Atomizer/.claude/skills/00_BOOTSTRAP.md

---
skill_id: SKILL_000
version: 2.0
last_updated: 2025-12-07
type: bootstrap
code_dependencies: []
requires_skills: []
---

# Atomizer LLM Bootstrap

**Version**: 2.0
**Updated**: 2025-12-07
**Purpose**: First file any LLM session reads. Provides instant orientation and task routing.

---

## Quick Orientation (30 Seconds)

**Atomizer** = LLM-first FEA optimization framework using NX Nastran + Optuna + Neural Networks.

**Your Role**: Help users set up, run, and analyze structural optimization studies through conversation.

**Core Philosophy**: "Talk, don't click." Users describe what they want; you configure and execute.

---

## Task Classification Tree

When a user request arrives, classify it:

```
User Request
    │
    ├─► CREATE something?
    │       ├─ "new study", "set up", "create", "optimize this"
    │       └─► Load: OP_01_CREATE_STUDY.md + core/study-creation-core.md
    │
    ├─► RUN something?
    │       ├─ "start", "run", "execute", "begin optimization"
    │       └─► Load: OP_02_RUN_OPTIMIZATION.md
    │
    ├─► CHECK status?
    │       ├─ "status", "progress", "how many trials", "what's happening"
    │       └─► Load: OP_03_MONITOR_PROGRESS.md
    │
    ├─► ANALYZE results?
    │       ├─ "results", "best design", "compare", "pareto"
    │       └─► Load: OP_04_ANALYZE_RESULTS.md
    │
    ├─► DEBUG/FIX error?
    │       ├─ "error", "failed", "not working", "crashed"
    │       └─► Load: OP_06_TROUBLESHOOT.md
    │
    ├─► CONFIGURE settings?
    │       ├─ "change", "modify", "settings", "parameters"
    │       └─► Load relevant SYS_* protocol
    │
    ├─► EXTEND functionality?
    │       ├─ "add extractor", "new hook", "create protocol"
    │       └─► Check privilege, then load EXT_* protocol
    │
    └─► EXPLAIN/LEARN?
            ├─ "what is", "how does", "explain"
            └─► Load relevant SYS_* protocol for reference
```

---

## Protocol Routing Table

| User Intent | Keywords | Protocol | Skill to Load | Privilege |
|-------------|----------|----------|---------------|-----------|
| Create study | "new", "set up", "create", "optimize" | OP_01 | **core/study-creation-core.md** | user |
| Run optimization | "start", "run", "execute", "begin" | OP_02 | - | user |
| Monitor progress | "status", "progress", "trials", "check" | OP_03 | - | user |
| Analyze results | "results", "best", "compare", "pareto" | OP_04 | - | user |
| Export training data | "export", "training data", "neural" | OP_05 | modules/neural-acceleration.md | user |
| Debug issues | "error", "failed", "not working", "help" | OP_06 | - | user |
| Understand IMSO | "protocol 10", "IMSO", "adaptive" | SYS_10 | - | user |
| Multi-objective | "pareto", "NSGA", "multi-objective" | SYS_11 | - | user |
| Extractors | "extractor", "displacement", "stress" | SYS_12 | modules/extractors-catalog.md | user |
| Dashboard | "dashboard", "visualization", "real-time" | SYS_13 | - | user |
| Neural surrogates | "neural", "surrogate", "NN", "acceleration" | SYS_14 | modules/neural-acceleration.md | user |
| Add extractor | "create extractor", "new physics" | EXT_01 | - | power_user |
| Add hook | "create hook", "lifecycle", "callback" | EXT_02 | - | power_user |
| Add protocol | "create protocol", "new protocol" | EXT_03 | - | admin |
| Add skill | "create skill", "new skill" | EXT_04 | - | admin |

---

## Role Detection

Determine user's privilege level:

| Role | How to Detect | Can Do | Cannot Do |
|------|---------------|--------|-----------|
| **user** | Default for all sessions | Run studies, monitor, analyze, configure | Create extractors, modify protocols |
| **power_user** | User states they're a developer, or session context indicates | Create extractors, add hooks | Create protocols, modify skills |
| **admin** | Explicit declaration, admin config present | Full access | - |

**Default**: Assume `user` unless explicitly told otherwise.

---

## Context Loading Rules

After classifying the task, load context in this order:

### 1. Always Loaded (via CLAUDE.md)
- This file (00_BOOTSTRAP.md)
- Python environment rules
- Code reuse protocol

### 2. Load Per Task Type
See `02_CONTEXT_LOADER.md` for complete loading rules.

**Quick Reference**:
```
CREATE_STUDY     → core/study-creation-core.md (PRIMARY)
                 → SYS_12_EXTRACTOR_LIBRARY.md (extractor reference)
                 → modules/zernike-optimization.md (if telescope/mirror)
                 → modules/neural-acceleration.md (if >50 trials)

RUN_OPTIMIZATION → OP_02_RUN_OPTIMIZATION.md
                 → SYS_15_METHOD_SELECTOR.md (method recommendation)
                 → SYS_14_NEURAL_ACCELERATION.md (if neural/turbo)

DEBUG           → OP_06_TROUBLESHOOT.md
                → Relevant SYS_* based on error type
```

---

## Execution Framework

For ANY task, follow this pattern:

```
1. ANNOUNCE  → State what you're about to do
2. VALIDATE  → Check prerequisites are met
3. EXECUTE   → Perform the action
4. VERIFY    → Confirm success
5. REPORT    → Summarize what was done
6. SUGGEST   → Offer logical next steps
```

See `PROTOCOL_EXECUTION.md` for detailed execution rules.

---

## Emergency Quick Paths

### "I just want to run an optimization"
1. Do you have a `.prt` and `.sim` file? → Yes: OP_01 → OP_02
2. Getting errors? → OP_06
3. Want to see progress? → OP_03

### "Something broke"
1. Read the error message
2. Load OP_06_TROUBLESHOOT.md
3. Follow diagnostic flowchart

### "What did my optimization find?"
1. Load OP_04_ANALYZE_RESULTS.md
2. Query the study database
3. Generate report

---

## Protocol Directory Map

```
docs/protocols/
├── operations/          # Layer 2: How-to guides
│   ├── OP_01_CREATE_STUDY.md
│   ├── OP_02_RUN_OPTIMIZATION.md
│   ├── OP_03_MONITOR_PROGRESS.md
│   ├── OP_04_ANALYZE_RESULTS.md
│   ├── OP_05_EXPORT_TRAINING_DATA.md
│   └── OP_06_TROUBLESHOOT.md
│
├── system/              # Layer 3: Core specifications
│   ├── SYS_10_IMSO.md
│   ├── SYS_11_MULTI_OBJECTIVE.md
│   ├── SYS_12_EXTRACTOR_LIBRARY.md
│   ├── SYS_13_DASHBOARD_TRACKING.md
│   └── SYS_14_NEURAL_ACCELERATION.md
│
└── extensions/          # Layer 4: Extensibility guides
    ├── EXT_01_CREATE_EXTRACTOR.md
    ├── EXT_02_CREATE_HOOK.md
    ├── EXT_03_CREATE_PROTOCOL.md
    ├── EXT_04_CREATE_SKILL.md
    └── templates/
```

---

## Key Constraints (Always Apply)

1. **Python Environment**: Always use `conda activate atomizer`
2. **Never modify master files**: Copy NX files to study working directory first
3. **Code reuse**: Check `optimization_engine/extractors/` before writing new extraction code
4. **Validation**: Always validate config before running optimization
5. **Documentation**: Every study needs README.md and STUDY_REPORT.md

---

## Next Steps After Bootstrap

1. If you know the task type → Go to relevant OP_* or SYS_* protocol
2. If unclear → Ask user clarifying question
3. If complex task → Read `01_CHEATSHEET.md` for quick reference
4. If need detailed loading rules → Read `02_CONTEXT_LOADER.md`