feat: Add AtomizerField training data export and intelligent model discovery

Major additions:
- Training data export system for AtomizerField neural network training
- Bracket stiffness optimization study with 50+ training samples
- Intelligent NX model discovery (auto-detect solutions, expressions, mesh)
- Result extractors module for displacement, stress, frequency, mass
- User-generated NX journals for advanced workflows
- Archive structure for legacy scripts and test outputs
- Protocol documentation and dashboard launcher

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

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

optimization_engine/extractors/extract_frequency.py

@@ -0,0 +1,100 @@
+"""
+Extract natural frequencies from modal analysis
+Auto-generated by Atomizer Phase 3 - pyNastran Research Agent
+
+Pattern: eigenvalue_extraction
+Element Type: General
+Result Type: eigenvalues
+API: model.eigenvalues[subcase]
+"""
+
+from pathlib import Path
+from typing import Dict, Any
+import numpy as np
+from pyNastran.op2.op2 import OP2
+
+
+def extract_frequency(op2_file: Path, subcase: int = 1, mode_number: int = 1):
+    """
+    Extract natural frequency results from modal analysis OP2 file.
+
+    Args:
+        op2_file: Path to OP2 file
+        subcase: Subcase ID for modal analysis (default: 1)
+        mode_number: Which mode to extract (1-indexed, default: 1 for fundamental frequency)
+
+    Returns:
+        Dictionary containing frequency data
+    """
+    from pyNastran.op2.op2 import OP2
+    import numpy as np
+
+    model = OP2()
+    model.read_op2(str(op2_file))
+
+    # Access eigenvalues from modal analysis
+    # NX Nastran often uses empty string '' as subcase key
+    available_subcases = list(model.eigenvalues.keys())
+    if not available_subcases:
+        raise ValueError(f"No eigenvalue data found in OP2 file: {op2_file}")
+
+    # Use the first available subcase (often '' for NX Nastran)
+    actual_subcase = available_subcases[0]
+    eigenvalues = model.eigenvalues[actual_subcase]
+
+    # Extract frequency data for the specified mode
+    # RealEigenvalues object has different attributes than expected
+    # Try to access frequencies - could be in different formats
+
+    # Mode number is 1-indexed, array is 0-indexed
+    mode_idx = mode_number - 1
+
+    # Try different attribute names for frequencies
+    if hasattr(eigenvalues, 'cycles'):
+        frequencies = eigenvalues.cycles
+    elif hasattr(eigenvalues, 'frequencies'):
+        frequencies = eigenvalues.frequencies
+    else:
+        # Try to get eigenvalues and convert to frequency
+        if hasattr(eigenvalues, 'eigenvalues'):
+            # eigenvalue (lambda) = (2*pi*f)^2, so f = sqrt(lambda) / (2*pi)
+            eigenvals = eigenvalues.eigenvalues
+            frequencies = np.sqrt(np.abs(eigenvals)) / (2.0 * np.pi)
+        else:
+            raise ValueError(f"Cannot find frequency data in eigenvalues object. Available attributes: {dir(eigenvalues)}")
+
+    if mode_idx >= len(frequencies):
+        raise ValueError(f"Mode {mode_number} not found. Only {len(frequencies)} modes available.")
+
+    frequency = frequencies[mode_idx]  # Hz
+
+    # Try to get eigenvalue if available
+    if hasattr(eigenvalues, 'eigenvalues'):
+        eigenvalue = eigenvalues.eigenvalues[mode_idx]
+    elif hasattr(eigenvalues, 'eigrs'):
+        eigenvalue = eigenvalues.eigrs[mode_idx]
+    else:
+        eigenvalue = (2.0 * np.pi * frequency) ** 2  # Convert back from frequency
+
+    # Also return all frequencies for reference
+    all_frequencies = list(frequencies)
+
+    return {
+        'frequency': float(frequency),
+        'mode_number': int(mode_number),
+        'eigenvalue': float(eigenvalue),
+        'all_frequencies': all_frequencies,
+        'n_modes': len(all_frequencies)
+    }
+
+
+if __name__ == '__main__':
+    # Example usage
+    import sys
+    if len(sys.argv) > 1:
+        op2_file = Path(sys.argv[1])
+        mode_num = int(sys.argv[2]) if len(sys.argv) > 2 else 1
+        result = extract_frequency(op2_file, mode_number=mode_num)
+        print(f"Extraction result: {result}")
+    else:
+        print(f"Usage: python {sys.argv[0]} <op2_file> [mode_number]")