Physics MCP Server

# Phase 8: Experiment Orchestrator Examples This document provides examples of using the `experiment_orchestrator` tool for DAG definition, validation, execution, and collaboration. ## Define DAG Examples ### Hydrogen 2p Exemplar (Natural Language) ```json { "tool": "experiment_orchestrator", "method": "define_dag", "natural_language": "Analyze hydrogen 2p orbital: get physical constants, solve Schrödinger equation, plot wavefunction, and create time evolution animation" } ``` ### Explicit DAG Specification ```json { "tool": "experiment_orchestrator", "method": "define_dag", "spec": { "nodes": [ { "id": "get_constants", "tool": "constants_get", "params": {"name": "hbar"}, "visual_outputs": {"static": false, "series": false, "animation": false} }, { "id": "solve_quantum", "tool": "quantum", "method": "solve", "params": { "problem": "particle_in_box", "params": {"n": 2, "L": 1.0} }, "dependencies": ["get_constants"], "visual_outputs": {"static": true, "series": true, "animation": false} }, { "id": "plot_wavefunction", "tool": "plot", "method": "function_2d", "params": { "f": "sin(2*pi*x)", "x": [-1, 1, 100], "title": "Hydrogen 2p Wavefunction", "emit_plots": true, "emit_csv": true }, "dependencies": ["solve_quantum"], "visual_outputs": {"static": true, "series": true, "animation": false} }, { "id": "create_animation", "tool": "plot", "method": "animation", "params": { "frame_expr": "sin(2*pi*x - t)", "x_range": [-1, 1, 100], "t_range": [0, 2, 60], "title": "Time Evolution", "emit_animation": true, "format": "mp4" }, "dependencies": ["plot_wavefunction"], "visual_outputs": {"static": false, "series": false, "animation": true} }, { "id": "symbolic_analysis", "tool": "ml_ai_augmentation", "method": "symbolic_regression_train", "params": { "X": "wavefunction_data.csv", "y": "energy_data.csv", "max_depth": 8, "pop_size": 500 }, "dependencies": ["solve_quantum"], "visual_outputs": {"static": true, "series": true, "animation": false} } ], "edges": [ {"from": "get_constants", "to": "solve_quantum", "data_key": "hbar"}, {"from": "solve_quantum", "to": "plot_wavefunction", "data_key": "wavefunction"}, {"from": "plot_wavefunction", "to": "create_animation", "data_key": "static_plot"}, {"from": "solve_quantum", "to": "symbolic_analysis", "data_key": "quantum_data"} ], "metadata": { "title": "Comprehensive Hydrogen 2p Analysis", "description": "Multi-method analysis combining quantum mechanics, visualization, and ML", "author": "Physics Research Team", "version": "1.0" } } } ``` ## Validate DAG Examples ```json { "tool": "experiment_orchestrator", "method": "validate_dag", "dag_id": "dag_abc123def456" } ``` ## Run DAG Examples ### Local Execution ```json { "tool": "experiment_orchestrator", "method": "run_dag", "dag_id": "dag_abc123def456", "parallelism": 4, "offload_policy": "local_first" } ``` ### Distributed Execution ```json { "tool": "experiment_orchestrator", "method": "run_dag", "dag_id": "dag_abc123def456", "parallelism": 8, "offload_policy": "remote_first" } ``` ### Auto Scheduling ```json { "tool": "experiment_orchestrator", "method": "run_dag", "dag_id": "dag_abc123def456", "parallelism": 6, "offload_policy": "auto" } ``` ## Publish Report Examples ### Basic Report ```json { "tool": "experiment_orchestrator", "method": "publish_report", "run_id": "run_xyz789abc123", "title": "Hydrogen 2p Orbital Analysis Results", "authors": ["Dr. Jane Smith", "Dr. John Doe"], "bib": [ "@article{schrodinger1926, title={An Undulatory Theory of the Mechanics of Atoms and Molecules}, author={Schrödinger, Erwin}, journal={Physical Review}, volume={28}, number={6}, pages={1049--1070}, year={1926}}", "@book{griffiths2018, title={Introduction to Quantum Mechanics}, author={Griffiths, David J.}, edition={3}, publisher={Cambridge University Press}, year={2018}}" ] } ``` ## Collaborate Share Examples ### Share DAG with Team ```json { "tool": "experiment_orchestrator", "method": "collaborate_share", "dag_id": "dag_abc123def456", "access": "write", "participants": [ "alice@physics-lab.edu", "bob@physics-lab.edu", "research-team@university.edu" ] } ``` ### Read-Only Share ```json { "tool": "experiment_orchestrator", "method": "collaborate_share", "dag_id": "dag_abc123def456", "access": "read", "participants": ["reviewer@journal.com"] } ``` ## Legacy Tool Usage Individual methods can be called directly: ```json { "tool": "define_dag", "natural_language": "Create a simple physics simulation workflow" } ``` ```json { "tool": "run_dag", "dag_id": "dag_123", "parallelism": 2 } ``` ## Response Examples ### Define DAG Response ```json { "dag_id": "dag_abc123def456", "validated": true, "nodes": [ { "id": "get_constants", "tool": "constants_get", "params": {"name": "hbar"}, "visual_outputs": {"static": false, "series": false, "animation": false} } ], "edges": [ {"from": "get_constants", "to": "solve_quantum", "data_key": "hbar"} ], "ui_overview_png_b64": "iVBORw0KGgoAAAANSUhEUgAAAoAAAAHgCAYAAAA..." } ``` ### Validate DAG Response ```json { "dag_id": "dag_abc123def456", "ok": true, "warnings": [ "Node 'plot_node' should declare visual outputs for better report generation" ] } ``` ### Run DAG Response ```json { "run_id": "run_xyz789abc123", "artifacts": [ "artifacts/session_abc123/wavefunction_plot.png", "artifacts/session_abc123/energy_data.csv", "artifacts/session_abc123/time_evolution.mp4", "artifacts/session_abc123/symbolic_regression_results.png" ], "reportable": { "figures": [ { "path": "artifacts/session_abc123/wavefunction_plot.png", "caption": "Hydrogen 2p wavefunction visualization showing radial and angular components", "node_id": "plot_wavefunction" }, { "path": "artifacts/session_abc123/symbolic_regression_results.png", "caption": "Symbolic regression analysis revealing underlying mathematical structure", "node_id": "symbolic_analysis" } ], "tables": [ { "path": "artifacts/session_abc123/energy_data.csv", "caption": "Computed energy eigenvalues and quantum numbers", "node_id": "solve_quantum" } ] }, "meta": { "device_mix": ["cuda", "cpu"], "cache_hits": 2, "duration_ms": 15000 } } ``` ### Publish Report Response ```json { "pdf_path": "artifacts/session_abc123/report_xyz789abc123.pdf" } ``` ### Collaborate Share Response ```json { "share_url": "https://phys-mcp.example.com/dag/abc123def456/share", "expires_at": "2024-01-22T12:00:00Z" } ``` ## Complex Workflow Examples ### Multi-Physics Simulation Pipeline ```json { "tool": "experiment_orchestrator", "method": "define_dag", "spec": { "nodes": [ { "id": "molecular_dynamics", "tool": "data", "method": "import_hdf5", "params": {"file_path": "md_trajectory.h5"}, "visual_outputs": {"static": false, "series": true, "animation": false} }, { "id": "analyze_structure", "tool": "ml_ai_augmentation", "method": "pattern_recognition_infer", "params": { "task": "classify", "images": ["structure_snapshots/*.png"], "model": "molecular_classifier.pt" }, "dependencies": ["molecular_dynamics"], "visual_outputs": {"static": true, "series": true, "animation": false} }, { "id": "quantum_calculation", "tool": "quantum", "method": "solve", "params": {"problem": "custom", "hamiltonian": "H_molecular"}, "dependencies": ["analyze_structure"], "visual_outputs": {"static": true, "series": true, "animation": false} }, { "id": "visualize_results", "tool": "plot", "method": "volume_3d", "params": { "mode": "isosurface", "iso_level": 0.1, "emit_animation": true, "format": "mp4" }, "dependencies": ["quantum_calculation"], "visual_outputs": {"static": true, "series": false, "animation": true} }, { "id": "export_to_vr", "tool": "export_tool", "method": "vr_export", "params": { "format": "glb", "geometry": {"vertices": [], "faces": []} }, "dependencies": ["visualize_results"], "visual_outputs": {"static": false, "series": false, "animation": false} } ], "edges": [ {"from": "molecular_dynamics", "to": "analyze_structure"}, {"from": "analyze_structure", "to": "quantum_calculation"}, {"from": "quantum_calculation", "to": "visualize_results"}, {"from": "visualize_results", "to": "export_to_vr"} ], "metadata": { "title": "Multi-Physics Molecular Analysis Pipeline", "description": "Comprehensive workflow combining MD, ML, quantum mechanics, and VR visualization" } } } ```