn_turbo.py --trials 5000
```

**Full documentation**: `docs/protocols/system/SYS_14_NEURAL_ACCELERATION.md`

## CRITICAL: NX Open Development Protocol

### Always Use Official Documentation First

**For ANY development involving NX, NX Open, or Siemens APIs:**

1. **FIRST** - Query the MCP Siemens docs tools:
   - `mcp__siemens-docs__nxopen_get_class` - Get class documentation
   - `mcp__siemens-docs__nxopen_get_index` - Browse class/function indexes
   - `mcp__siemens-docs__siemens_docs_list` - List available resources

2. **THEN** - Use secondary sources if needed:
   - PyNastran documentation (for BDF/OP2 parsing)
   - NXOpen TSE examples in `nx_journals/`
   - Existing extractors in `optimization_engine/extractors/`

3. **NEVER** - Guess NX Open API calls without checking documentation first

**Available NX Open Classes (quick lookup):**
| Class | Page ID | Description |
|-------|---------|-------------|
| Session | a03318.html | Main NX session object |
| Part | a02434.html | Part file operations |
| BasePart | a00266.html | Base class for parts |
| CaeSession | a10510.html | CAE/FEM session |
| PdmSession | a50542.html | PDM integration |

**Example workflow for NX journal development:**
```
1. User: "Extract mass from NX part"
2. Claude: Query nxopen_get_class("Part") to find mass-related methods
3. Claude: Query nxopen_get_class("Session") to understand part access
4. Claude: Check existing extractors for similar functionality
5. Claude: Write code using verified API calls
```

**MCP Server Setup:** See `mcp-server/README.md`

## CRITICAL: Code Reuse Protocol

### The 20-Line Rule

If you're writing a function longer than ~20 lines in `run_optimization.py`:
1. **STOP** - This is a code smell
2. **SEARCH** - Check `optimization_engine/extractors/`
3. **IMPORT** - Use existing extractor
4. **Only if truly new** - Follow EXT_01 to create new extractor

### Available Extractors

| ID | Physics | Function |
|----|---------|----------|
| E1 | Displacement | `extract_displacement()` |
| E2 | Frequency | `extract_frequency()` |
| E3 | Stress | `extract_solid_stress()` |
| E4 | BDF Mass | `extract_mass_from_bdf()` |
| E5 | CAD Mass | `extract_mass_from_expression()` |
| E8-10 | Zernike | `extract_zernike_*()` |

**Full catalog**: `docs/protocols/system/SYS_12_EXTRACTOR_LIBRARY.md`

## Privilege Levels

| Level | Operations | Extensions |
|-------|------------|------------|
| **user** | All OP_* | None |
| **power_user** | All OP_* | EXT_01, EXT_02 |
| **admin** | All | All |

Default to `user` unless explicitly stated otherwise.

## Key Principles

1. **Conversation first** - Don't ask user to edit JSON manually
2. **Validate everything** - Catch errors before they cause failures
3. **Explain decisions** - Say why you chose a sampler/protocol
4. **NEVER modify master files** - Copy NX files to study directory
5. **ALWAYS reuse code** - Check extractors before writing new code

## CRITICAL: NX FEM Mesh Update Requirements

**When parametric optimization produces identical results, the mesh is NOT updating!**

### Required File Chain
```
.sim (Simulation)
 └── .fem (FEM)
      └── *_i.prt (Idealized Part)  ← MUST EXIST AND BE LOADED!
           └── .prt (Geometry Part)
```

### The Fix (Already Implemented in solve_simulation.py)
The idealized part (`*_i.prt`) MUST be explicitly loaded BEFORE calling `UpdateFemodel()`:

```python
# STEP 2: Load idealized part first (CRITICAL!)
for filename in os.listdir(working_dir):
    if '_i.prt' in filename.lower():
        idealized_part, status = theSession.Parts.Open(path)
        break

# THEN update FEM - now it will actually regenerate the mesh
feModel.UpdateFemodel()
```

**Without loading the `_i.prt`, `UpdateFemodel()` runs but the mesh doesn't change!**

### Study Setup Checklist
When creating a new study, ensure ALL these files are copied:
- [ ] `Model.prt` - Geometry part
- [ ] `Model_fem1_i.prt` - Idealized part ← **OFTEN MISSING!**
- [ ] `Model_fem1.fem` - FEM file
- [ ] `Model_sim1.sim` - Simulation file

See `docs/protocols/operations/OP_06_TROUBLESHOOT.md` for full troubleshooting guide.

## Developer Documentation

**For developers maintaining Atomizer**:
- Read `.claude/skills/DEV_DOCUMENTATION.md`
- Use self-documenting commands: "Document the {feature} I added"
- Commit code + docs together

## When Uncertain

1. Check `.claude/skills/00_BOOTSTRAP.md` for task routing
2. Check `.claude/skills/01_CHEATSHEET.md` for quick lookup
3. Load relevant protocol from `docs/protocols/`
4. Ask user for clarification

---

## Subagent Architecture

For complex tasks, spawn specialized subagents using the Task tool:

### Available Subagent Patterns

| Task Type | Subagent | Context to Provide |
|-----------|----------|-------------------|
| **Create Study** | `general-purpose` | Load `core/study-creation-core.md`, SYS_12. Task: Create complete study from description. |
| **NX Automation** | `general-purpose` | Use MCP siemens-docs tools. Query NXOpen classes before writing journals. |
| **Codebase Search** | `Explore` | Search for patterns, extractors, or understand existing code |
| **Architecture** | `Plan` | Design implementation approach for complex features |
| **Protocol Audit** | `general-purpose` | Validate config against SYS_12 extractors, check for issues |

### When to Use Subagents

**Use subagents for**:
- Creating new studies (complex, multi-file generation)
- NX API lookups and journal development
- Searching for patterns across multiple files
- Planning complex architectural changes

**Don't use subagents for**:
- Simple file reads/edits
- Running Python scripts
- Quick DB queries
- Direct user questions

### Subagent Prompt Template

When spawning a subagent, provide comprehensive context:
```
Context: [What the user wants]
Study: [Current study name if applicable]
Files to check: [Specific paths]
Task: [Specific deliverable expected]
Output: [What to return - files created, analysis, etc.]
```

---

## Auto-Documentation Protocol

When creating or modifying extractors/protocols, **proactively update docs**:

1. **New extractor created** →
   - Add to `optimization_engine/extractors/__init__.py`
   - Update `SYS_12_EXTRACTOR_LIBRARY.md`
   - Update `.claude/skills/01_CHEATSHEET.md`
   - Commit with: `feat: Add E{N} {name} extractor`

2. **Protocol updated** →
   - Update version in protocol header
   - Update `ATOMIZER_CONTEXT.md` version table
   - Mention in commit message

3. **New study template** →
   - Add to `optimization_engine/templates/registry.json`
   - Update `ATOMIZER_CONTEXT.md` template table

---

*Atomizer: Where engineers talk, AI optimizes.*