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Resonant Fractal Nature Theory — a mathematical framework for coherent patterns on graph-coupled networks.

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© 2026 TNFR project — MIT licensed.DOI 10.5281/zenodo.17602860
docs
grammar
PHYSICS_VERIFICATION.md
API_CONTRACTS.mdCANONICAL_OZ_SEQUENCES.mdEMPIRICAL_CONFRONTATION_EEG.mdREADME.mdSTRUCTURAL_FIELDS_TETRAD.mdSTRUCTURAL_INTERFACE_THEORY.md
theory
APPLIED_STRUCTURAL_ANALYSIS.mdCATALOG_TYPE_HYGIENE_PROGRAMME.mdDISSIPATIVE_AND_OPEN_SYSTEMS.mdEMERGENT_ONTOLOGY.mdEXTENDED_FIELDS_AND_DERIVED_QUANTITIES.mdFUNDAMENTAL_THEORY.mdGAUGE_SYMMETRY_AND_UNIFICATION.mdGLOSSARY.mdMATHEMATICAL_DYNAMICS_BASIS.mdMINIMAL_STRUCTURAL_DEGREES.mdNUCLEUS_A_PRIME_LADDER_ATLAS.mdNUCLEUS_B_EQUIVARIANCE_OBSTRUCTIONS.mdPHYSICAL_REGIME_CORRESPONDENCES.mdREADME.mdREMESH_INFINITY_DERIVATION.mdSTRUCTURAL_CONSERVATION_THEOREM.mdSTRUCTURAL_OPERATORS.mdSTRUCTURAL_STABILITY_AND_DYNAMICS.mdTNFR_BSD_RESEARCH_NOTES.mdTNFR_HODGE_RESEARCH_NOTES.mdTNFR_NAVIER_STOKES_RESEARCH_NOTES.mdTNFR_NUMBER_THEORY.mdTNFR_P_VS_NP_RESEARCH_NOTES.mdTNFR_RIEMANN_RESEARCH_NOTES.mdTNFR_VARIATIONAL_PRINCIPLE.mdTNFR_YANG_MILLS_RESEARCH_NOTES.mdTNFR.pdfUNIFIED_GRAMMAR_RULES.md
factorization-lab
analysis
analyze_patterns.pycertificate_manifest.py
benchmarks
benchmark_analysis.pybenchmark_expansion_suite.pyfull_spectrum_factorization.pypaley_gap_extended.pypaley_gap_smoke.pytest_benchmark_suite.py
demos
experiment_contexts
exp_0b1663cd19b7.jsonexp_0bf0054b7474.jsonexp_75a4c8ca616a.jsonexp_848ee0fd1857.jsonexp_f6fe00562193.jsonexp_fdf3da424e1e.json
failure_telemetry_batch.pyfeedback_integration_demo.pyintegration_demo_snapshots.dbseed_management_integration_demo.pysnapshot_integration_demo.pytrajectory_143.jsontrajectory_77.jsontrajectory_89.jsontrajectory_91.jsontrajectory_97.json
docs
FACTORING_PLAYBOOK.mdFALSE_POSITIVE_TEST_SUITE.mdOPERATOR_CERTIFICATES.mdROADMAP.mdSPECTRAL_ROUTE.md
experiment_contexts
exp_cebe1d9e7d8e.json
notebooks
spectral_history.ipynb
scripts
run_false_positive_tests.py
tests
run_false_positive_test_suite.pytest_cli.pytest_false_positive_methodology.pytest_false_positive_verifier.pytest_feedback_integration.pytest_partitioning.pytest_seed_management.pytest_self_opt_support.pytest_snapshot_system.pytest_spectral_paley.pytest_verification_robustness.py
tnfr_factorization
__init__.pyapi.pycli.pyfailure_telemetry.pyfeedback_adapter.pyfeedback_integration.pypartitioning.pyself_opt_support.pyspectral_paley.py
demo_snapshots.dbLICENSE_SNAPSHOT.mdPACKAGE_SUMMARY.mdREADME.mdseed_management.pysnapshot_system.pytest_certificate_hashing.pytest_installation.pyverification_trajectory_77.json
benchmarks
analyze_tetrad_universality.pyb0star_alpha_canonical_product_graphs.pybenchmark_optimization_tracks.pybenchmark_utils.pyboundary_vibration.pybridge_primes_riemann.pychiral_involution.pycli_utils.pycoherence_projector_sense_index.pycommutant_bridge.pycomposition_arithmetic.pyconfinement_zones_test.pyconservation_law_validation.pydirected_paley_bridge.pyemergent_arithmetic_pulse.pyemergent_atom_dynamics.pyemergent_atomic_shells.pyemergent_base_dimension.pyemergent_dimension_dynamics.pyemergent_fractal_pulse.pyemergent_fractal_simplex_dimension.pyemergent_integers_symmetry.pyemergent_musical_nfr.pyemergent_nfr_geometry.pyemergent_nfr_where.pyemergent_rationals.pyemergent_rhythm.pyemergent_screening.pyemergent_shell_cardinals.pyemergent_shell_ordering.pyemergent_simplex_dimension.pyemergent_substrate_symmetry.pyequivariance_wall.pyexternal_phase_gate_validation.pyfield_methods_battery.pygolden_residue_remesh_bridge.pyintegrated_force_regime_study.pyinverse_spectrum_to_symmetry.pyk_phi_safety_demo.pykuramoto_farey_bridge.pymissing_piece_bridge.pymultichannel_interface_benchmark.pynavier_stokes_recipe_bridge.pynodal_propagator_residue_bridge.pyns_moment_hierarchy_cascade.pyoperational_irreducibility.pypaley_bridge.pyphase_curvature_investigation.pyphase_wall.pyphi_s_confinement_investigation.pyprimes_as_consequence.pypulse_phase_coherence_budget.pyREADME.mdremesh_infinity_riemann_baseline.pyremesh_infinity_riemann_composed.pyremesh_infinity_riemann_modified_graph.pyremesh_infinity_riemann_operator.pyremesh_infinity_riemann_spectral_basis.pyremesh_infinity_riemann_spectral_robustness.pyremesh_infinity_riemann_spectral.pyresidue_phase_vs_riemann.pystructural_interface_benchmark.pytemporal_interface_benchmark.pytetrad_results_aggregate.pyu2_destabilization_irreversibility.pyuniversality_clusters.pyxi_c_fast_experiment.py
primality-test
benchmarks
comprehensive_benchmark.py
docs
ADVANCED_INTEGRATION.mdmathematical_foundation.mdperformance_analysis.md
examples
advanced_examples.pybasic_usage.py
tnfr_primality
__init__.py__main__.pyadvanced_cli.pyadvanced_core.pycli.pyconstants.pycore.pyoptimized.py
MANIFEST.inPACKAGE_SUMMARY.mdREADME.mdRELEASE_NOTES_v1.0.mdsetup.pytest_installation.py
tests
core_physics
__init__.pytest_conservation_laws.pytest_delta_nfr_computation_paths.pytest_delta_nfr.pytest_dispersion_coherence_sign_invariance.pytest_emergent_constants_guard.pytest_lyapunov_operators.pytest_nodal_equation.pytest_structural_triad.py
data
replay_manifests
sample_run
_manifest_summary.json_manifest.json_partition_files.txt.gz
self_opt_validation
seed_alpha
paley.json
seed_beta
integration.json
seed_gamma
unknown.json
self_optimization
test_run
partitioned
test_run
test_run_p0.jsontest_run_p1.json
_manifest_summary.json_manifest.json
engines
test_pattern_discovery_manifest.pytest_self_optimization_engine.py
mathematics
__init__.pytest_autodiff.pytest_backends.pytest_dissipative_dynamics.pytest_epi.pytest_factory_patterns.pytest_metrics.pytest_navier_stokes_refounded.pytest_number_theory_canonical.pytest_operators.pytest_residue_networks.pytest_riemann_nodal_pulse.pytest_riemann_pulse_coherence.pytest_spaces.pytest_transforms.pytest_validator.py
operators
test_canonical_operators_modern.pytest_grammar_canon.pytest_grammar_canonical_consistency.pytest_grammar_dynamics.pytest_operator_contracts.pytest_operator_strategies.py
parallel
test_fractal_partition_manifest.py
physics
test_conservation_gauge_unification.pytest_dissipative_conservation.pytest_emergent_chemistry.pytest_field_cache_invalidation.pytest_gauge.pytest_phase_transition.pytest_signatures.pytest_spectral_conservation.pytest_structural_diffusion.pytest_structural_integrity.pytest_symplectic_substrate.pytest_tetrad_bounds.pytest_variational.pytest_yang_mills_closure.pytest_yang_mills_derivability.pytest_yang_mills_scaling.pytest_yang_mills_structural_gap.pytest_yang_mills_u6_sweep.py
scripts
test_run_self_opt_validation.pytest_run_self_optimization.py
sdk
__init__.pytest_simple_advanced.py
__init__.pyconftest.pyREADME.mdtest_breast_cancer_phase_gate_demo.pytest_classical_mechanics.pytest_distributed_fft.pytest_external_phase_gate_validation.pytest_factorization_entrypoint.pytest_multichannel_interface.pytest_nodal_optimizer.pytest_phase_gate_api.pytest_replay_register_manifest.pytest_signal_confrontation.pytest_structural_interface_api.pytest_structural_interface_baselines.pytest_structural_interface_benchmark.pytest_temporal_interface.pytest_vectorized_coherence_length_regression.pytest_wine_quality_phase_gate_demo.pyutils.py
examples
01_foundations
01_hello_world.py02_musical_resonance.py03_network_formation.py04_operator_sequences.py05_coherence_evolution.py06_network_topologies.py07_phase_transitions.py08_emergent_phenomena.py09_visualization_suite.py10_simplified_sdk_showcase.py
02_physics_regimes
11_classical_limit_comparison.py115_operator_contract_audit.py12_classical_mechanics_demo.py13_quantum_mechanics_demo.py14_uncertainty_and_interference.py15_train_crossing_demo.py17_conservation_law_demo.py26_gauge_structure_demo.py27_variational_principle_demo.py28_dissipative_systems_demo.py29_lyapunov_stability_demo.py30_self_optimization_demo.py31_mathematical_constants_basis.py33_complex_field_unification.py34_conservation_protocol_suite.py35_tetrad_irreducibility.py36_grammar_violation_detector.py37_operator_tetrad_synergy.py38_grammar_energy_landscape.py39_nodal_equation_decomposition.py
03_riemann_zeta
157_nodal_pulse_phase_attack.py41_von_mangoldt_zeta_demo.py42_riemann_zeros_as_resonances.py43_prime_ladder_hamiltonian_demo.py44_weil_explicit_formula_demo.py45_li_keiper_demo.py46_weil_tnfr_positivity_demo.py47_alpha_sweep_demo.py48_admissible_family_sweep_demo.py49_nodeaware_gauge_sweep_demo.py50_uniform_coercivity_demo.py51_adaptive_coercivity_demo.py52_paley_gap_coercivity_demo.py53_lyapunov_spectral_positivity_demo.py54_hilbert_polya_demo.py55_structural_zero_density_demo.py56_spectral_emergence_demo.py57_admissible_rescaling_demo.py58_oscillatory_correction_demo.py
04_riemann_L_twisted
59_dirichlet_l_function_demo.py60_dirichlet_l_continuation_demo.py61_dirichlet_l_hamiltonian_demo.py62_dirichlet_weil_explicit_formula_demo.py63_dirichlet_li_keiper_demo.py64_twisted_weil_positivity_demo.py65_twisted_alpha_sweep_demo.py66_twisted_admissible_family_sweep_demo.py67_twisted_nodeaware_gauge_sweep_demo.py68_twisted_hermite_family_demo.py69_twisted_coercivity_uniform_demo.py70_twisted_paley_gap_coercivity_demo.py71_twisted_lyapunov_spectral_demo.py72_twisted_hilbert_polya_demo.py73_twisted_structural_zero_density_demo.py74_twisted_spectral_emergence_demo.py75_twisted_admissible_rescaling_demo.py76_twisted_oscillatory_correction_demo.py
05_type_hygiene
77_remesh_infinity_residue_split_demo.py78_nuf_type_signature_demo.py79_epi_type_signature_demo.py80_phi_type_signature_demo.py81_dnfr_type_signature_demo.py82_remesh_window_type_signature_demo.py83_delta_phi_max_type_signature_demo.py84_coupling_weights_type_signature_demo.py85_tetrad_closure_signature_demo.py86_currents_closure_signature_demo.py87_aggregates_closure_signature_demo.py88_urules_consistency_signature_demo.py89_operator_catalog_discipline_signature_demo.py
06_navier_stokes
158_navier_stokes_two_face_refounded.py
07_number_theory
100_prime_families_orbits.py101_numbers_as_coupled_network.py102_nodal_flow_primes_equilibria.py116_nuf_emergent_prime_visibility.py146_primality_grammatical_inertness.py147_numbers_as_free_monoid_words.py148_capacity_arm_carries_von_mangoldt.py149_p14_is_the_capacity_arm_operator.py153_structural_frequency_rank_cyclotomy.py40_arithmetic_number_theory.py94_generative_number_construction.py95_primes_from_spectral_waves.py96_spectral_vibration_of_coherence.py97_goldbach_additive_multiplicative.pyemergent_chemistry_particles_demo.py
08_emergent_geometry
103_emergent_substrate_meets_riemann.py106_per_node_polarization_geometry.py107_orthogonal_structure_emergent_geometry.py108_emergent_field_generating_structure.py112_structure_predicts_coherence_flow.py113_overdamped_projection_bridge.py114_substrate_conserved_quantities.py117_emergent_geometry_residue_graph.py118_emergent_vs_classical_operator.py119_phase_sector_directed_residue.py120_symmetry_wall_substrate_vs_spectrum.py121_canonical_symmetry_break_negative.py122_factorization_phase_sector.py123_symmetry_sector_decomposition.py124_emergent_metric_fractal_consistency.py125_node_is_the_emergent_substrate.py126_two_layers_base_fiber.py127_base_is_emergent_not_imposed.py128_base_substrate_coemergence.py129_spectral_gap_base_fiber_clock.py130_operators_break_substrate_charges.py131_coemergent_loop_convergence.py132_geometric_phase_holonomy.py133_psi_topological_defects.py134_spectral_dimension_heat_kernel.py135_arrow_of_time_h_theorem.py136_heat_kernel_coefficients.py137_synchronization_transition.py138_structure_frequency_synchronization.py139_grammar_formal_language.py140_grammar_automaton.py141_grammar_rule_decomposition.py142_grammar_operator_quotient.py143_glyphic_function_sublanguage.py144_branching_combinator.py145_syntactic_monoid_starfree.py150_emergent_grammatical_pattern_parry.py151_grammar_in_emergent_geometry.py152_operator_contract_tetrahedron.py154_conductor_annotated_qr_spectrum.py155_ontological_position_of_numbers.py156_emergence_directness_law.py98_emergent_symplectic_substrate.py99_structural_diffusion.pyunified_fields_showcase.py
09_millennium
109_p_vs_np_coherence_synthesis.py110_bsd_rank_structural_pressure.py111_hodge_discrete_and_honest_gap.py
10_applications
159_empirical_confrontation_pipeline.py90_phase_gate_monitor_demo.py91_breast_cancer_phase_gate_demo.py92_wine_quality_phase_gate_demo.py93_structural_interface_demo.pypytorch_cuda_demo.py
README.md
scripts
replay
__init__.pyregister_manifest.py
__init__.pyREADME.mdrebuild_failure_manifest.pyrun_reproducible_benchmarks.pyrun_self_opt_validation.pyrun_self_optimization.pytnfr_is_prime.pyvalidate_conservation_law.pyverify_internal_references.py
src
core
__init__.pyevaluation.py
tnfr
backends
__init__.pyjax_backend.pynumpy_backend.pyoptimized_numpy.pyREADME.mdtorch_backend.py
cli
__init__.py__init__.pyiarguments.pyarguments.pyiexecution.pyexecution.pyiinteractive_validator.pyREADME.mdutils.pyutils.pyi
compat
__init__.pydataclass.pyjsonschema_stub.pymatplotlib_stub.pynumpy_stub.pyREADME.md
config
__init__.py__init__.pyiconstants.pyconstants.pyidefaults_core.pydefaults_init.pydefaults_metric.pydefaults.pyfeature_flags.pyfeature_flags.pyiglyph_constants.pyoperator_names.pyoperator_names.pyiphysics_derivation.pyprecision_modes.pypresets.pypresets.pyiREADME.mdsecurity.pythresholds.pytnfr_config.py
constants
__init__.py__init__.pyialiases.pyaliases.pyicanonical.pymetric.pymetric.pyioperational.py
core
__init__.pycontainer.pydefault_implementations.pyexceptions.pyinterfaces.pyREADME.md
dynamics
__init__.py__init__.pyiadaptation.pyadaptation.pyiadaptive_sequences.pyadaptive_sequences.pyiadelic.pyadvanced_cache_optimizer.pyadvanced_fft_arithmetic.pyaliases.pyaliases.pyibifurcation.pycache_aware_fft_engine.pycanonical.pycanonical.pyicomputational_hub.pycoordination.pycoordination.pyidistributed_fft.pydnfr.pydnfr.pyidynamic_limits.pyemergent_centralization.pyemergent_integration_engine.pyfeedback.pyfeedback.pyifft_backend.pyfft_cache_coordinator.pyfft_dispatchers.pyfft_engine.pyfft_workers.pyfused_dnfr.pyhomeostasis.pyhomeostasis.pyiintegrators.pyintegrators.pyilearning.pylearning.pyimetabolism.pymulti_modal_cache.pynbody_tnfr.pynbody.pynodal_optimizer.pyoptimization_orchestrator.pypropagation.pyREADME.mdruntime.pyruntime.pyisampling.pysampling.pyiselectors.pyselectors.pyiself_optimizing_engine.pyspectral_structural_fusion.pystructural_cache.pystructural_clip.pysymplectic.pyunified_backend.pyunified_mathematical_cache_orchestrator.py
engines
computation
__init__.pyfft_engine.pyunified_fft_engine.pyunified_gpu_system.py
constants
__init__.pycanonical.pyoperational.py
integration
__init__.pyemergent_integration.py
pattern_discovery
__init__.pymathematical_patterns.pymulti_modal_cache.py
self_optimization
__init__.pyengine.py
__init__.pyREADME.md
errors
__init__.pycontextual.py
factorization
__init__.py
flatten
README.md
gamma
README.md
glyph_history
README.md
glyph_runtime
README.md
immutable
README.md
initialization
README.md
io
README.md
math
__init__.pyfields_symbolic.pygrammar_validators.pyoptimizer.pyREADME.mdsymbolic.py
mathematics
__init__.pybackend.pybackend.pyidynamics.pydynamics.pyiepi.pyepi.pyigenerators.pygenerators.pyiliouville.pymetrics.pymetrics.pyinumber_theory.pyoperators_factory.pyoperators_factory.pyioperators.pyoperators.pyioptimized_primality.pyprojection.pyprojection.pyiREADME.mdruntime.pyruntime.pyispaces.pyspaces.pyispectral.pytransforms.pytransforms.pyiunified_cache.pyunified_numerical.pyzeta.py
metrics
__init__.py__init__.pyibuffer_cache.pybuffer_cache.pyicache_utils.pycoherence.pycoherence.pyicommon.pycommon.pyicore.pycore.pyidiagnosis.pydiagnosis.pyiemergence.pyexport.pyexport.pyiglyph_timing.pyglyph_timing.pyilearning_metrics.pylearning_metrics.pyilocal_coherence.pyphase_coherence.pyphase_compatibility.pyREADME.mdreporting.pyreporting.pyisense_index.pysense_index.pyitelemetry.pytetrad.pytrig_cache.pytrig_cache.pyitrig.pytrig.pyi
multiscale
__init__.pyhierarchical.pyREADME.md
navier_stokes
__init__.pyconservative_face.pyoperator.py
node
README.md
observers
README.md
operators
network_analysis
__init__.pysource_detection.py
postconditions
__init__.pymutation.py
preconditions
__init__.pycoherence.pydissonance.pyemission.pymutation.pyreception.pyresonance.py
strategies
__init__.pydefaults.pygpu_strategies.pystrategy.py
__init__.py__init__.pyialgebra.pycanonical_patterns.pycascade.pycoherence.pycontraction.pycoupling.pycycle_detection.pydefinitions_base.pydefinitions.pydefinitions.pyidissonance.pyemission.pyexpansion.pygrammar_application.pygrammar_canon.pygrammar_context.pygrammar_core.pygrammar_dynamics.pygrammar_error_factory.pygrammar_memoization.pygrammar_patterns.pygrammar_telemetry.pygrammar_types.pygrammar_u6.pygrammar_validate.pygrammar.pygrammar.pyihamiltonian.pyhealth_analyzer.pyintrospection.pyjitter.pyjitter.pyilifecycle.pymetabolism.pymetrics_basic.pymetrics_core.pymetrics_network.pymetrics_structural.pymetrics_u6.pymetrics.pymutation.pynodal_equation.pyoperator_contracts.pypattern_detection.pypatterns.pyREADME.mdreception.pyrecursivity.pyregistry.pyregistry.pyiremesh.pyremesh.pyiresonance.pyself_organization.pysilence.pystructural_units.pytransition.py
parallel
__init__.pyauto_scaler.pydistributed.pyengine.pymonitoring.pypartitioner.pyREADME.md
performance
guardrails.py
physics
__init__.py_helpers.pycalibration.pycanonical.pycell.pyclassical_mechanics.pyconservation_gauge_unification.pyconservation.pydissipative_conservation.pyemergent_chemistry.pyemergent_particles.pyextended.pyfields.pygauge.pyintegrity.pyinteractions.pylife.pylyapunov.pypatterns.pyphase_transition.pyquantum_mechanics.pyREADME.mdsignatures.pyspectral_conservation.pyspectral_metrics.pystructural_diffusion.pysymplectic_substrate.pytelemetry.pyunified.pyvariational.pyvectorized_ops.py
primality
__init__.py
recipes
__init__.pycookbook.pyREADME.md
riemann
__init__.pyadmissible_family_sweep.pyadmissible_rescaling.pyaggregates_closure_signature.pyalpha_sweep.pyanalytic_continuation_dirichlet.pyanalytic_continuation.pycoercivity_uniform.pycoupling_weights_type_signature.pycurrents_closure_signature.pydelta_phi_max_type_signature.pydirichlet_l.pydnfr_type_signature.pyepi_type_signature.pyhilbert_polya.pyli_keiper.pylyapunov_spectral_positivity.pynodal_pulse.pynodeaware_gauge_sweep.pynuf_type_signature.pyoperator_catalog_discipline_signature.pyoperator.pyoscillatory_correction.pypaley_gap_coercivity.pyphi_type_signature.pyprime_ladder_hamiltonian.pypulse_coherence.pyremesh_infinity_residue_split.pyremesh_window_type_signature.pyspectral_emergence.pystructural_zero_density.pytelemetry.pytetrad_closure_signature.pytwisted_admissible_family_sweep.pytwisted_admissible_rescaling.pytwisted_alpha_sweep.pytwisted_coercivity_uniform.pytwisted_hermite_family.pytwisted_hilbert_polya.pytwisted_li_keiper.pytwisted_lyapunov_spectral_positivity.pytwisted_nodeaware_gauge_sweep.pytwisted_oscillatory_correction.pytwisted_paley_gap_coercivity.pytwisted_prime_ladder_hamiltonian.pytwisted_spectral_emergence.pytwisted_structural_zero_density.pytwisted_weil_explicit_formula.pytwisted_weil_positivity.pyurules_consistency_signature.pyvon_mangoldt.pyweil_explicit_formula.pyweil_positivity.py
schemas
__init__.pygrammar.jsonREADME.md
sdk
__init__.py__init__.pyiadaptive_system.pyadaptive_system.pyibuilders.pybuilders.pyifluent.pyfluent.pyiREADME.mdself_opt.pysimple.pytemplates.pytemplates.pyiutils.py
security
__init__.pycrypto.pydatabase.pyREADME.mdsubprocess.pyvalidation.py
sequencing
__init__.pypatterns.pyREADME.md
services
__init__.pyorchestrator.pyREADME.md
sparse
__init__.pyREADME.mdrepresentations.py
structural
README.md
telemetry
__init__.pycache_metrics.pycache_metrics.pyiconstants.pynu_f.pynu_f.pyiREADME.mdunified_telemetry_system.pyverbosity.pyverbosity.pyi
tools
__init__.pydomain_templates.pyREADME.mdsequence_generator.pytnfr_is_prime_cli_optimized.pytnfr_is_prime_cli.py
topology
__init__.pyasymmetry.pyREADME.md
utils
cache_layers.pycache.pycache.pyicallbacks.pycallbacks.pyichunks.pychunks.pyidata.pydata.pyifast_diameter.pygraph.pygraph.pyiinit.pyinit.pyiio.pyio.pyinumeric.pynumeric.pyiREADME.mdtopology.pyunified_cache.py
validation
__init__.py__init__.pyiaggregator.pybase.pycompatibility.pycompatibility.pyiconfig.pygraph.pygraph.pyihealth.pyinput_validation.pyinterface_baselines.pyinvariants.pymultichannel_interface.pyphase_gate.pyREADME.mdrules.pyrules.pyiruntime.pyruntime.pyisequence_validator.pysignal_confrontation.pysoft_filters.pysoft_filters.pyispectral.pyspectral.pyistructural_interface.pytemporal_interface.pyunified_validation_system.pyvalidator.pywindow.pywindow.pyi
visualization
__init__.pycascade_viz.pyhierarchy.pyREADME.mdsequence_plotter.py
yang_mills
__init__.pyclosure.pyderivability.pyscaling.pystructural_gap.pyu6_sweep.py
__init__.py__init__.pyi_compat.py_version.py_version.pyialias.pyalias.pyibackend_config.pycache.pycache.pyiexecution.pyexecution.pyiflatten.pyflatten.pyigamma.pygamma.pyiglyph_history.pyglyph_history.pyiglyph_runtime.pyglyph_runtime.pyiimmutable.pyimmutable.pyiinitialization.pyinitialization.pyiio.pyio.pyilocking.pylocking.pyinode.pynode.pyiobservers.pyobservers.pyiontosim.pyontosim.pyipy.typedrng.pyrng.pyisecure_config.pyselector.pyselector.pyisense.pysense.pyistructural.pystructural.pyitokens.pytokens.pyitrace.pytrace.pyitypes.pytypes.pyiunits.pyunits.pyi
tetrad_evaluator.py
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FILE: benchmarks/phase_curvature_investigation.py

phase_curvature_investigation.py

Phase Curvature K_φ Confinement Mechanism Investigation

Research pipeline to validate K_φ as canonical field through:

  1. Critical threshold validation (fragmentation predictor)
  2. Confinement zone mapping (strong-like interaction regime)
  3. Asymptotic freedom testing (scale-dependent variance)
  4. Mutation candidate prediction (ZHIR optimization)
  5. Complementary safety criteria (local hotspot detection)
  6. Cross-domain validation

Based on §10-11 evidence: |K_φ| > 4.88 threshold, weak correlation but threshold behavior.

Source Code

python
#!/usr/bin/env python3
"""
Phase Curvature K_φ Confinement Mechanism Investigation

Research pipeline to validate K_φ as canonical field through:
1. Critical threshold validation (fragmentation predictor)
2. Confinement zone mapping (strong-like interaction regime)
3. Asymptotic freedom testing (scale-dependent variance)
4. Mutation candidate prediction (ZHIR optimization)
5. Complementary safety criteria (local hotspot detection)
6. Cross-domain validation

Based on §10-11 evidence: |K_φ| > 4.88 threshold, weak correlation
but threshold behavior.
"""

import json
import random
import sys
from dataclasses import dataclass
from pathlib import Path
from typing import Any, Dict, List, Tuple

import networkx as nx
import numpy as np
from sklearn.metrics import roc_auc_score, roc_curve

# Add project root to path for imports
PROJECT_ROOT = Path(__file__).parent.parent
sys.path.insert(0, str(PROJECT_ROOT))


@dataclass
class CurvatureExperiment:
    """Single K_φ threshold experiment result."""

    topology: str
    nodes: int
    edges: int
    k_phi_max: float
    k_phi_mean: float
    k_phi_var: float
    coherence: float
    fragmented: bool
    intensity: float
    sequence: str
    seed: int


class CurvatureInvestigator:
    """Phase curvature K_φ confinement mechanism research pipeline."""

    def __init__(self, output_dir: str = "benchmarks/results"):
        """Initialize K_φ investigator.

        Parameters
        ----------
        output_dir : str
            Directory for experiment results storage
        """
        # Import here to avoid module-level import errors
        from benchmarks.benchmark_utils import (
            create_tnfr_topology,
            generate_grammar_valid_sequence,
            initialize_tnfr_nodes,
        )
        from src.tnfr.physics.fields import compute_phase_curvature

        # Store imports as class attributes
        self.compute_phase_curvature = compute_phase_curvature
        self.create_tnfr_topology = create_tnfr_topology
        self.initialize_tnfr_nodes = initialize_tnfr_nodes
        self.generate_grammar_valid_sequence = generate_grammar_valid_sequence

        self.output_dir = Path(output_dir)
        self.output_dir.mkdir(exist_ok=True)

        # Research parameters based on §11 evidence
        self.candidate_threshold = 4.88  # From fragmentation analysis
        self.threshold_range = (4.0, 6.0)  # Fine-grained sweep range
        self.critical_intensity = 2.015  # From §11 I_c value

        # Experiment configurations
        self.topologies = [
            "scale_free",
            "tree",
            "grid",
            "ring",
            "ws",  # Watts-Strogatz (small world)
        ]

        self.node_sizes = [20, 50, 100]
        self.sequences = [
            "OZ_heavy",  # High instability
            "balanced",  # Moderate dynamics
            "RA_dominated",  # Low dynamics (resonance-heavy)
        ]

    def run_threshold_validation(
        self, n_experiments: int = 200
    ) -> List[CurvatureExperiment]:
        """Task 1: Critical Threshold Validation.

        Test if |K_φ| ≈ 4.88 acts as universal fragmentation threshold
        across topologies with ≥90% classification accuracy.

        Parameters
        ----------
        n_experiments : int
            Number of experiments per configuration

        Returns
        -------
        List[CurvatureExperiment]
            Experiment results for ROC analysis
        """
        print("🔬 Task 1: Critical Threshold Validation")
        print(f"Target: |K_φ| > {self.candidate_threshold} → fragmentation")
        print(f"Testing range: {self.threshold_range}")
        print()

        experiments = []
        total_runs = (
            len(self.topologies)
            * len(self.node_sizes)
            * len(self.sequences)
            * n_experiments
        )
        run_count = 0

        for topology in self.topologies:
            for n_nodes in self.node_sizes:
                for sequence in self.sequences:
                    print(f"Testing {topology} n={n_nodes} seq={sequence}")

                    for i in range(n_experiments):
                        run_count += 1
                        seed = random.randint(1000, 99999)

                        try:
                            # Create graph and apply sequence
                            G = self.create_tnfr_topology(topology, n_nodes, seed=seed)
                            self.initialize_tnfr_nodes(G, seed=seed)

                            # Apply sequence with intensity sweep around I_c
                            noise = np.random.uniform(-0.5, 0.5)
                            intensity = self.critical_intensity + noise

                            # Generate and apply sequence
                            ops = self.generate_grammar_valid_sequence(
                                sequence, intensity=intensity
                            )
                            # Apply operators to graph (simplified)
                            for op in ops:
                                try:
                                    op.apply(G)
                                except Exception:
                                    pass  # Skip failed operations

                            # Compute K_φ and coherence metrics
                            k_phi = self.compute_phase_curvature(G)
                            k_phi_values = list(k_phi.values())

                            if not k_phi_values:
                                continue

                            k_phi_max = max(abs(k) for k in k_phi_values)
                            k_phi_mean = np.mean([abs(k) for k in k_phi_values])
                            k_phi_var = np.var(k_phi_values)

                            # Coherence assessment (simplified)
                            coherence = self._assess_coherence(G)
                            fragmented = coherence < 0.3

                            experiment = CurvatureExperiment(
                                topology=topology.name,
                                nodes=len(G.nodes()),
                                edges=len(G.edges()),
                                k_phi_max=k_phi_max,
                                k_phi_mean=k_phi_mean,
                                k_phi_var=k_phi_var,
                                coherence=coherence,
                                fragmented=fragmented,
                                intensity=intensity,
                                sequence=sequence.name,
                                seed=seed,
                            )

                            experiments.append(experiment)

                            if run_count % 20 == 0:
                                pct = 100 * run_count / total_runs
                                print(
                                    f"  Progress: {run_count}/{total_runs} "
                                    + f"({pct:.1f}%)"
                                )

                        except Exception as e:
                            print(f"  Error in experiment {run_count}: {e}")
                            continue

        # Save raw results
        results_file = self.output_dir / "k_phi_threshold_validation.jsonl"
        with open(results_file, "w") as f:
            for exp in experiments:
                f.write(json.dumps(exp.__dict__) + "\n")

        print(f"✅ Completed {len(experiments)} experiments")
        print(f"Results saved to: {results_file}")

        # ROC analysis
        self._analyze_threshold_roc(experiments)

        return experiments

    def _analyze_threshold_roc(self, experiments: List[CurvatureExperiment]) -> None:
        """Perform ROC analysis to optimize K_φ threshold."""
        if not experiments:
            return

        print("\n📊 ROC Analysis for K_φ Fragmentation Threshold")

        # Extract data for ROC
        k_phi_max_values = [exp.k_phi_max for exp in experiments]
        fragmentation_labels = [int(exp.fragmented) for exp in experiments]

        if len(set(fragmentation_labels)) < 2:
            print("❌ No fragmentation variation - cannot compute ROC")
            return

        # Compute ROC curve
        fpr, tpr, thresholds = roc_curve(fragmentation_labels, k_phi_max_values)
        auc_score = roc_auc_score(fragmentation_labels, k_phi_max_values)

        # Find optimal threshold (max Youden's J statistic)
        j_scores = tpr - fpr
        optimal_idx = np.argmax(j_scores)
        optimal_threshold = thresholds[optimal_idx]
        optimal_tpr = tpr[optimal_idx]
        optimal_fpr = fpr[optimal_idx]

        print(f"🎯 AUC Score: {auc_score:.4f}")
        print(f"🎯 Optimal Threshold: |K_φ| > {optimal_threshold:.3f}")
        print(f"   - True Positive Rate: {optimal_tpr:.3f}")
        print(f"   - False Positive Rate: {optimal_fpr:.3f}")
        print(f"   - Accuracy: {optimal_tpr - optimal_fpr:.3f}")

        # Compare with candidate threshold
        candidate_predictions = [k > self.candidate_threshold for k in k_phi_max_values]
        candidate_accuracy = np.mean(
            [
                pred == label
                for pred, label in zip(candidate_predictions, fragmentation_labels)
            ]
        )

        print(f"📋 Candidate threshold |K_φ| > {self.candidate_threshold}:")
        print(f"   - Accuracy: {candidate_accuracy:.3f}")
        print(f"   - Target: ≥0.90 for canonical promotion")

        # Topology breakdown
        print("\n🗺️ Topology-wise Performance:")
        topology_stats = {}
        for topology in set(exp.topology for exp in experiments):
            topo_exps = [exp for exp in experiments if exp.topology == topology]
            topo_k_phi = [exp.k_phi_max for exp in topo_exps]
            topo_frag = [int(exp.fragmented) for exp in topo_exps]

            if len(set(topo_frag)) >= 2:  # Need variation
                topo_auc = roc_auc_score(topo_frag, topo_k_phi)
                topo_acc = np.mean(
                    [
                        k > self.candidate_threshold == f
                        for k, f in zip(topo_k_phi, topo_frag)
                    ]
                )
                topology_stats[topology] = {"auc": topo_auc, "accuracy": topo_acc}
                print(f"   {topology}: AUC={topo_auc:.3f}, Acc={topo_acc:.3f}")
            else:
                print(f"   {topology}: No fragmentation variation")

        # Save ROC results
        roc_results = {
            "overall_auc": float(auc_score),
            "optimal_threshold": float(optimal_threshold),
            "optimal_tpr": float(optimal_tpr),
            "optimal_fpr": float(optimal_fpr),
            "candidate_threshold": self.candidate_threshold,
            "candidate_accuracy": float(candidate_accuracy),
            "topology_stats": topology_stats,
            "n_experiments": len(experiments),
        }

        roc_file = self.output_dir / "k_phi_roc_analysis.json"
        with open(roc_file, "w") as f:
            json.dump(roc_results, f, indent=2)

        print(f"\n💾 ROC analysis saved to: {roc_file}")

    def identify_confinement_zones(
        self, G: Any, k_phi_threshold: float = 4.5
    ) -> Tuple[Any, int, Dict]:
        """Task 2: Confinement Zone Mapping.

        Identify subgraphs where |K_φ| > threshold as confinement regions.

        Parameters
        ----------
        G : networkx.Graph
            Network to analyze
        k_phi_threshold : float
            Threshold for confinement zone identification

        Returns
        -------
        subgraph : networkx.Graph
            Subgraph of confined nodes
        n_components : int
            Number of connected components in confinement zones
        zone_stats : dict
            Statistics about confinement zones
        """
        k_phi = compute_phase_curvature(G)

        # Identify nodes with high curvature
        confined_nodes = [n for n, k in k_phi.items() if abs(k) > k_phi_threshold]

        if not confined_nodes:
            return G.subgraph([]), 0, {"total_nodes": 0, "coverage": 0.0}

        # Create confinement subgraph
        subgraph = G.subgraph(confined_nodes).copy()
        n_components = nx.number_connected_components(subgraph)

        # Compute zone statistics
        zone_stats = {
            "total_nodes": len(confined_nodes),
            "coverage": len(confined_nodes) / len(G.nodes()),
            "n_components": n_components,
            "max_component_size": (
                max(len(c) for c in nx.connected_components(subgraph))
                if confined_nodes
                else 0
            ),
            "avg_k_phi": np.mean([abs(k_phi[n]) for n in confined_nodes]),
            "threshold_used": k_phi_threshold,
        }

        return subgraph, n_components, zone_stats

    def measure_scale_dependent_curvature(
        self, G: Any, scales: List[int] = None
    ) -> Dict[int, float]:
        """Task 3: Asymptotic Freedom Investigation.

        Test if |K_φ| variance decreases at larger scales (asymptotic freedom).

        Parameters
        ----------
        G : networkx.Graph
            Network to analyze
        scales : List[int], optional
            Neighborhood radii to test. Default: [1, 2, 3, 5, 10]

        Returns
        -------
        Dict[int, float]
            K_φ variance at each scale
        """
        if scales is None:
            scales = [1, 2, 3, 5, 10]

        k_phi_base = compute_phase_curvature(G)
        scale_variances = {}

        for r in scales:
            k_phi_coarse = {}

            for node in G.nodes():
                # Get r-hop ego network
                try:
                    ego_nodes = nx.ego_graph(G, node, radius=r).nodes()
                    ego_k_phi = [k_phi_base[n] for n in ego_nodes if n in k_phi_base]

                    if ego_k_phi:
                        k_phi_coarse[node] = np.mean(ego_k_phi)
                    else:
                        k_phi_coarse[node] = 0.0
                except:
                    k_phi_coarse[node] = 0.0

            # Compute variance at this scale
            if k_phi_coarse:
                scale_variances[r] = np.var(list(k_phi_coarse.values()))
            else:
                scale_variances[r] = 0.0

        return scale_variances

    def predict_mutation_candidates(
        self, G: Any, top_k: int = 5
    ) -> List[Tuple[Any, float]]:
        """Task 4: Mutation Candidate Prediction.

        Identify nodes with highest |K_φ| as optimal ZHIR targets.

        Parameters
        ----------
        G : networkx.Graph
            Network to analyze
        top_k : int
            Number of top candidates to return

        Returns
        -------
        List[Tuple[Any, float]]
            List of (node, |K_φ|) for top candidates
        """
        k_phi = compute_phase_curvature(G)

        # Sort by absolute curvature
        sorted_candidates = sorted(k_phi.items(), key=lambda x: abs(x[1]), reverse=True)

        return sorted_candidates[:top_k]

    def _assess_coherence(self, G: Any) -> float:
        """Simple coherence assessment for fragmentation detection."""
        try:
            # Use connected component analysis as proxy
            largest_component_size = max(len(c) for c in nx.connected_components(G))
            coherence = largest_component_size / len(G.nodes())
            return coherence
        except:
            return 0.0


def main():
    """Run K_φ confinement mechanism investigation."""
    print("🌊 Phase Curvature K_φ Confinement Mechanism Investigation")
    print("=" * 60)
    print()

    investigator = CurvatureInvestigator()

    # Task 1: Critical Threshold Validation
    experiments = investigator.run_threshold_validation(n_experiments=50)

    print("\n" + "=" * 60)
    print("✅ Investigation Phase 1 Complete")
    print(f"📊 {len(experiments)} experiments conducted")
    print("📈 Check results/k_phi_threshold_validation.jsonl for detailed data")
    print("📈 Check results/k_phi_roc_analysis.json for threshold optimization")


if __name__ == "__main__":
    main()