feat: Complete Phase 3.1 - Extractor Orchestration & End-to-End Automation

Phase 3.1 completes the ZERO-MANUAL-CODING automation pipeline by
integrating all phases into a seamless workflow from natural language
request to final objective value.

Key Features:
- ExtractorOrchestrator integrates Phase 2.7 LLM + Phase 3.0 Research Agent
- Automatic extractor generation from LLM workflow output
- Dynamic loading and execution on real OP2 files
- Smart parameter filtering per extraction pattern type
- Multi-extractor support in single workflow
- Complete end-to-end test passed on real bracket OP2

Complete Automation Pipeline:
  User Natural Language Request
      ↓
  Phase 2.7 LLM Analysis
      ↓
  Phase 3.1 Orchestrator
      ↓
  Phase 3.0 Research Agent (auto OP2 code gen)
      ↓
  Generated Extractor Modules
      ↓
  Dynamic Execution on Real OP2
      ↓
  Phase 2.8 Inline Calculations
      ↓
  Phase 2.9 Post-Processing Hooks
      ↓
  Final Objective → Optuna

Test Results:
- Generated displacement extractor: PASSED
- Executed on bracket OP2: PASSED
- Extracted max_displacement: 0.361783mm at node 91
- Calculated normalized objective: 0.072357
- Multi-extractor generation: PASSED

New Files:
- optimization_engine/extractor_orchestrator.py (380+ lines)
- tests/test_phase_3_1_integration.py (200+ lines)
- docs/SESSION_SUMMARY_PHASE_3_1.md (comprehensive documentation)
- optimization_engine/result_extractors/generated/ (auto-generated extractors)

Modified Files:
- README.md - Added Phase 3.1 completion status

ZERO MANUAL CODING - Complete automation achieved!

Generated with Claude Code

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

optimization_engine/result_extractors/generated/extract_1d_element_forces.py

@@ -0,0 +1,73 @@
+"""
+Extract element forces from CBAR in Z direction from OP2
+Auto-generated by Atomizer Phase 3 - pyNastran Research Agent
+
+Pattern: cbar_force
+Element Type: CBAR
+Result Type: force
+API: model.cbar_force[subcase]
+"""
+
+from pathlib import Path
+from typing import Dict, Any
+import numpy as np
+from pyNastran.op2.op2 import OP2
+
+
+def extract_cbar_force(op2_file: Path, subcase: int = 1, direction: str = 'Z'):
+    """
+    Extract forces from CBAR elements.
+
+    Args:
+        op2_file: Path to OP2 file
+        subcase: Subcase ID
+        direction: Force direction ('X', 'Y', 'Z', 'axial', 'torque')
+
+    Returns:
+        Dict with force statistics
+    """
+    from pyNastran.op2.op2 import OP2
+    import numpy as np
+
+    model = OP2()
+    model.read_op2(str(op2_file))
+
+    if not hasattr(model, 'cbar_force'):
+        raise ValueError("No CBAR force results in OP2")
+
+    force = model.cbar_force[subcase]
+    itime = 0
+
+    # CBAR force data structure:
+    # [bending_moment_a1, bending_moment_a2,
+    #  bending_moment_b1, bending_moment_b2,
+    #  shear1, shear2, axial, torque]
+
+    direction_map = {
+        'shear1': 4,
+        'shear2': 5,
+        'axial': 6,
+        'Z': 6,  # Commonly axial is Z direction
+        'torque': 7
+    }
+
+    col_idx = direction_map.get(direction, direction_map.get(direction.lower(), 6))
+    forces = force.data[itime, :, col_idx]
+
+    return {
+        f'max_{direction}_force': float(np.max(np.abs(forces))),
+        f'avg_{direction}_force': float(np.mean(np.abs(forces))),
+        f'min_{direction}_force': float(np.min(np.abs(forces))),
+        'forces_array': forces.tolist()
+    }
+
+
+if __name__ == '__main__':
+    # Example usage
+    import sys
+    if len(sys.argv) > 1:
+        op2_file = Path(sys.argv[1])
+        result = extract_cbar_force(op2_file)
+        print(f"Extraction result: {result}")
+    else:
+        print("Usage: python {sys.argv[0]} <op2_file>")

optimization_engine/result_extractors/generated/extract_displacement.py

@@ -0,0 +1,56 @@
+"""
+Extract displacement from OP2
+Auto-generated by Atomizer Phase 3 - pyNastran Research Agent
+
+Pattern: displacement
+Element Type: General
+Result Type: displacement
+API: model.displacements[subcase]
+"""
+
+from pathlib import Path
+from typing import Dict, Any
+import numpy as np
+from pyNastran.op2.op2 import OP2
+
+
+def extract_displacement(op2_file: Path, subcase: int = 1):
+    """Extract displacement results from OP2 file."""
+    from pyNastran.op2.op2 import OP2
+    import numpy as np
+
+    model = OP2()
+    model.read_op2(str(op2_file))
+
+    disp = model.displacements[subcase]
+    itime = 0  # static case
+
+    # Extract translation components
+    txyz = disp.data[itime, :, :3]  # [tx, ty, tz]
+
+    # Calculate total displacement
+    total_disp = np.linalg.norm(txyz, axis=1)
+    max_disp = np.max(total_disp)
+
+    # Get node info
+    node_ids = [nid for (nid, grid_type) in disp.node_gridtype]
+    max_disp_node = node_ids[np.argmax(total_disp)]
+
+    return {
+        'max_displacement': float(max_disp),
+        'max_disp_node': int(max_disp_node),
+        'max_disp_x': float(np.max(np.abs(txyz[:, 0]))),
+        'max_disp_y': float(np.max(np.abs(txyz[:, 1]))),
+        'max_disp_z': float(np.max(np.abs(txyz[:, 2])))
+    }
+
+
+if __name__ == '__main__':
+    # Example usage
+    import sys
+    if len(sys.argv) > 1:
+        op2_file = Path(sys.argv[1])
+        result = extract_displacement(op2_file)
+        print(f"Extraction result: {result}")
+    else:
+        print("Usage: python {sys.argv[0]} <op2_file>")

optimization_engine/result_extractors/generated/extract_solid_stress.py

@@ -0,0 +1,58 @@
+"""
+Extract von Mises stress from solid elements
+Auto-generated by Atomizer Phase 3 - pyNastran Research Agent
+
+Pattern: solid_stress
+Element Type: CTETRA
+Result Type: stress
+API: model.ctetra_stress[subcase] or model.chexa_stress[subcase]
+"""
+
+from pathlib import Path
+from typing import Dict, Any
+import numpy as np
+from pyNastran.op2.op2 import OP2
+
+
+def extract_solid_stress(op2_file: Path, subcase: int = 1, element_type: str = 'ctetra'):
+    """Extract stress from solid elements."""
+    from pyNastran.op2.op2 import OP2
+    import numpy as np
+
+    model = OP2()
+    model.read_op2(str(op2_file))
+
+    # Get stress object for element type
+    stress_attr = f"{element_type}_stress"
+    if not hasattr(model, stress_attr):
+        raise ValueError(f"No {element_type} stress results in OP2")
+
+    stress = getattr(model, stress_attr)[subcase]
+    itime = 0
+
+    # Extract von Mises if available
+    if stress.is_von_mises():
+        von_mises = stress.data[itime, :, 9]  # Column 9 is von Mises
+        max_stress = float(np.max(von_mises))
+
+        # Get element info
+        element_ids = [eid for (eid, node) in stress.element_node]
+        max_stress_elem = element_ids[np.argmax(von_mises)]
+
+        return {
+            'max_von_mises': max_stress,
+            'max_stress_element': int(max_stress_elem)
+        }
+    else:
+        raise ValueError("von Mises stress not available")
+
+
+if __name__ == '__main__':
+    # Example usage
+    import sys
+    if len(sys.argv) > 1:
+        op2_file = Path(sys.argv[1])
+        result = extract_solid_stress(op2_file)
+        print(f"Extraction result: {result}")
+    else:
+        print("Usage: python {sys.argv[0]} <op2_file>")