Archive Management:
- Moved RALPH_LOOP, CANVAS, and dashboard implementation plans to archive/review/ for CEO review
- Moved completed restructuring plan and protocol v1 to archive/historical/
- Moved old session summaries to archive/review/
New HQ Documentation (docs/hq/):
- README.md: Overview of Atomizer-HQ multi-agent optimization team
- PROJECT_STRUCTURE.md: Standard KB-integrated project layout with Hydrotech reference
- KB_CONVENTIONS.md: Knowledge Base accumulation principles with generation tracking
- AGENT_WORKFLOWS.md: Project lifecycle phases and agent handoffs (OP_09 integration)
- STUDY_CONVENTIONS.md: Technical study execution standards and atomizer_spec.json format
Index Update:
- Reorganized docs/00_INDEX.md with HQ docs prominent
- Updated structure to reflect new agent-focused organization
- Maintained core documentation access for engineers
No files deleted, only moved to appropriate archive locations.
New project structure with knowledge base integration:
- kb/ with components, materials, fea, dev generations
- models/ for reference NX files (golden copies)
- studies/ for self-contained optimization campaigns
- deliverables/ for final outputs
- DECISIONS.md decision log (6 decisions tracked)
- BREAKDOWN.md (moved from 1_breakdown/)
- Gen 001 created from intake + technical breakdown
KB extension file: atomizer/shared/skills/knowledge-base-atomizer-ext.md
Refs: DEC-HB-004, DEC-HB-005, DEC-HB-006
- Embed Plotly.js inline for offline viewing (fixes CDN loading issues)
- Add 4x resolution PNG export for all charts via toImageButtonOptions
- Add SAT3_Trajectory_V7 study (TPE warm-start from V5, 86 trials, WS=277.37)
- Include V7 optimization report and configuration
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Generates publication-ready PSD figures from OP2 FEA data:
- psd_multi_angle.png: PSD curves for all elevation angles
- psd_band_decomposition.png: LSF/MSF/HSF bar chart
- psd_40deg_composite.png: WFE surface + PSD side-by-side
- psd_trajectory.png: Band evolution vs elevation
Uses Atomizer's full OPD pipeline for consistency with CDR WFE numbers.
- tools/wfe_psd.py: Quick PSD computation for WFE surfaces
- optimization_engine/insights/wfe_psd.py: Full PSD module with band
decomposition (LSF/MSF/HSF), radial averaging, Hann windowing,
and visualization support
- knowledge_base/lac/session_insights/stopp_command_20260129.jsonl:
Session insight from stopp command implementation
PSD analysis decomposes WFE into spatial frequency bands per Tony Hull's
JWST methodology. Used for CDR V7 to validate that MSF (support
print-through) dominates the residual WFE at 85-89% of total RMS.
- X-axis now auto-ranges from data (was going to 10^21)
- Band annotations clamped to actual data extent
- Legend moved to upper-right (was overlapping data)
- Thicker lines (2.5px), larger axis labels
- dtick=1 for clean log-scale tick marks
- Band RMS now uses direct Parseval: sqrt(sum(|FFT|²) / N⁴ / hann_power)
- Previous approach had dimensional mismatch (cycles/apt vs cycles/mm)
- Results now match Zernike filtered RMS within ~10%:
40° vs 20°: PSD=6.18nm vs Zernike=7.70nm
60° vs 20°: PSD=15.83nm vs Zernike=17.69nm
90° Abs: PSD=27.01nm vs Zernike=22.33nm
- PSD plot curve uses separate normalization (shape, not absolute)
- Refactored compute_surface_psd to return dict with freqs, psd, bands
- Remove compute_spatial_freq_metrics() and _spatial_freq_html()
- Add compute_surface_psd(): 2D FFT + Hann window + radial averaging
- Add compute_psd_band_rms(): gravity/support/HF band decomposition
- Add make_psd_plot(): interactive log-log PSD plot with band annotations
- Add _psd_summary_html(): band RMS cards with % breakdown
- New section in report: Power Spectral Density Analysis
- Zernike details now show only coefficient bar charts (cleaner)
- Methodology: Tony Hull JWST approach for WFE spatial frequency analysis
New tool: tools/generate_optical_report.py
- CDR-ready single HTML report from OP2 results
- Executive summary with pass/fail vs targets
- Per-angle WFE analysis with 3D surface plots
- Zernike trajectory analysis (mode-specific RMS)
- Axial vs lateral sensitivity matrix
- Manufacturing correction metrics
- Collapsible Zernike coefficient bar charts
- Optional study DB integration for design params
- Annular aperture support (default M1 inner R=135.75mm)
- Dark theme, interactive Plotly charts, print-friendly
- Replace brittle order-based subcase mapping with name-based search
- Tools now directly search for required angles (20, 40, 60, 90) by label
- Ignores extra subcases (e.g., 30, 50 degrees) without errors
- Falls back to numeric IDs (1,2,3,4) if angle labels not found
- Clear error messages show exactly which subcases are missing
This allows running WFE analysis on simulations with >4 subcases
without manual file/code modifications.
Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
## DevLoop - Closed-Loop Development System
- Orchestrator for plan → build → test → analyze cycle
- Gemini planning via OpenCode CLI
- Claude implementation via CLI bridge
- Playwright browser testing integration
- Test runner with API, filesystem, and browser tests
- Persistent state in .devloop/ directory
- CLI tool: tools/devloop_cli.py
Usage:
python tools/devloop_cli.py start 'Create new feature'
python tools/devloop_cli.py plan 'Fix bug in X'
python tools/devloop_cli.py test --study support_arm
python tools/devloop_cli.py browser --level full
## HTML Reports (optimization_engine/reporting/)
- Interactive Plotly-based reports
- Convergence plot, Pareto front, parallel coordinates
- Parameter importance analysis
- Self-contained HTML (offline-capable)
- Tailwind CSS styling
## Playwright E2E Tests
- Home page tests
- Test results in test-results/
## LAC Knowledge Base Updates
- Session insights (failures, workarounds, patterns)
- Optimization memory for arm support study
Phase 4 - Live Updates:
- Create useOptimizationStream hook for real-time trial updates
- Replace polling with WebSocket subscription in SpecRenderer
- Auto-report errors to ErrorPanel via panel store
- Add progress tracking (FEA count, NN count, best trial)
Phase 5 - Convergence Visualization:
- Add ConvergenceSparkline component for mini line charts
- Add ProgressRing component for circular progress indicator
- Update ObjectiveNode to show convergence trend sparkline
- Add history field to ObjectiveNodeData schema
- Add live progress indicator centered on canvas when running
Bug fixes:
- Fix TypeScript errors in FloatingIntrospectionPanel (type casts)
- Fix ValidationPanel using wrong store method (selectNode vs setSelectedNodeId)
- Fix NodeConfigPanelV2 unused state variable
- Fix specValidator source.extractor_id path
- Clean up unused imports across components
Phase 1 - Panel Management System:
- Create usePanelStore.ts for centralized panel state management
- Add PanelContainer.tsx for draggable floating panels
- Create FloatingIntrospectionPanel.tsx (persistent, doesn't disappear on node click)
- Create ResultsPanel.tsx for trial result details
- Refactor NodeConfigPanelV2 to use panel store for introspection
- Integrate PanelContainer into CanvasView
Phase 2 - Pre-run Validation:
- Create specValidator.ts with comprehensive validation rules
- Add ValidationPanel (enhanced version with error navigation)
- Add Validate button to SpecRenderer with status indicator
- Block run if validation fails
- Check for: design vars, objectives, extractors, bounds, connections
Phase 3 - Error Handling & Recovery:
- Create ErrorPanel.tsx for displaying optimization errors
- Add error classification (nx_crash, solver_fail, extractor_error, etc.)
- Add recovery suggestions based on error type
- Update status endpoint to return error info
- Add _get_study_error_info helper to check error_status.json and DB
- Integrate error detection into status polling
Documentation:
- Add CANVAS_ROBUSTNESS_PLAN.md with full implementation plan
Phase 2 - Execution Bridge:
- Update /start endpoint to fallback to generic runner when no study script exists
- Auto-detect model files (.prt, .sim) from 1_setup/model/ directory
- Pass atomizer_spec.json path to generic runner
Phase 3 - Live Monitoring & Results Overlay:
- Add ResultBadge component for displaying values on canvas nodes
- Extend schema with resultValue and isFeasible fields
- Update DesignVarNode, ObjectiveNode, ConstraintNode, ExtractorNode to show results
- Add Run/Stop buttons and Results toggle to SpecRenderer
- Poll /status endpoint every 3s and map best_trial values to nodes
- Show green/red badges for constraint feasibility
- Create introspect_sim.py NX journal to extract solutions, BCs from SIM files
- Update introspect_sim_file() to optionally call NX journal for full introspection
- Add FEM mesh section (nodes, elements, materials, properties) to IntrospectionPanel
- Add SIM solutions and boundary conditions sections to IntrospectionPanel
- Show introspection method and NX errors in panel
- Fetch available parts from /nx/parts on panel mount
- Dropdown to select which part to introspect (default = assembly)
- Hides idealized parts (*_i.prt) from dropdown
- Shows part size in dropdown (KB or MB)
- Header shows selected part name in primary color
- Refresh button respects current part selection
- Auto-introspects when part selection changes
Backend:
- GET /nx/parts - List all .prt files in model directory
- GET /nx/introspect/{part_name} - Introspect a specific part file
(e.g., M1_Blank.prt instead of just the assembly)
- Each part gets its own cache file (_introspection_{stem}.json)
Frontend IntrospectionPanel:
- Add 'FEA Results' section showing existing OP2/F06 sources
- Green checkmark when results exist, shows recommended source
- Expand file_deps and fea_results sections by default
- Add CheckCircle2 and Database icons
This allows introspecting component parts that contain the actual
design variable expressions (e.g., M1_Blank has 56 expressions
while the assembly ASSY_M1 only has 5).
- scan_existing_fea_results() scans study for existing OP2/F06 files
- Introspection now returns existing_fea_results with recommended source
- New POST /nx/extract endpoint runs extractors on existing OP2 files
- Supports: displacement, stress, frequency, mass_bdf, zernike
- No NX solve needed - uses PyNastran and Atomizer extractors directly
This allows users to test extractors and get physics data from existing
simulation results without re-running the FEA solver.
- Use same approach as run_optimization.py with use_iteration_folders=True
- NXSolver.create_iteration_folder() handles proper file copying
- Read NX settings from atomizer_spec.json or optimization_config.json
- Extract Nastran version from NX install path
- Creates iter0 folder for baseline (consistent with optimization numbering)
This fixes the issue where manually copying files didn't preserve
NX file dependency chain (.sim -> .afm -> .fem -> _i.prt -> .prt)
- Parse Nastran log file to detect memory allocation failures
- Extract requested vs available memory from log
- Provide actionable error message with specific values
- Include log files in result_files response
- Read nx_install_path from atomizer_spec.json if available
- Auto-detect from common Siemens installation paths
- Fixes issue where NX2512 wasn't found (actual path is DesigncenterNX2512)
Drag-drop fixes:
- Fix Objective default data: use nested 'source' object with extractor_id/output_name
- Fix Constraint default data: use 'type' field (not constraint_type), 'threshold' (not limit)
Undo/Redo fixes:
- Remove dependency on isDirty flag (which is always false due to auto-save)
- Record snapshots based on actual spec changes via deep comparison
Code generation improvements:
- Update system prompt to support multiple extractor types:
* OP2-based extractors for FEA results (stress, displacement, frequency)
* Expression-based extractors for NX model values (dimensions, volumes)
* Computed extractors for derived values (no FEA needed)
- Claude will now choose appropriate signature based on user's description
Backend:
- Add POST /api/optimization/studies/{study_id}/nx/run-baseline endpoint
- Creates trial_baseline folder in 2_iterations/
- Copies all model files and runs NXSolver
- Returns paths to result files (.op2, .f06, .bdf) for extractor testing
Frontend:
- Add 'Run Baseline Simulation' button to IntrospectionPanel
- Show progress spinner during simulation
- Display result files when complete (OP2, F06, BDF)
- Show error messages if simulation fails
This enables:
- Testing custom extractors against real FEA results
- Validating the simulation pipeline before optimization
- Inspecting boundary conditions and loads
