Antoine/Atomizer
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Anto01 f13563d7ab feat: Major update - Physics docs, Zernike OPD, insights, NX journals, tools 
Documentation:
- Add docs/06_PHYSICS/ with Zernike fundamentals and OPD method docs
- Add docs/guides/CMA-ES_EXPLAINED.md optimization guide
- Update CLAUDE.md and ATOMIZER_CONTEXT.md with current architecture
- Update OP_01_CREATE_STUDY protocol

Planning:
- Add DYNAMIC_RESPONSE plans for random vibration/PSD support
- Add OPTIMIZATION_ENGINE_MIGRATION_PLAN for code reorganization

Insights System:
- Update design_space, modal_analysis, stress_field, thermal_field insights
- Improve error handling and data validation

NX Journals:
- Add analyze_wfe_zernike.py for Zernike WFE analysis
- Add capture_study_images.py for automated screenshots
- Add extract_expressions.py and introspect_part.py utilities
- Add user_generated_journals/journal_top_view_image_taking.py

Tests & Tools:
- Add comprehensive Zernike OPD test suite
- Add audit_v10 tests for WFE validation
- Add tools for Pareto graphs and mirror data extraction
- Add migrate_studies_to_topics.py utility

Knowledge Base:
- Initialize LAC (Learning Atomizer Core) with failure/success patterns

Dashboard:
- Update Setup.tsx and launch_dashboard.py
- Add restart-dev.bat helper script

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

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
2025-12-23 19:47:37 -05:00
..
test_output/task_1_2_integration/generated_hooks
fix: Remove redundant save() call that overwrote NX expression updates
2025-11-17 21:24:02 -05:00
__init__.py
feat: Implement Option A - MCP Model Discovery tool
2025-11-15 13:23:05 +00:00
analyze_v11.py
feat: Add OPD method support to Zernike visualization with Standard/OPD toggle
2025-12-22 21:03:19 -05:00
audit_v10_fix.py
feat: Major update - Physics docs, Zernike OPD, insights, NX journals, tools
2025-12-23 19:47:37 -05:00
audit_v10_method_diff.py
feat: Major update - Physics docs, Zernike OPD, insights, NX journals, tools
2025-12-23 19:47:37 -05:00
audit_v10_wfe.py
feat: Major update - Physics docs, Zernike OPD, insights, NX journals, tools
2025-12-23 19:47:37 -05:00
Bracket_fem1_i.prt
feat: Add substudy system with live history tracking and workflow fixes
2025-11-16 21:29:54 -05:00
Bracket_fem1.fem
feat: Update model discovery to handle real binary NX files
2025-11-15 13:44:42 +00:00
bracket_sim1-solution_1.dat
feat: Add substudy system with live history tracking and workflow fixes
2025-11-16 21:29:54 -05:00
bracket_sim1-solution_1.t13980_32.asg
feat: Add substudy system with live history tracking and workflow fixes
2025-11-16 21:29:54 -05:00
Bracket_sim1.sim
feat: Add substudy system with live history tracking and workflow fixes
2025-11-16 21:29:54 -05:00
Bracket.prt
feat: Add substudy system with live history tracking and workflow fixes
2025-11-16 21:29:54 -05:00
check_api_routes.py
feat: Major update - Physics docs, Zernike OPD, insights, NX journals, tools
2025-12-23 19:47:37 -05:00
compare_v8_zernike_methods.py
feat: Add OPD method support to Zernike visualization with Standard/OPD toggle
2025-12-22 21:03:19 -05:00
debug_figure_coords.py
feat: Major update - Physics docs, Zernike OPD, insights, NX journals, tools
2025-12-23 19:47:37 -05:00
debug_insights.py
feat: Major update - Physics docs, Zernike OPD, insights, NX journals, tools
2025-12-23 19:47:37 -05:00
debug_lateral_discrepancy.py
feat: Add debug script for lateral displacement analysis
2025-12-23 15:03:32 -05:00
demo_research_agent.py
feat: Complete Phase 2.5-2.7 - Intelligent LLM-Powered Workflow Analysis
2025-11-16 13:35:41 -05:00
interactive_optimization_setup.py
feat: Add substudy system with live history tracking and workflow fixes
2025-11-16 21:29:54 -05:00
journal_apply_expression.py
fix: Apply expression updates directly in NX journal
2025-11-15 12:47:55 -05:00
journal_open_run_sim_and_save.py
feat: Add journal-based NX solver integration for optimization
2025-11-15 12:23:57 -05:00
journal_open_run_sim.py
feat: Add journal-based NX solver integration for optimization
2025-11-15 12:23:57 -05:00
journal_reload_master.py
feat: Add journal-based NX solver integration for optimization
2025-11-15 12:23:57 -05:00
journal_with_regenerate.py
feat: Implement complete FEM regeneration workflow
2025-11-15 12:43:31 -05:00
run_5trial_test.py
docs: Reorganize documentation structure
2025-11-16 08:40:53 -05:00
run_beam_benchmarking_clean.py
fix: Remove redundant save() call that overwrote NX expression updates
2025-11-17 21:24:02 -05:00
run_beam_benchmarking.py
fix: Remove redundant save() call that overwrote NX expression updates
2025-11-17 21:24:02 -05:00
run_benchmarking_simple.py
fix: Remove redundant save() call that overwrote NX expression updates
2025-11-17 21:24:02 -05:00
setup_beam_optimization.py
fix: Remove redundant save() call that overwrote NX expression updates
2025-11-17 21:24:02 -05:00
test_api_verification.py
test: Add API verification test with hardcoded key for periodic checks
2025-11-17 09:27:52 -05:00
test_beam_workflow.py
fix: Remove redundant save() call that overwrote NX expression updates
2025-11-17 21:24:02 -05:00
test_bracket_full_optimization.py
feat: Add substudy system with live history tracking and workflow fixes
2025-11-16 21:29:54 -05:00
test_bracket_llm_runner.py
feat: Add substudy system with live history tracking and workflow fixes
2025-11-16 21:29:54 -05:00
test_cbar_genetic_algorithm.py
feat: Complete Phase 2.5-2.7 - Intelligent LLM-Powered Workflow Analysis
2025-11-16 13:35:41 -05:00
test_cbush_optimization.py
feat: Complete Phase 2.5-2.7 - Intelligent LLM-Powered Workflow Analysis
2025-11-16 13:35:41 -05:00
test_code_generation.py
feat: Complete Phase 2.5-2.7 - Intelligent LLM-Powered Workflow Analysis
2025-11-16 13:35:41 -05:00
test_complete_research_workflow.py
feat: Complete Phase 2.5-2.7 - Intelligent LLM-Powered Workflow Analysis
2025-11-16 13:35:41 -05:00
test_complex_multiobj_request.py
feat: Complete Phase 2.5-2.7 - Intelligent LLM-Powered Workflow Analysis
2025-11-16 13:35:41 -05:00
test_hooks_with_bracket.py
docs: Reorganize documentation structure
2025-11-16 08:40:53 -05:00
test_insights_import.py
feat: Major update - Physics docs, Zernike OPD, insights, NX journals, tools
2025-12-23 19:47:37 -05:00
test_interactive_session.py
feat: Complete Phase 2.5-2.7 - Intelligent LLM-Powered Workflow Analysis
2025-11-16 13:35:41 -05:00
test_journal_optimization.py
docs: Reorganize documentation structure
2025-11-16 08:40:53 -05:00
test_knowledge_base_search.py
feat: Complete Phase 2.5-2.7 - Intelligent LLM-Powered Workflow Analysis
2025-11-16 13:35:41 -05:00
test_lifecycle_hook_integration.py
feat: Complete Phase 3 - pyNastran Documentation Integration
2025-11-16 16:33:48 -05:00
test_llm_complex_request.py
feat: Complete Phase 2.5-2.7 - Intelligent LLM-Powered Workflow Analysis
2025-11-16 13:35:41 -05:00
test_llm_runner_init.py
feat: Add substudy system with live history tracking and workflow fixes
2025-11-16 21:29:54 -05:00
test_modal_deformation_request.py
feat: Complete Phase 2.5-2.7 - Intelligent LLM-Powered Workflow Analysis
2025-11-16 13:35:41 -05:00
test_nxopen_intellisense.py
fix: Update intellisense test to prevent execution errors
2025-11-17 08:57:08 -05:00
test_optimization_setup_wizard.py
feat: Add substudy system with live history tracking and workflow fixes
2025-11-16 21:29:54 -05:00
test_phase_2_5_intelligent_gap_detection.py
feat: Complete Phase 2.5-2.7 - Intelligent LLM-Powered Workflow Analysis
2025-11-16 13:35:41 -05:00
test_phase_3_1_integration.py
feat: Complete Phase 3.1 - Extractor Orchestration & End-to-End Automation
2025-11-16 19:39:04 -05:00
test_phase_3_2_e2e.py
refactor: Implement centralized extractor library to eliminate code duplication
2025-11-18 09:00:10 -05:00
test_phase_3_2_llm_mode.py
feat: Phase 3.2 Task 1.2 - Wire LLMOptimizationRunner to production
2025-11-17 20:48:40 -05:00
test_plugin_system.py
feat: Implement Phase 1 - Plugin & Hook System
2025-11-15 14:46:49 -05:00
test_research_agent.py
feat: Complete Phase 2.5-2.7 - Intelligent LLM-Powered Workflow Analysis
2025-11-16 13:35:41 -05:00
test_step_classifier.py
feat: Complete Phase 2.5-2.7 - Intelligent LLM-Powered Workflow Analysis
2025-11-16 13:35:41 -05:00
test_task_1_2_integration.py
feat: Phase 3.2 Task 1.2 - Wire LLMOptimizationRunner to production
2025-11-17 20:48:40 -05:00
test_timestamp_verification.py
feat: Add substudy system with live history tracking and workflow fixes
2025-11-16 21:29:54 -05:00
test_training_data_exporter.py
feat: Add AtomizerField training data export and intelligent model discovery
2025-11-26 12:01:50 -05:00
test_zernike_import.py
feat: Major update - Physics docs, Zernike OPD, insights, NX journals, tools
2025-12-23 19:47:37 -05:00
test_zernike_insight.py
feat: Major update - Physics docs, Zernike OPD, insights, NX journals, tools
2025-12-23 19:47:37 -05:00
test_zernike_methods_comparison.py
feat: Add OPD method support to Zernike visualization with Standard/OPD toggle
2025-12-22 21:03:19 -05:00
test_zernike_opd_comparison.py
feat: Major update - Physics docs, Zernike OPD, insights, NX journals, tools
2025-12-23 19:47:37 -05:00
test_zernike_opd_with_prescription.py
feat: Major update - Physics docs, Zernike OPD, insights, NX journals, tools
2025-12-23 19:47:37 -05:00
verify_parametric_link.py
feat: Implement complete FEM regeneration workflow
2025-11-15 12:43:31 -05:00