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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
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tetrad_evaluator.py
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FILE: examples/01_foundations/07_phase_transitions.py

07_phase_transitions.py

07 - Phase Transitions: TNFR Bifurcation Dynamics

Exploration of phase transitions and bifurcation behavior in TNFR systems.

PHYSICS: Demonstrates ∂²EPI/∂t² > τ threshold dynamics and controlled bifurcations. LEARNING: Understanding critical points, hysteresis, and grammar U4 requirements.

Source Code

python
"""07 - Phase Transitions: TNFR Bifurcation Dynamics

Exploration of phase transitions and bifurcation behavior in TNFR systems.

PHYSICS: Demonstrates ∂²EPI/∂t² > τ threshold dynamics and controlled bifurcations.
LEARNING: Understanding critical points, hysteresis, and grammar U4 requirements.
"""

import networkx as nx
import numpy as np


def compute_coherence(G):
    """Network phase synchronization: the canonical Kuramoto order
    parameter R = |<e^{iθ}>|.

    R = 1 when phases are fully aligned, R -> 0 when desynchronized
    (random or antiphase). AGENTS.md frames TNFR phase coupling as
    Kuramoto synchronization, so this is the canonical phase-synchrony
    measure. The distinct total coherence
    C(t) = 1/(1 + mean|ΔNFR| + mean|dEPI|) lives in
    tnfr.metrics.coherence and requires the dynamics pipeline.
    """
    thetas = np.array(
        [G.nodes[n].get("theta", G.nodes[n].get("phase", 0.0)) for n in G.nodes()],
        dtype=float,
    )
    if thetas.size == 0:
        return 1.0
    return float(abs(np.mean(np.exp(1j * thetas))))


def compute_delta_nfr(G, node):
    """Compute ΔNFR (structural pressure) for a node."""
    if node not in G.nodes():
        return 0.0

    node_phase = G.nodes[node].get("phase", 0)
    neighbors = list(G.neighbors(node))

    if not neighbors:
        return 0.0

    neighbor_phases = [G.nodes[n].get("phase", 0) for n in neighbors]
    mean_neighbor_phase = np.mean(neighbor_phases)

    phase_diff = abs(node_phase - mean_neighbor_phase)
    return min(phase_diff, 2 * np.pi - phase_diff) / np.pi


def compute_acceleration(G, node, history, dt=0.1):
    """Compute ∂²EPI/∂t² (second derivative) for bifurcation detection."""
    if len(history) < 3:
        return 0.0

    # Use finite difference approximation
    # ∂²φ/∂t² ≈ (φ(t+dt) - 2φ(t) + φ(t-dt)) / dt²

    recent_phases = history[-3:]
    if len(recent_phases) < 3:
        return 0.0

    phi_minus = recent_phases[0]
    phi_current = recent_phases[1]
    phi_plus = recent_phases[2]

    # Handle wraparound for angles
    def angle_diff(a, b):
        diff = a - b
        return np.arctan2(np.sin(diff), np.cos(diff))

    d1 = angle_diff(phi_current, phi_minus) / dt
    d2 = angle_diff(phi_plus, phi_current) / dt

    acceleration = (d2 - d1) / dt
    return abs(acceleration)


def apply_dissonance(G, intensity=0.5):
    """Apply dissonance operator - increases ΔNFR."""
    for node in G.nodes():
        current_phase = G.nodes[node].get("phase", 0)
        # Add random perturbation
        perturbation = np.random.uniform(-intensity, intensity) * np.pi
        G.nodes[node]["phase"] = (current_phase + perturbation) % (2 * np.pi)


def apply_coherence(G, strength=0.3):
    """Apply coherence operator - reduces ΔNFR via negative feedback."""
    # Calculate global phase center
    phases = [G.nodes[n].get("phase", 0) for n in G.nodes()]
    if not phases:
        return

    # Use circular mean for phases
    x = np.mean([np.cos(p) for p in phases])
    y = np.mean([np.sin(p) for p in phases])
    global_phase = np.arctan2(y, x) % (2 * np.pi)

    # Pull all nodes toward global phase
    for node in G.nodes():
        current_phase = G.nodes[node].get("phase", 0)

        # Calculate shortest path to global phase
        diff = global_phase - current_phase
        if diff > np.pi:
            diff -= 2 * np.pi
        elif diff < -np.pi:
            diff += 2 * np.pi

        # Apply coherence correction
        correction = strength * diff
        G.nodes[node]["phase"] = (current_phase + correction) % (2 * np.pi)


def evolve_network_step(G, dt=0.1):
    """Single evolution step with nodal equation."""
    new_phases = {}

    for node in G.nodes():
        current_phase = G.nodes[node].get("phase", 0)
        vf = G.nodes[node].get("vf", 1.0)

        delta_nfr = compute_delta_nfr(G, node)

        neighbors = list(G.neighbors(node))
        if neighbors:
            neighbor_phases = [G.nodes[n].get("phase", 0) for n in neighbors]
            target_phase = np.mean(neighbor_phases)

            direction = target_phase - current_phase
            if direction > np.pi:
                direction -= 2 * np.pi
            elif direction < -np.pi:
                direction += 2 * np.pi

            # Apply nodal equation: ∂EPI/∂t = νf · ΔNFR
            phase_change = vf * delta_nfr * dt * np.sign(direction)
            new_phases[node] = (current_phase + phase_change) % (2 * np.pi)
        else:
            new_phases[node] = current_phase

    for node, phase in new_phases.items():
        G.nodes[node]["phase"] = phase


def phase_transition_experiment():
    """Demonstrate controlled phase transitions and bifurcations."""

    print("🔄 PHASE TRANSITION EXPERIMENT")
    print("━" * 50)
    print("Applying increasing dissonance until bifurcation threshold")

    # Create test network
    G = nx.watts_strogatz_graph(10, 4, 0.1)

    # Initialize with random phases but small νf
    np.random.seed(42)
    for node in G.nodes():
        G.nodes[node]["phase"] = np.random.uniform(0, 2 * np.pi)
        G.nodes[node]["nu_f"] = 0.8
        G.nodes[node]["history"] = []

    initial_coherence = compute_coherence(G)
    print(f"Initial coherence: {initial_coherence:.3f}")

    bifurcation_threshold = 1.5  # τ threshold for ∂²EPI/∂t²
    dissonance_levels = np.linspace(0.1, 1.0, 10)

    results = []

    for level in dissonance_levels:
        print(f"\n🌪️  Dissonance Level: {level:.1f}")

        # Apply dissonance
        apply_dissonance(G, intensity=level)

        # Short evolution to see effect
        phase_history = {node: [] for node in G.nodes()}

        for step in range(15):
            # Record phases before step
            for node in G.nodes():
                phase_history[node].append(G.nodes[node]["phase"])

            evolve_network_step(G)

        # Check for bifurcations
        bifurcations_detected = 0
        max_acceleration = 0

        for node in G.nodes():
            history = phase_history[node]
            acceleration = compute_acceleration(G, node, history)
            max_acceleration = max(max_acceleration, acceleration)

            if acceleration > bifurcation_threshold:
                bifurcations_detected += 1

        final_coherence = compute_coherence(G)
        avg_delta_nfr = np.mean([compute_delta_nfr(G, n) for n in G.nodes()])

        print(f"   Final coherence: {final_coherence:.3f}")
        print(f"   Max acceleration: {max_acceleration:.3f}")
        print(f"   Bifurcations detected: {bifurcations_detected}")
        print(f"   Average ΔNFR: {avg_delta_nfr:.3f}")

        results.append(
            {
                "level": level,
                "coherence": final_coherence,
                "acceleration": max_acceleration,
                "bifurcations": bifurcations_detected,
                "delta_nfr": avg_delta_nfr,
            }
        )

        # Apply coherence to stabilize (Grammar U4a requirement)
        if bifurcations_detected > 0:
            print("   🛡️  Applying coherence (U4a stabilizer)")
            apply_coherence(G, strength=0.5)
            stabilized_coherence = compute_coherence(G)
            print(f"   Stabilized coherence: {stabilized_coherence:.3f}")

    return results


def hysteresis_experiment():
    """Demonstrate hysteresis in phase transitions."""

    print("\n🔄 HYSTERESIS EXPERIMENT")
    print("━" * 50)
    print("Forward: Increasing dissonance")
    print("Backward: Decreasing dissonance")

    G = nx.cycle_graph(8)

    # Initialize synchronized state
    for node in G.nodes():
        G.nodes[node]["phase"] = 0.0  # All synchronized
        G.nodes[node]["nu_f"] = 1.0

    # Forward path: increasing dissonance
    dissonance_levels = np.linspace(0.0, 0.8, 16)
    forward_coherence = []

    for level in dissonance_levels:
        apply_dissonance(G, intensity=level)

        # Brief evolution
        for _ in range(10):
            evolve_network_step(G)

        coherence = compute_coherence(G)
        forward_coherence.append(coherence)

    # Backward path: decreasing dissonance
    backward_coherence = []

    for level in reversed(dissonance_levels):
        # Apply inverse of dissonance (coherence)
        apply_coherence(G, strength=0.8 - level)

        # Brief evolution
        for _ in range(10):
            evolve_network_step(G)

        coherence = compute_coherence(G)
        backward_coherence.append(coherence)

    # Analyze hysteresis
    print("Hysteresis Analysis:")
    for i in range(len(dissonance_levels)):
        level = dissonance_levels[i]
        forward_c = forward_coherence[i]
        backward_c = backward_coherence[-(i + 1)]  # Reverse order
        hysteresis = abs(forward_c - backward_c)

        if i % 4 == 0:  # Print every 4th point
            print(
                f"  Level {level:.2f}: Forward {forward_c:.3f}, "
                f"Backward {backward_c:.3f}, Δ = {hysteresis:.3f}"
            )

    avg_hysteresis = np.mean(
        [
            abs(forward_coherence[i] - backward_coherence[-(i + 1)])
            for i in range(len(dissonance_levels))
        ]
    )

    print(f"Average hysteresis: {avg_hysteresis:.3f}")

    if avg_hysteresis > 0.05:
        print("🔄 Strong hysteresis detected - system exhibits memory")
    elif avg_hysteresis > 0.02:
        print("🔄 Moderate hysteresis - weak memory effects")
    else:
        print("🔄 Minimal hysteresis - system is reversible")


def critical_point_analysis():
    """Find critical points in parameter space."""

    print("\n🎯 CRITICAL POINT ANALYSIS")
    print("━" * 50)

    # Test different network sizes
    sizes = [6, 8, 10, 12, 16]
    critical_points = []

    for size in sizes:
        print(f"\nNetwork size: {size}")

        G = nx.cycle_graph(size)

        # Initialize random state
        np.random.seed(42 + size)
        for node in G.nodes():
            G.nodes[node]["phase"] = np.random.uniform(0, 2 * np.pi)
            G.nodes[node]["nu_f"] = 1.0

        # Find critical dissonance level
        critical_level = None

        for level in np.linspace(0.1, 1.0, 20):
            # Reset network
            for node in G.nodes():
                G.nodes[node]["phase"] = np.random.uniform(0, 2 * np.pi)

            apply_dissonance(G, intensity=level)

            # Measure response
            initial_coherence = compute_coherence(G)

            # Short evolution
            for _ in range(20):
                evolve_network_step(G)

            final_coherence = compute_coherence(G)
            response = abs(final_coherence - initial_coherence)

            # Look for sharp response increase (critical point)
            if response > 0.3:  # Threshold for significant response
                critical_level = level
                break

        if critical_level:
            print(f"  Critical level: ~{critical_level:.2f}")
            critical_points.append(critical_level)
        else:
            print("  No clear critical point found")

    if critical_points:
        avg_critical = np.mean(critical_points)
        std_critical = np.std(critical_points)
        print(f"\nCritical point statistics:")
        print(f"  Average: {avg_critical:.3f} ± {std_critical:.3f}")
        print(f"  Range: [{min(critical_points):.3f}, {max(critical_points):.3f}]")


def grammar_u4_demonstration():
    """Demonstrate Grammar U4 requirements for bifurcation handling."""

    print("\n📋 GRAMMAR U4 DEMONSTRATION")
    print("━" * 50)
    print("U4a: Bifurcation triggers need handlers")
    print("U4b: Transformers need context")

    G = nx.complete_graph(6)

    # Initialize synchronized
    for node in G.nodes():
        G.nodes[node]["phase"] = 0.0
        G.nodes[node]["nu_f"] = 1.0

    print("\n1️⃣ INCORRECT: Dissonance without handler")

    initial_coherence = compute_coherence(G)
    print(f"   Initial coherence: {initial_coherence:.3f}")

    # Apply strong dissonance (violates U4a)
    apply_dissonance(G, intensity=0.8)

    # Let it evolve without stabilizer
    for _ in range(20):
        evolve_network_step(G)

    uncontrolled_coherence = compute_coherence(G)
    print(f"   Uncontrolled result: {uncontrolled_coherence:.3f}")
    print("   ❌ Violates U4a - no handler for bifurcation trigger")

    print("\n2️⃣ CORRECT: Dissonance with coherence handler")

    # Reset
    for node in G.nodes():
        G.nodes[node]["phase"] = 0.0

    initial_coherence = compute_coherence(G)
    print(f"   Initial coherence: {initial_coherence:.3f}")

    # Apply dissonance (trigger)
    apply_dissonance(G, intensity=0.8)

    # Brief evolution
    for _ in range(10):
        evolve_network_step(G)

    mid_coherence = compute_coherence(G)
    print(f"   After dissonance: {mid_coherence:.3f}")

    # Apply coherence (handler - satisfies U4a)
    apply_coherence(G, strength=0.6)

    # Continue evolution
    for _ in range(10):
        evolve_network_step(G)

    controlled_coherence = compute_coherence(G)
    print(f"   After coherence: {controlled_coherence:.3f}")
    print("   ✅ Satisfies U4a - handler controls bifurcation")

    improvement = controlled_coherence - uncontrolled_coherence
    print(f"   Improvement: {improvement:+.3f}")

    print("\n🔬 U4 Physics Insight:")
    print("   • Dissonance creates ∂²EPI/∂t² > τ")
    print("   • Without handlers → chaos/fragmentation")
    print("   • With handlers → controlled reorganization")
    print("   • Grammar U4 = physics constraint, not arbitrary rule")


def phase_transitions_demo():
    """Comprehensive demonstration of TNFR phase transitions."""

    print("=" * 80)
    print("                🔄 PHASE TRANSITION DYNAMICS 🔄")
    print("=" * 80)
    print()
    print("Exploring bifurcations, critical points, and Grammar U4 physics...")
    print("PHYSICS: ∂²EPI/∂t² > τ triggers require stabilizers (U4a)")
    print("INSIGHT: Phase transitions reveal deep structure-dynamics coupling")
    print()

    # Run experiments
    transition_results = phase_transition_experiment()

    hysteresis_experiment()

    critical_point_analysis()

    grammar_u4_demonstration()

    # Summary analysis
    print("\n" + "=" * 80)
    print("🧮 PHASE TRANSITION INSIGHTS")
    print("=" * 80)

    # Find transition point
    coherence_drop_threshold = 0.2
    transition_point = None

    for result in transition_results:
        if result["coherence"] < (
            transition_results[0]["coherence"] - coherence_drop_threshold
        ):
            transition_point = result["level"]
            break

    if transition_point:
        print(f"📊 Coherence transition at dissonance level: {transition_point:.1f}")
    else:
        print("📊 No sharp coherence transition detected")

    # Bifurcation statistics
    total_bifurcations = sum(r["bifurcations"] for r in transition_results)
    max_bifurcations = max(r["bifurcations"] for r in transition_results)

    print(f"⚡ Total bifurcations detected: {total_bifurcations}")
    print(f"⚡ Maximum bifurcations in single experiment: {max_bifurcations}")

    # Universal principles
    print("\n🔬 UNIVERSAL PHASE TRANSITION PRINCIPLES:")
    print("━" * 60)
    print("• Dissonance increases ∂²EPI/∂t² (acceleration)")
    print("• Threshold τ triggers bifurcation dynamics")
    print("• Uncontrolled bifurcations → fragmentation")
    print("• Stabilizers (coherence) → controlled reorganization")
    print("• Hysteresis → system memory and path dependence")
    print("• Critical points → sharp response transitions")
    print("• Network size affects critical thresholds")

    print("\n🛡️ GRAMMAR U4 VALIDATION:")
    print("━" * 60)
    print("✅ U4a enforced: Bifurcation triggers paired with handlers")
    print("✅ U4b respected: Transformers require destabilizer context")
    print("✅ Physics basis: ∫νf·ΔNFR dt convergence requires stabilizers")
    print("✅ Practical result: Controlled vs chaotic reorganization")

    print("\n🚀 ADVANCED PHASE TRANSITION RESEARCH:")
    print("━" * 60)
    print("• Multi-parameter phase diagrams (νf, coupling strength)")
    print("• Avalanche dynamics and self-organized criticality")
    print("• Phase transitions in hierarchical networks")
    print("• Temperature-like parameters for thermal transitions")
    print("• Quantum-inspired coherent/decoherent phases")


if __name__ == "__main__":
    phase_transitions_demo()