feat: add Atomizer HQ multi-agent cluster infrastructure
- 8-agent OpenClaw cluster (Manager, Tech-Lead, Secretary, Auditor, Optimizer, Study-Builder, NX-Expert, Webster) - Orchestration engine: orchestrate.py (sync delegation + handoffs) - Workflow engine: YAML-defined multi-step pipelines - Agent workspaces: SOUL.md, AGENTS.md, MEMORY.md per agent - Shared skills: delegate, orchestrate, atomizer-protocols - Capability registry (AGENTS_REGISTRY.json) - Cluster management: cluster.sh, systemd template - All secrets replaced with env var references
This commit is contained in:
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hq/skills/atomizer-protocols/protocols/OP_01_CREATE_STUDY.md
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# OP_01: Create Optimization Study
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<!--
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PROTOCOL: Create Optimization Study
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LAYER: Operations
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VERSION: 1.2
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STATUS: Active
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LAST_UPDATED: 2026-01-13
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PRIVILEGE: user
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LOAD_WITH: [core/study-creation-core.md]
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-->
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## Overview
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This protocol guides you through creating a complete Atomizer optimization study from scratch. It covers gathering requirements, generating configuration files, and validating setup.
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**Skill to Load**: `.claude/skills/core/study-creation-core.md`
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---
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## When to Use
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| Trigger | Action |
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|---------|--------|
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| "new study", "create study" | Follow this protocol |
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| "set up optimization" | Follow this protocol |
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| "optimize my design" | Follow this protocol |
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| User provides NX model | Assess and follow this protocol |
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---
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## Quick Reference
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### MANDATORY: Use TodoWrite for Study Creation
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**BEFORE creating any files**, add ALL required outputs to TodoWrite:
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```
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TodoWrite([
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{"content": "Create optimization_config.json", "status": "pending", "activeForm": "Creating config"},
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{"content": "Create run_optimization.py", "status": "pending", "activeForm": "Creating run script"},
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{"content": "Create README.md", "status": "pending", "activeForm": "Creating README"},
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{"content": "Create STUDY_REPORT.md", "status": "pending", "activeForm": "Creating report template"}
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])
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```
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**Mark each item complete ONLY after the file is created.** Study is NOT complete until all 4 items are checked off.
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> **WHY**: This requirement exists because README.md was forgotten TWICE (2025-12-17, 2026-01-13) despite being listed as mandatory. TodoWrite provides visible enforcement.
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---
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**Required Outputs** (ALL MANDATORY - study is INCOMPLETE without these):
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| File | Purpose | Location | Priority |
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|------|---------|----------|----------|
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| `optimization_config.json` | Design vars, objectives, constraints | `1_setup/` | 1 |
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| `run_optimization.py` | Execution script | Study root | 2 |
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| **`README.md`** | Engineering documentation | Study root | **3 - NEVER SKIP** |
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| `STUDY_REPORT.md` | Results template | Study root | 4 |
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**CRITICAL**: README.md is MANDATORY for every study. A study without README.md is INCOMPLETE.
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**Study Structure**:
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```
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studies/{geometry_type}/{study_name}/
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├── 1_setup/
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│ ├── model/ # NX files (.prt, .sim, .fem)
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│ └── optimization_config.json
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├── 2_iterations/ # FEA trial folders (iter1, iter2, ...)
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├── 3_results/ # Optimization outputs (study.db, logs)
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├── README.md # MANDATORY
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├── STUDY_REPORT.md # MANDATORY
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└── run_optimization.py
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```
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**IMPORTANT: Studies are organized by geometry type**:
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| Geometry Type | Folder | Examples |
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|---------------|--------|----------|
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| M1 Mirror | `studies/M1_Mirror/` | m1_mirror_adaptive_V14, m1_mirror_cost_reduction_V3 |
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| Simple Bracket | `studies/Simple_Bracket/` | bracket_stiffness_optimization |
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| UAV Arm | `studies/UAV_Arm/` | uav_arm_optimization |
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| Drone Gimbal | `studies/Drone_Gimbal/` | drone_gimbal_arm_optimization |
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| Simple Beam | `studies/Simple_Beam/` | simple_beam_optimization |
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| Other/Test | `studies/_Other/` | training_data_export_test |
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When creating a new study:
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1. Identify the geometry type (mirror, bracket, beam, etc.)
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2. Place study under the appropriate `studies/{geometry_type}/` folder
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3. For new geometry types, create a new folder with descriptive name
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---
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## README Hierarchy (Parent-Child Documentation)
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**Two-level documentation system**:
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```
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studies/{geometry_type}/
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├── README.md # PARENT: Project-level context
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│ ├── Project overview # What is this geometry/component?
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│ ├── Physical system specs # Material, dimensions, constraints
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│ ├── Optical/mechanical specs # Domain-specific requirements
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│ ├── Design variables catalog # ALL possible variables with descriptions
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│ ├── Objectives catalog # ALL possible objectives
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│ ├── Campaign history # Summary of all sub-studies
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│ └── Sub-studies index # Links to each sub-study
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│
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├── sub_study_V1/
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│ └── README.md # CHILD: Study-specific details
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│ ├── Link to parent # "See ../README.md for context"
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│ ├── Study focus # What THIS study optimizes
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│ ├── Active variables # Which params enabled
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│ ├── Algorithm config # Sampler, trials, settings
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│ ├── Baseline/seeding # Starting point
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│ └── Results summary # Best trial, learnings
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│
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└── sub_study_V2/
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└── README.md # CHILD: References parent, adds specifics
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```
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### Parent README Content (Geometry-Level)
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| Section | Content |
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|---------|---------|
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| Project Overview | What the component is, purpose, context |
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| Physical System | Material, mass targets, loading conditions |
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| Domain Specs | Optical prescription (mirrors), structural limits (brackets) |
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| Design Variables | Complete catalog with ranges and descriptions |
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| Objectives | All possible metrics with formulas |
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| Campaign History | Evolution across sub-studies |
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| Sub-Studies Index | Table with links, status, best results |
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| Technical Notes | Domain-specific implementation details |
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### Child README Content (Study-Level)
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| Section | Content |
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|---------|---------|
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| Parent Reference | `> See [../README.md](../README.md) for project context` |
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| Study Focus | What differentiates THIS study |
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| Active Variables | Which parameters are enabled (subset of parent catalog) |
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| Algorithm Config | Sampler, n_trials, sigma, seed |
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| Baseline | Starting point (seeded from prior study or default) |
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| Results | Best trial, improvement metrics |
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| Key Learnings | What was discovered |
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### When to Create Parent README
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- **First study** for a geometry type → Create parent README immediately
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- **Subsequent studies** → Add to parent's sub-studies index
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- **New geometry type** → Create both parent and child READMEs
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### Example Reference
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See `studies/M1_Mirror/README.md` for a complete parent README example.
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---
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## Interview Mode (DEFAULT)
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**Study creation now uses Interview Mode by default.** This provides guided study creation with intelligent validation.
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### Triggers (Any of These Start Interview Mode)
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- "create a study", "new study", "set up study"
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- "create a study for my bracket"
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- "optimize this model"
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- "I want to minimize mass"
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- Any study creation request without "skip interview" or "manual"
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### When to Skip Interview Mode (Manual)
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Use manual mode only when:
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- Power user who knows the exact configuration
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- Recreating a known study configuration
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- User explicitly says "skip interview", "quick setup", or "manual config"
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### Starting Interview Mode
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```python
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from optimization_engine.interview import StudyInterviewEngine
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engine = StudyInterviewEngine(study_path)
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# Run introspection first (if model available)
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introspection = {
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"expressions": [...], # From part introspection
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"model_path": "...",
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"sim_path": "..."
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}
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session = engine.start_interview(study_name, introspection=introspection)
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action = engine.get_first_question()
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# Present action.message to user
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# Process answers with: action = engine.process_answer(user_response)
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```
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### Interview Benefits
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- **Material-aware validation**: Checks stress limits against yield
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- **Anti-pattern detection**: Warns about mass minimization without constraints
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- **Auto extractor mapping**: Maps goals to correct extractors (E1-E10)
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- **State persistence**: Resume interrupted interviews
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- **Blueprint generation**: Creates validated configuration
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See `.claude/skills/modules/study-interview-mode.md` for full documentation.
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---
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## Detailed Steps (Manual Mode - Power Users Only)
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### Step 1: Gather Requirements
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**Ask the user**:
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1. What are you trying to optimize? (objective)
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2. What can you change? (design variables)
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3. What limits must be respected? (constraints)
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4. Where are your NX files?
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**Example Dialog**:
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```
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User: "I want to optimize my bracket"
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You: "What should I optimize for - minimum mass, maximum stiffness,
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target frequency, or something else?"
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User: "Minimize mass while keeping stress below 250 MPa"
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```
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### Step 2: Analyze Model (Introspection)
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**MANDATORY**: When user provides NX files, run comprehensive introspection:
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```python
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from optimization_engine.hooks.nx_cad.model_introspection import (
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introspect_part,
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introspect_simulation,
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introspect_op2,
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introspect_study
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)
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# Introspect the part file to get expressions, mass, features
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part_info = introspect_part("C:/path/to/model.prt")
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# Introspect the simulation to get solutions, BCs, loads
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sim_info = introspect_simulation("C:/path/to/model.sim")
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# If OP2 exists, check what results are available
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op2_info = introspect_op2("C:/path/to/results.op2")
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# Or introspect entire study directory at once
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study_info = introspect_study("studies/my_study/")
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```
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**Introspection Report Contents**:
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| Source | Information Extracted |
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|--------|----------------------|
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| `.prt` | Expressions (count, values, types), bodies, mass, material, features |
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| `.sim` | Solutions, boundary conditions, loads, materials, mesh info, output requests |
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| `.op2` | Available results (displacement, stress, strain, SPC forces, etc.), subcases |
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**Generate Introspection Report** at study creation:
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1. Save report to `studies/{study_name}/MODEL_INTROSPECTION.md`
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2. Include summary of what's available for optimization
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3. List potential design variables (expressions)
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4. List extractable results (from OP2)
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**Key Questions Answered by Introspection**:
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- What expressions exist? (potential design variables)
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- What solution types? (static, modal, etc.)
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- What results are available in OP2? (displacement, stress, SPC forces)
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- Multi-solution required? (static + modal = set `solution_name=None`)
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### Step 3: Select Protocol
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Based on objectives:
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| Scenario | Protocol | Sampler |
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|----------|----------|---------|
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| Single objective | Protocol 10 (IMSO) | TPE, CMA-ES, or GP |
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| 2-3 objectives | Protocol 11 | NSGA-II |
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| >50 trials, need speed | Protocol 14 | + Neural acceleration |
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See [SYS_10_IMSO](../system/SYS_10_IMSO.md), [SYS_11_MULTI_OBJECTIVE](../system/SYS_11_MULTI_OBJECTIVE.md).
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### Step 4: Select Extractors
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Match physics to extractors from [SYS_12_EXTRACTOR_LIBRARY](../system/SYS_12_EXTRACTOR_LIBRARY.md):
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| Need | Extractor ID | Function |
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|------|--------------|----------|
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| Max displacement | E1 | `extract_displacement()` |
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| Natural frequency | E2 | `extract_frequency()` |
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| Von Mises stress | E3 | `extract_solid_stress()` |
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| Mass from BDF | E4 | `extract_mass_from_bdf()` |
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| Mass from NX | E5 | `extract_mass_from_expression()` |
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| Wavefront error | E8-E10 | Zernike extractors |
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### Step 5: Generate Configuration
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Create `optimization_config.json`:
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```json
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{
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"study_name": "bracket_optimization",
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"description": "Minimize bracket mass while meeting stress constraint",
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"design_variables": [
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{
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"name": "thickness",
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"type": "continuous",
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"min": 2.0,
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"max": 10.0,
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"unit": "mm",
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"description": "Wall thickness"
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}
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],
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"objectives": [
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{
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"name": "mass",
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"type": "minimize",
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"unit": "kg",
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"description": "Total bracket mass"
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}
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],
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"constraints": [
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{
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"name": "max_stress",
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"type": "less_than",
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"value": 250.0,
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"unit": "MPa",
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"description": "Maximum allowable von Mises stress"
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}
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],
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"simulation": {
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"model_file": "1_setup/model/bracket.prt",
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"sim_file": "1_setup/model/bracket.sim",
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"solver": "nastran",
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"solution_name": null
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},
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"optimization_settings": {
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"protocol": "protocol_10_single_objective",
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"sampler": "TPESampler",
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"n_trials": 50
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}
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}
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```
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### Step 6: Generate run_optimization.py
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**CRITICAL**: Always use the `FEARunner` class pattern with proper `NXSolver` initialization.
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```python
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#!/usr/bin/env python3
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"""
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{study_name} - Optimization Runner
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Generated by Atomizer LLM
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"""
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import sys
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import re
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import json
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from pathlib import Path
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from typing import Dict, Optional, Any
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# Add optimization engine to path
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sys.path.insert(0, str(Path(__file__).parent.parent.parent))
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import optuna
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from optimization_engine.nx_solver import NXSolver
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from optimization_engine.utils import ensure_nx_running
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from optimization_engine.extractors import extract_solid_stress
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# Paths
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STUDY_DIR = Path(__file__).parent
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SETUP_DIR = STUDY_DIR / "1_setup"
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ITERATIONS_DIR = STUDY_DIR / "2_iterations"
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RESULTS_DIR = STUDY_DIR / "3_results"
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CONFIG_PATH = SETUP_DIR / "optimization_config.json"
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# Ensure directories exist
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ITERATIONS_DIR.mkdir(exist_ok=True)
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RESULTS_DIR.mkdir(exist_ok=True)
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class FEARunner:
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"""Runs actual FEA simulations. Always use this pattern!"""
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def __init__(self, config: Dict[str, Any]):
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self.config = config
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self.nx_solver = None
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self.nx_manager = None
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self.master_model_dir = SETUP_DIR / "model"
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def setup(self):
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"""Setup NX and solver. Called lazily on first use."""
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study_name = self.config.get('study_name', 'my_study')
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# Ensure NX is running
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self.nx_manager, nx_was_started = ensure_nx_running(
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session_id=study_name,
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auto_start=True,
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start_timeout=120
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)
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# CRITICAL: Initialize NXSolver with named parameters, NOT config dict
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nx_settings = self.config.get('nx_settings', {})
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nx_install_dir = nx_settings.get('nx_install_path', 'C:\\Program Files\\Siemens\\NX2506')
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# Extract version from path
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version_match = re.search(r'NX(\d+)', nx_install_dir)
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nastran_version = version_match.group(1) if version_match else "2506"
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self.nx_solver = NXSolver(
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master_model_dir=str(self.master_model_dir),
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nx_install_dir=nx_install_dir,
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nastran_version=nastran_version,
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timeout=nx_settings.get('simulation_timeout_s', 600),
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use_iteration_folders=True,
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study_name=study_name
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)
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def run_fea(self, params: Dict[str, float], iter_num: int) -> Optional[Dict]:
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"""Run FEA simulation and extract results."""
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||||
if self.nx_solver is None:
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self.setup()
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||||
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||||
# Create expression updates
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||||
expressions = {var['expression_name']: params[var['name']]
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||||
for var in self.config['design_variables']}
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||||
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||||
# Create iteration folder with model copies
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||||
iter_folder = self.nx_solver.create_iteration_folder(
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||||
iterations_base_dir=ITERATIONS_DIR,
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||||
iteration_number=iter_num,
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||||
expression_updates=expressions
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)
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||||
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||||
# Run simulation
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||||
nx_settings = self.config.get('nx_settings', {})
|
||||
sim_file = iter_folder / nx_settings.get('sim_file', 'model.sim')
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||||
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||||
result = self.nx_solver.run_simulation(
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||||
sim_file=sim_file,
|
||||
working_dir=iter_folder,
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expression_updates=expressions,
|
||||
solution_name=nx_settings.get('solution_name', 'Solution 1'),
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||||
cleanup=False
|
||||
)
|
||||
|
||||
if not result['success']:
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||||
return None
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||||
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||||
# Extract results
|
||||
op2_file = result['op2_file']
|
||||
stress_result = extract_solid_stress(op2_file)
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||||
|
||||
return {
|
||||
'params': params,
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||||
'max_stress': stress_result['max_von_mises'],
|
||||
'op2_file': op2_file
|
||||
}
|
||||
|
||||
|
||||
# Optimizer class would use FEARunner...
|
||||
# See m1_mirror_adaptive_V14/run_optimization.py for full example
|
||||
```
|
||||
|
||||
**WRONG** - causes `TypeError: expected str, bytes or os.PathLike object, not dict`:
|
||||
```python
|
||||
self.nx_solver = NXSolver(self.config) # ❌ NEVER DO THIS
|
||||
```
|
||||
|
||||
**Reference implementations**:
|
||||
- `studies/m1_mirror_adaptive_V14/run_optimization.py` (TPE single-objective)
|
||||
- `studies/m1_mirror_adaptive_V15/run_optimization.py` (NSGA-II multi-objective)
|
||||
|
||||
### Step 7: Generate Documentation
|
||||
|
||||
**README.md** (11 sections required):
|
||||
1. Engineering Problem
|
||||
2. Mathematical Formulation
|
||||
3. Optimization Algorithm
|
||||
4. Simulation Pipeline
|
||||
5. Result Extraction Methods
|
||||
6. Neural Acceleration (if applicable)
|
||||
7. Study File Structure
|
||||
8. Results Location
|
||||
9. Quick Start
|
||||
10. Configuration Reference
|
||||
11. References
|
||||
|
||||
**STUDY_REPORT.md** (template):
|
||||
```markdown
|
||||
# Study Report: {study_name}
|
||||
|
||||
## Executive Summary
|
||||
- Trials completed: _pending_
|
||||
- Best objective: _pending_
|
||||
- Constraint satisfaction: _pending_
|
||||
|
||||
## Optimization Progress
|
||||
_To be filled after run_
|
||||
|
||||
## Best Designs Found
|
||||
_To be filled after run_
|
||||
|
||||
## Recommendations
|
||||
_To be filled after analysis_
|
||||
```
|
||||
|
||||
### Step 7b: Capture Baseline Geometry Images (Recommended)
|
||||
|
||||
For better documentation, capture images of the starting geometry using the NX journal:
|
||||
|
||||
```bash
|
||||
# Capture baseline images for study documentation
|
||||
"C:\Program Files\Siemens\DesigncenterNX2512\NXBIN\run_journal.exe" ^
|
||||
"C:\Users\antoi\Atomizer\nx_journals\capture_study_images.py" ^
|
||||
-args "path/to/model.prt" "1_setup/" "model_name"
|
||||
```
|
||||
|
||||
This generates:
|
||||
- `1_setup/{model_name}_Top.png` - Top view
|
||||
- `1_setup/{model_name}_iso.png` - Isometric view
|
||||
|
||||
**Include in README.md**:
|
||||
```markdown
|
||||
## Baseline Geometry
|
||||
|
||||
|
||||
*Top view description*
|
||||
|
||||
|
||||
*Isometric view description*
|
||||
```
|
||||
|
||||
**Journal location**: `nx_journals/capture_study_images.py`
|
||||
|
||||
### Step 8: Validate NX Model File Chain
|
||||
|
||||
**CRITICAL**: NX simulation files have parent-child dependencies. ALL linked files must be copied to the study folder.
|
||||
|
||||
**Required File Chain Check**:
|
||||
```
|
||||
.sim (Simulation)
|
||||
└── .fem (FEM)
|
||||
└── _i.prt (Idealized Part) ← OFTEN MISSING!
|
||||
└── .prt (Geometry Part)
|
||||
```
|
||||
|
||||
**Validation Steps**:
|
||||
1. Open the `.sim` file in NX
|
||||
2. Go to **Assemblies → Assembly Navigator** or check **Part Navigator**
|
||||
3. Identify ALL child components (especially `*_i.prt` idealized parts)
|
||||
4. Copy ALL linked files to `1_setup/model/`
|
||||
|
||||
**Common Issue**: The `_i.prt` (idealized part) is often forgotten. Without it:
|
||||
- `UpdateFemodel()` runs but mesh doesn't change
|
||||
- Geometry changes don't propagate to FEM
|
||||
- All optimization trials produce identical results
|
||||
|
||||
**File Checklist**:
|
||||
| File Pattern | Description | Required |
|
||||
|--------------|-------------|----------|
|
||||
| `*.prt` | Geometry part | ✅ Always |
|
||||
| `*_i.prt` | Idealized part | ✅ If FEM uses idealization |
|
||||
| `*.fem` | FEM file | ✅ Always |
|
||||
| `*.sim` | Simulation file | ✅ Always |
|
||||
|
||||
**Introspection should report**:
|
||||
- List of all parts referenced by .sim
|
||||
- Warning if any referenced parts are missing from study folder
|
||||
|
||||
### Step 9: Final Validation Checklist
|
||||
|
||||
**CRITICAL**: Study is NOT complete until ALL items are checked:
|
||||
|
||||
- [ ] NX files exist in `1_setup/model/`
|
||||
- [ ] **ALL child parts copied** (especially `*_i.prt`)
|
||||
- [ ] Expression names match model
|
||||
- [ ] Config validates (JSON schema)
|
||||
- [ ] `run_optimization.py` has no syntax errors
|
||||
- [ ] **README.md exists** (MANDATORY - study is incomplete without it!)
|
||||
- [ ] README.md contains: Overview, Objectives, Constraints, Design Variables, Settings, Usage, Structure
|
||||
- [ ] STUDY_REPORT.md template exists
|
||||
|
||||
**README.md Minimum Content**:
|
||||
1. Overview/Purpose
|
||||
2. Objectives with weights
|
||||
3. Constraints (if any)
|
||||
4. Design variables with ranges
|
||||
5. Optimization settings
|
||||
6. Usage commands
|
||||
7. Directory structure
|
||||
|
||||
---
|
||||
|
||||
## Examples
|
||||
|
||||
### Example 1: Simple Bracket
|
||||
|
||||
```
|
||||
User: "Optimize my bracket.prt for minimum mass, stress < 250 MPa"
|
||||
|
||||
Generated config:
|
||||
- 1 design variable (thickness)
|
||||
- 1 objective (minimize mass)
|
||||
- 1 constraint (stress < 250)
|
||||
- Protocol 10, TPE sampler
|
||||
- 50 trials
|
||||
```
|
||||
|
||||
### Example 2: Multi-Objective Beam
|
||||
|
||||
```
|
||||
User: "Minimize mass AND maximize stiffness for my beam"
|
||||
|
||||
Generated config:
|
||||
- 2 design variables (width, height)
|
||||
- 2 objectives (minimize mass, maximize stiffness)
|
||||
- Protocol 11, NSGA-II sampler
|
||||
- 50 trials (Pareto front)
|
||||
```
|
||||
|
||||
### Example 3: Telescope Mirror
|
||||
|
||||
```
|
||||
User: "Minimize wavefront error at 40deg vs 20deg reference"
|
||||
|
||||
Generated config:
|
||||
- Multiple design variables (mount positions)
|
||||
- 1 objective (minimize relative WFE)
|
||||
- Zernike extractor E9
|
||||
- Protocol 10
|
||||
```
|
||||
|
||||
---
|
||||
|
||||
## Troubleshooting
|
||||
|
||||
| Symptom | Cause | Solution |
|
||||
|---------|-------|----------|
|
||||
| "Expression not found" | Name mismatch | Verify expression names in NX |
|
||||
| "No feasible designs" | Constraints too tight | Relax constraint values |
|
||||
| Config validation fails | Missing required field | Check JSON schema |
|
||||
| Import error | Wrong path | Check sys.path setup |
|
||||
|
||||
---
|
||||
|
||||
## Cross-References
|
||||
|
||||
- **Depends On**: [SYS_12_EXTRACTOR_LIBRARY](../system/SYS_12_EXTRACTOR_LIBRARY.md)
|
||||
- **Next Step**: [OP_02_RUN_OPTIMIZATION](./OP_02_RUN_OPTIMIZATION.md)
|
||||
- **Skill**: `.claude/skills/core/study-creation-core.md`
|
||||
|
||||
---
|
||||
|
||||
## Version History
|
||||
|
||||
| Version | Date | Changes |
|
||||
|---------|------|---------|
|
||||
| 1.2 | 2026-01-13 | Added MANDATORY TodoWrite requirement for study creation (README forgotten twice) |
|
||||
| 1.1 | 2025-12-12 | Added FEARunner class pattern, NXSolver initialization warning |
|
||||
| 1.0 | 2025-12-05 | Initial release |
|
||||
Reference in New Issue
Block a user