feat: Complete Phase 3 - pyNastran Documentation Integration

Phase 3 implements automated OP2 extraction code generation using
pyNastran documentation research. This completes the zero-manual-coding
pipeline for FEA optimization workflows.

Key Features:
- PyNastranResearchAgent for automated OP2 code generation
- Documentation research via WebFetch integration
- 3 core extraction patterns (displacement, stress, force)
- Knowledge base architecture for learned patterns
- Successfully tested on real OP2 files

Phase 2.9 Integration:
- Updated HookGenerator with lifecycle hook generation
- Added POST_CALCULATION hook point to hooks.py
- Created post_calculation/ plugin directory
- Generated hooks integrate seamlessly with HookManager

New Files:
- optimization_engine/pynastran_research_agent.py (600+ lines)
- optimization_engine/hook_generator.py (800+ lines)
- optimization_engine/inline_code_generator.py
- optimization_engine/plugins/post_calculation/
- tests/test_lifecycle_hook_integration.py
- docs/SESSION_SUMMARY_PHASE_3.md
- docs/SESSION_SUMMARY_PHASE_2_9.md
- docs/SESSION_SUMMARY_PHASE_2_8.md
- docs/HOOK_ARCHITECTURE.md

Modified Files:
- README.md - Added Phase 3 completion status
- optimization_engine/plugins/hooks.py - Added POST_CALCULATION hook

Test Results:
- Phase 3 research agent: PASSED
- Real OP2 extraction: PASSED (max_disp=0.362mm)
- Lifecycle hook integration: PASSED

Generated with Claude Code

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

generated_extractors/cbar_force_extractor.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>")

generated_extractors/test_displacement_extractor.py

@@ -0,0 +1,56 @@
+"""
+Extract displacement from bracket 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>")