feat: Add neural loop automation - templates, auto-trainer, CLI

Closes the neural training loop with automated workflow:
- atomizer.py: One-command neural workflow CLI
- auto_trainer.py: Auto-training trigger system (50pt threshold)
- template_loader.py: Study creation from templates
- study_reset.py: Study reset/cleanup utility
- 3 templates: beam stiffness, bracket stress, frequency tuning
- State assessment document (Nov 25)

Usage: python atomizer.py neural-optimize --study my_study --trials 500

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

Co-Authored-By: Claude <noreply@anthropic.com>

templates/frequency_tuning.json

@@ -0,0 +1,133 @@
+{
+  "study_name": "frequency_tuning_optimization",
+  "description": "Natural Frequency Tuning - Adjust structural dynamics to avoid resonance",
+  "engineering_context": "Modal optimization for avoiding resonance with excitation sources (motors, rotors, vibration). Tune natural frequencies away from operating frequencies while minimizing mass.",
+  "template_info": {
+    "category": "dynamics",
+    "analysis_type": "modal",
+    "typical_applications": ["motor mounts", "drone arms", "rotating equipment supports", "vibration isolation"],
+    "required_nx_expressions": ["section_width", "section_height", "arm_length"],
+    "notes": "Requires modal analysis (SOL 103) solution in NX"
+  },
+
+  "optimization_settings": {
+    "protocol": "protocol_11_multi_objective",
+    "n_trials": 60,
+    "sampler": "NSGAIISampler",
+    "pruner": null,
+    "timeout_per_trial": 500
+  },
+
+  "design_variables": [
+    {
+      "parameter": "section_width",
+      "bounds": [10, 40],
+      "description": "Cross-section width (mm) - affects stiffness",
+      "units": "mm"
+    },
+    {
+      "parameter": "section_height",
+      "bounds": [10, 60],
+      "description": "Cross-section height (mm) - affects stiffness in bending plane",
+      "units": "mm"
+    },
+    {
+      "parameter": "arm_length",
+      "bounds": [80, 200],
+      "description": "Arm/cantilever length (mm) - strongly affects frequency",
+      "units": "mm"
+    },
+    {
+      "parameter": "wall_thickness",
+      "bounds": [1, 5],
+      "description": "Wall thickness for hollow sections (mm)",
+      "units": "mm"
+    }
+  ],
+
+  "objectives": [
+    {
+      "name": "mass",
+      "goal": "minimize",
+      "weight": 1.0,
+      "description": "Total mass (grams) - minimize for weight savings",
+      "target": 50,
+      "extraction": {
+        "action": "extract_mass",
+        "domain": "result_extraction",
+        "params": {
+          "result_type": "mass",
+          "metric": "total"
+        }
+      }
+    },
+    {
+      "name": "first_frequency",
+      "goal": "maximize",
+      "weight": 1.0,
+      "description": "First natural frequency (Hz) - push away from excitation",
+      "target": 200,
+      "extraction": {
+        "action": "extract_frequency",
+        "domain": "result_extraction",
+        "params": {
+          "result_type": "frequency",
+          "mode_number": 1
+        }
+      }
+    }
+  ],
+
+  "constraints": [
+    {
+      "name": "min_frequency_limit",
+      "type": "greater_than",
+      "threshold": 120,
+      "description": "First natural frequency > 120 Hz (above rotor harmonics)",
+      "extraction": {
+        "action": "extract_frequency",
+        "domain": "result_extraction",
+        "params": {
+          "result_type": "frequency",
+          "mode_number": 1
+        }
+      }
+    },
+    {
+      "name": "max_stress_limit",
+      "type": "less_than",
+      "threshold": 150,
+      "description": "Maximum stress < 150 MPa under static load",
+      "extraction": {
+        "action": "extract_stress",
+        "domain": "result_extraction",
+        "params": {
+          "result_type": "stress",
+          "metric": "max_von_mises"
+        }
+      }
+    }
+  ],
+
+  "simulation": {
+    "model_file": "Arm.prt",
+    "sim_file": "Arm_sim1.sim",
+    "fem_file": "Arm_fem1.fem",
+    "solver": "nastran",
+    "analysis_types": ["modal", "static"]
+  },
+
+  "reporting": {
+    "generate_plots": true,
+    "save_incremental": true,
+    "llm_summary": false
+  },
+
+  "training_data_export": {
+    "enabled": true,
+    "export_dir": "atomizer_field_training_data/${study_name}",
+    "export_every_n_trials": 1,
+    "include_mesh": true,
+    "compress": false
+  }
+}