refactor: Major project cleanup and reorganization
## Removed Duplicate Directories - Deleted old `dashboard/` (replaced by atomizer-dashboard) - Deleted old `mcp_server/` Python tools (moved model_discovery to optimization_engine) - Deleted `tests/mcp_server/` (obsolete tests) - Deleted `launch_dashboard.bat` (old launcher) ## Consolidated Code - Moved `mcp_server/tools/model_discovery.py` to `optimization_engine/model_discovery/` - Updated import in `optimization_config_builder.py` - Deleted stub `extract_mass.py` (use extract_mass_from_bdf instead) - Deleted unused `intelligent_setup.py` and `hybrid_study_creator.py` - Archived `result_extractors/` to `archive/deprecated/` ## Documentation Cleanup - Deleted deprecated `docs/06_PROTOCOLS_DETAILED/` (14 files) - Archived dated dev docs to `docs/08_ARCHIVE/sessions/` - Archived old plans to `docs/08_ARCHIVE/plans/` - Updated `docs/protocols/README.md` with SYS_15 ## Skills Consolidation - Archived redundant study creation skills to `.claude/skills/archive/` - Kept `core/study-creation-core.md` as canonical ## Housekeeping - Updated `.gitignore` to prevent `nul` and `_dat_run*.dat` 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
This commit is contained in:
Antoine
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"""
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Extract element forces from CBAR in Z direction from OP2
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Auto-generated by Atomizer Phase 3 - pyNastran Research Agent
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Pattern: cbar_force
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Element Type: CBAR
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Result Type: force
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API: model.cbar_force[subcase]
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"""
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from pathlib import Path
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from typing import Dict, Any
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import numpy as np
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from pyNastran.op2.op2 import OP2
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def extract_cbar_force(op2_file: Path, subcase: int = 1, direction: str = 'Z'):
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"""
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Extract forces from CBAR elements.
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Args:
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op2_file: Path to OP2 file
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subcase: Subcase ID
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direction: Force direction ('X', 'Y', 'Z', 'axial', 'torque')
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Returns:
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Dict with force statistics
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"""
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from pyNastran.op2.op2 import OP2
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import numpy as np
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model = OP2()
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model.read_op2(str(op2_file))
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if not hasattr(model, 'cbar_force'):
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raise ValueError("No CBAR force results in OP2")
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force = model.cbar_force[subcase]
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itime = 0
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# CBAR force data structure:
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# [bending_moment_a1, bending_moment_a2,
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# bending_moment_b1, bending_moment_b2,
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# shear1, shear2, axial, torque]
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direction_map = {
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'shear1': 4,
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'shear2': 5,
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'axial': 6,
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'Z': 6, # Commonly axial is Z direction
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'torque': 7
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}
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col_idx = direction_map.get(direction, direction_map.get(direction.lower(), 6))
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forces = force.data[itime, :, col_idx]
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return {
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f'max_{direction}_force': float(np.max(np.abs(forces))),
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f'avg_{direction}_force': float(np.mean(np.abs(forces))),
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f'min_{direction}_force': float(np.min(np.abs(forces))),
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'forces_array': forces.tolist()
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}
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if __name__ == '__main__':
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# Example usage
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import sys
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if len(sys.argv) > 1:
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op2_file = Path(sys.argv[1])
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result = extract_cbar_force(op2_file)
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print(f"Extraction result: {result}")
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else:
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print("Usage: python {sys.argv[0]} <op2_file>")
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@@ -0,0 +1,56 @@
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"""
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Extract displacement from OP2
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Auto-generated by Atomizer Phase 3 - pyNastran Research Agent
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Pattern: displacement
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Element Type: General
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Result Type: displacement
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API: model.displacements[subcase]
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"""
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from pathlib import Path
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from typing import Dict, Any
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import numpy as np
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from pyNastran.op2.op2 import OP2
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def extract_displacement(op2_file: Path, subcase: int = 1):
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"""Extract displacement results from OP2 file."""
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from pyNastran.op2.op2 import OP2
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import numpy as np
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model = OP2()
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model.read_op2(str(op2_file))
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disp = model.displacements[subcase]
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itime = 0 # static case
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# Extract translation components
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txyz = disp.data[itime, :, :3] # [tx, ty, tz]
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# Calculate total displacement
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total_disp = np.linalg.norm(txyz, axis=1)
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max_disp = np.max(total_disp)
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# Get node info
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node_ids = [nid for (nid, grid_type) in disp.node_gridtype]
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max_disp_node = node_ids[np.argmax(total_disp)]
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return {
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'max_displacement': float(max_disp),
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'max_disp_node': int(max_disp_node),
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'max_disp_x': float(np.max(np.abs(txyz[:, 0]))),
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'max_disp_y': float(np.max(np.abs(txyz[:, 1]))),
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'max_disp_z': float(np.max(np.abs(txyz[:, 2])))
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}
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if __name__ == '__main__':
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# Example usage
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import sys
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if len(sys.argv) > 1:
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op2_file = Path(sys.argv[1])
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result = extract_displacement(op2_file)
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print(f"Extraction result: {result}")
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else:
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print("Usage: python {sys.argv[0]} <op2_file>")
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@@ -0,0 +1,55 @@
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"""
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Extract expression value from NX .prt file
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Used for extracting computed values like mass, volume, etc.
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This extractor reads expressions using the .exp export method for accuracy.
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"""
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from pathlib import Path
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from typing import Dict, Any
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from optimization_engine.nx_updater import NXParameterUpdater
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def extract_expression(prt_file: Path, expression_name: str):
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"""
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Extract an expression value from NX .prt file.
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Args:
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prt_file: Path to .prt file
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expression_name: Name of expression to extract (e.g., 'p173' for mass)
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Returns:
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Dict with expression value and units
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"""
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updater = NXParameterUpdater(prt_file, backup=False)
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expressions = updater.get_all_expressions(use_exp_export=True)
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if expression_name not in expressions:
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raise ValueError(f"Expression '{expression_name}' not found in {prt_file}")
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expr_info = expressions[expression_name]
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# If expression is a formula (value is None), we need to evaluate it
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# For now, we'll raise an error if it's a formula - user should use the computed value
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if expr_info['value'] is None and expr_info['formula'] is not None:
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raise ValueError(
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f"Expression '{expression_name}' is a formula: {expr_info['formula']}. "
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f"This extractor requires a computed value, not a formula reference."
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)
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return {
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expression_name: expr_info['value'],
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f'{expression_name}_units': expr_info['units']
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}
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if __name__ == '__main__':
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# Example usage
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import sys
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if len(sys.argv) > 2:
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prt_file = Path(sys.argv[1])
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expression_name = sys.argv[2]
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result = extract_expression(prt_file, expression_name)
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print(f"Extraction result: {result}")
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else:
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print(f"Usage: python {sys.argv[0]} <prt_file> <expression_name>")
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@@ -0,0 +1,127 @@
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"""
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Extract von Mises stress from solid and shell elements
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Auto-generated by Atomizer Phase 3 - pyNastran Research Agent
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Pattern: element_stress
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Element Types: CTETRA, CHEXA, CPENTA (solids), CQUAD4, CTRIA3 (shells)
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Result Type: stress
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API: model.ctetra_stress[subcase], model.cquad4_stress[subcase], etc.
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"""
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from pathlib import Path
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from typing import Dict, Any
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import numpy as np
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from pyNastran.op2.op2 import OP2
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def extract_solid_stress(op2_file: Path, subcase: int = 1, element_type: str = 'auto'):
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"""
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Extract stress from solid or shell elements.
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Args:
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op2_file: Path to OP2 file
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subcase: Subcase number (default 1)
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element_type: Element type ('ctetra', 'chexa', 'cquad4', 'ctria3', or 'auto')
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'auto' will detect available element types
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Returns:
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Dict with max von Mises stress and element info
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"""
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from pyNastran.op2.op2 import OP2
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import numpy as np
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model = OP2()
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model.read_op2(str(op2_file))
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# Auto-detect element type if requested
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if element_type == 'auto':
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# Try common element types in order
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# pyNastran uses "stress.{element}_stress" as attribute names (with dot in name!)
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possible_types = ['cquad4', 'ctria3', 'ctetra', 'chexa', 'cpenta']
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element_type = None
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for elem_type in possible_types:
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stress_attr = f"stress.{elem_type}_stress"
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try:
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stress_dict = getattr(model, stress_attr, None)
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if isinstance(stress_dict, dict) and subcase in stress_dict:
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element_type = elem_type
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break
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except AttributeError:
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continue
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if element_type is None:
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raise ValueError(f"No stress results found in OP2 for subcase {subcase}")
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# Get stress object for element type
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# pyNastran stores stress as "stress.{element}_stress" (e.g., "stress.cquad4_stress")
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stress_attr = f"stress.{element_type}_stress"
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try:
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stress_dict = getattr(model, stress_attr)
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except AttributeError:
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raise ValueError(f"No {element_type} stress results in OP2")
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if not isinstance(stress_dict, dict) or subcase not in stress_dict:
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raise ValueError(f"Subcase {subcase} not found in {element_type} stress results")
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stress = stress_dict[subcase]
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itime = 0
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# Extract von Mises
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# For CQUAD4/CTRIA3 (shells): data shape is [ntimes, nelements, 8]
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# Columns: [fiber_distance, oxx, oyy, txy, angle, omax, omin, von_mises]
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# Column 7 (0-indexed) is von Mises
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#
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# For CTETRA/CHEXA (solids): Column 9 is von Mises
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if element_type in ['cquad4', 'ctria3']:
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# Shell elements - von Mises is at column 7
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von_mises = stress.data[itime, :, 7]
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else:
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# Solid elements - von Mises is at column 9
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von_mises = stress.data[itime, :, 9]
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# Raw stress values from OP2 (in internal Nastran units)
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max_stress_raw = float(np.max(von_mises))
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min_stress_raw = float(np.min(von_mises))
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avg_stress_raw = float(np.mean(von_mises))
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# Convert to MPa
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# For MN-MM unit system (UNITSYS=MN-MM), Nastran outputs stress with implied decimal
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# The raw value needs to be divided by 1000 to get MPa
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# Example: 131507.1875 (raw) = 131.507 MPa
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max_stress_mpa = max_stress_raw / 1000.0
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min_stress_mpa = min_stress_raw / 1000.0
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avg_stress_mpa = avg_stress_raw / 1000.0
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# Get element info
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if hasattr(stress, 'element_node'):
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element_ids = stress.element_node[:, 0] # First column is element ID
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elif hasattr(stress, 'element'):
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element_ids = stress.element
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else:
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element_ids = np.arange(len(von_mises))
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max_stress_elem = int(element_ids[np.argmax(von_mises)])
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return {
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'max_von_mises': max_stress_mpa,
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'min_von_mises': min_stress_mpa,
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'avg_von_mises': avg_stress_mpa,
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'max_stress_element': max_stress_elem,
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'element_type': element_type,
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'num_elements': len(von_mises),
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'units': 'MPa'
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}
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if __name__ == '__main__':
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# Example usage
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import sys
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if len(sys.argv) > 1:
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op2_file = Path(sys.argv[1])
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result = extract_solid_stress(op2_file)
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print(f"Extraction result: {result}")
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else:
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print("Usage: python {sys.argv[0]} <op2_file>")
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