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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: examples/02_physics_regimes/28_dissipative_systems_demo.py

28_dissipative_systems_demo.py

TNFR Dissipative Systems — Lindblad Decoherence and Grammar Violations.

Demonstrates how TNFR structural conservation extends to dissipative (open-system) regimes via the Lindblad master equation, and reveals WHY grammar rules U1-U6 exist: violations act as collapse operators that drive decoherence and purity loss.

Key results shown:

  1. Density operator snapshots: trace, purity, von Neumann entropy
  2. Lindblad dissipator action D[rho] from collapse operators
  3. Dissipation bound: |D[rho]| <= Sum_k ||L_k||^2 * (1 - Tr(rho^2))
  4. Purity decay and entropy production tracking
  5. Dissipative balance verification (contractivity, charge leak rate)
  6. Regime classification: weak / moderate / strong / decoherence
  7. Grammar violations as collapse operators (U2 -> decoherence mapping)
  8. Analytical predictions: amplitude damping and dephasing channels

See: theory/DISSIPATIVE_AND_OPEN_SYSTEMS.md for the full treatment.

Source Code

python
"""TNFR Dissipative Systems — Lindblad Decoherence and Grammar Violations.

Demonstrates how TNFR structural conservation extends to dissipative
(open-system) regimes via the Lindblad master equation, and reveals
WHY grammar rules U1-U6 exist: violations act as collapse operators
that drive decoherence and purity loss.

Key results shown:
1. Density operator snapshots: trace, purity, von Neumann entropy
2. Lindblad dissipator action D[rho] from collapse operators
3. Dissipation bound: |D[rho]| <= Sum_k ||L_k||^2 * (1 - Tr(rho^2))
4. Purity decay and entropy production tracking
5. Dissipative balance verification (contractivity, charge leak rate)
6. Regime classification: weak / moderate / strong / decoherence
7. Grammar violations as collapse operators (U2 -> decoherence mapping)
8. Analytical predictions: amplitude damping and dephasing channels

See: theory/DISSIPATIVE_AND_OPEN_SYSTEMS.md for the full treatment.
"""

from __future__ import annotations

import os
import sys

sys.path.insert(0, os.path.join(os.path.dirname(__file__), "..", "..", "src"))

import numpy as np

from tnfr.physics.dissipative_conservation import (
    DissipativeTimeSeries,
    capture_dissipative_snapshot,
    classify_dissipative_regime,
    compute_dissipation_bound,
    compute_dissipator_action,
    compute_purity_decay_bound,
    predict_amplitude_damping_purity,
    predict_dephasing_purity,
    verify_dissipative_balance,
)

SEED = 42


# ------------------------------------------------------------------
# Helpers
# ------------------------------------------------------------------


def _make_pure_state(dim: int = 4) -> np.ndarray:
    """Create a random pure-state density operator |psi><psi|."""
    rng = np.random.default_rng(SEED)
    psi = rng.standard_normal(dim) + 1j * rng.standard_normal(dim)
    psi /= np.linalg.norm(psi)
    return np.outer(psi, psi.conj())


def _make_mixed_state(dim: int = 4, purity_target: float = 0.5) -> np.ndarray:
    """Create a mixed-state density operator with approximate purity."""
    rng = np.random.default_rng(SEED + 1)
    # Blend pure state with maximally mixed
    pure = _make_pure_state(dim)
    identity = np.eye(dim, dtype=np.complex128) / dim
    # alpha * pure + (1-alpha) * I/d  gives purity ~ alpha^2 + (1-alpha)^2/d
    alpha = min(1.0, max(0.0, purity_target))
    rho = alpha * pure + (1 - alpha) * identity
    return rho / np.trace(rho).real


def _make_collapse_operators(dim: int = 4, strength: float = 0.1) -> list[np.ndarray]:
    """Create collapse operators for dephasing and amplitude damping."""
    ops: list[np.ndarray] = []

    # Dephasing: L_deph = sqrt(gamma) * |k><k| (diagonal projectors)
    for k in range(dim):
        L = np.zeros((dim, dim), dtype=np.complex128)
        L[k, k] = np.sqrt(strength)
        ops.append(L)

    # Amplitude damping: L_ad = sqrt(gamma) * |k><k+1| (lowering operators)
    for k in range(dim - 1):
        L = np.zeros((dim, dim), dtype=np.complex128)
        L[k, k + 1] = np.sqrt(strength * 0.5)
        ops.append(L)

    return ops


def _lindblad_step(
    rho: np.ndarray,
    collapse_operators: list[np.ndarray],
    hamiltonian: np.ndarray | None = None,
    dt: float = 0.1,
) -> np.ndarray:
    """One Euler step of the Lindblad master equation.

    d rho/dt = -i[H, rho] + D[rho]
    """
    # Hamiltonian contribution
    if hamiltonian is not None:
        drho = -1j * (hamiltonian @ rho - rho @ hamiltonian)
    else:
        drho = np.zeros_like(rho)

    # Dissipator D[rho]
    drho += compute_dissipator_action(rho, collapse_operators)

    rho_new = rho + dt * drho

    # Enforce Hermiticity and trace preservation
    rho_new = 0.5 * (rho_new + rho_new.conj().T)
    rho_new /= np.trace(rho_new).real

    return rho_new


# ------------------------------------------------------------------
# 1. Density operator snapshots
# ------------------------------------------------------------------


def demo_snapshots() -> None:
    """Capture and compare structural invariants of pure vs mixed states."""
    print("=" * 60)
    print("1. DENSITY OPERATOR SNAPSHOTS — pure vs mixed states")
    print("=" * 60)

    dim = 4

    pure = _make_pure_state(dim)
    mixed = _make_mixed_state(dim, purity_target=0.4)
    maximally_mixed = np.eye(dim, dtype=np.complex128) / dim

    for label, rho in [
        ("Pure state", pure),
        ("Mixed (P~0.4)", mixed),
        ("Maximally mixed", maximally_mixed),
    ]:
        snap = capture_dissipative_snapshot(rho)
        print(f"\n  {label}:")
        print(f"    Trace   = {snap.trace:.6f}  (should be 1)")
        print(
            f"    Purity  = {snap.purity:.6f}  (1=pure, 1/{dim}={1/dim:.4f}=max mixed)"
        )
        print(
            f"    Entropy = {snap.von_neumann_entropy:.6f}  (0=pure, ln({dim})={np.log(dim):.4f}=max)"
        )
    print()


# ------------------------------------------------------------------
# 2. Dissipation bound
# ------------------------------------------------------------------


def demo_dissipation_bound() -> None:
    """Verify the theoretical bound |D[rho]| <= Sum ||L_k||^2 * (1 - P)."""
    print("=" * 60)
    print("2. DISSIPATION BOUND — |D[rho]| <= Sum ||L_k||^2 * (1 - Tr(rho^2))")
    print("=" * 60)

    dim = 4
    collapse_ops = _make_collapse_operators(dim, strength=0.1)

    for label, rho in [
        ("Pure", _make_pure_state(dim)),
        ("Mixed", _make_mixed_state(dim, 0.5)),
        ("Max mixed", np.eye(dim, dtype=np.complex128) / dim),
    ]:
        snap = capture_dissipative_snapshot(rho)
        bound = compute_dissipation_bound(collapse_ops, snap.purity)
        D_action = compute_dissipator_action(rho, collapse_ops)
        actual = float(np.linalg.norm(D_action, ord="fro"))
        satisfied = actual <= bound + 1e-10

        print(f"\n  {label}:")
        print(f"    Purity P = {snap.purity:.6f}")
        print(f"    |D[rho]| actual = {actual:.6f}")
        print(f"    |D[rho]| bound  = {bound:.6f}")
        print(f"    Bound satisfied = {satisfied}")
    print()


# ------------------------------------------------------------------
# 3. Purity decay and entropy production tracking
# ------------------------------------------------------------------


def demo_purity_tracking() -> None:
    """Track purity decay and entropy growth under Lindblad evolution."""
    print("=" * 60)
    print("3. PURITY DECAY & ENTROPY PRODUCTION — Lindblad trajectory")
    print("=" * 60)

    dim = 4
    rho = _make_pure_state(dim)
    collapse_ops = _make_collapse_operators(dim, strength=0.08)
    dt = 0.1
    steps = 30

    series = DissipativeTimeSeries()
    current = rho.copy()

    for step in range(steps + 1):
        snap = capture_dissipative_snapshot(current)
        series.times.append(step * dt)
        series.purity.append(snap.purity)
        series.entropy.append(snap.von_neumann_entropy)

        if step < steps:
            current = _lindblad_step(current, collapse_ops, dt=dt)

    print(f"\n  Evolution: {steps} steps, dt = {dt}")
    print(
        f"  Purity:  {series.purity[0]:.4f} → {series.purity[-1]:.4f}  "
        f"(change: {series.purity[-1] - series.purity[0]:+.4f})"
    )
    print(
        f"  Entropy: {series.entropy[0]:.4f} → {series.entropy[-1]:.4f}  "
        f"(change: {series.entropy[-1] - series.entropy[0]:+.4f})"
    )
    print(f"  Total entropy produced: {series.entropy[-1] - series.entropy[0]:.4f}")

    # Show a few milestones
    milestones = [0, 5, 10, 20, steps]
    print("\n  Step  |  t    |  Purity  |  Entropy")
    print("  ------|-------|----------|----------")
    for m in milestones:
        if m <= steps:
            print(
                f"  {m:4d}  | {series.times[m]:5.2f} | {series.purity[m]:.4f}   | {series.entropy[m]:.4f}"
            )
    print()


# ------------------------------------------------------------------
# 4. Dissipative balance verification
# ------------------------------------------------------------------


def demo_dissipative_balance() -> None:
    """Verify the dissipative continuity equation between snapshots."""
    print("=" * 60)
    print("4. DISSIPATIVE BALANCE — continuity equation verification")
    print("=" * 60)

    dim = 4
    rho = _make_mixed_state(dim, purity_target=0.7)
    collapse_ops = _make_collapse_operators(dim, strength=0.05)
    dt = 0.1

    snap_before = capture_dissipative_snapshot(rho)
    rho_after = _lindblad_step(rho, collapse_ops, dt=dt)
    snap_after = capture_dissipative_snapshot(rho_after)

    balance = verify_dissipative_balance(
        snap_before,
        snap_after,
        dt=dt,
        collapse_operators=collapse_ops,
    )

    print(f"\n  Purity:  {balance.purity_before:.6f} → {balance.purity_after:.6f}")
    print(
        f"  Purity decay rate:       {balance.purity_decay_rate:.6f} (should be <= 0)"
    )
    print(
        f"  Entropy production rate: {balance.entropy_production_rate:.6f} (should be >= 0)"
    )
    print(f"  Trace drift:             {balance.trace_drift:.2e}")
    print(f"  Dissipation bound:       {balance.dissipation_bound:.6f}")
    print(f"  Actual dissipation:      {balance.actual_dissipation:.6f}")
    print(f"  Charge leak rate:        {balance.charge_leak_rate:.6f}")
    print(f"  Contractivity gap:       {balance.contractivity_gap:.6f}")
    print(f"  Is contractive?          {balance.is_contractive}")
    print()


# ------------------------------------------------------------------
# 5. Regime classification
# ------------------------------------------------------------------


def demo_regime_classification() -> None:
    """Classify dissipative strength into TNFR grammar tiers."""
    print("=" * 60)
    print("5. REGIME CLASSIFICATION — four dissipative tiers")
    print("=" * 60)

    dim = 4
    strengths = [0.001, 0.02, 0.1, 0.5]
    dt = 0.5  # Larger dt amplifies dissipation

    for strength in strengths:
        rho = _make_mixed_state(dim, purity_target=0.8)
        collapse_ops = _make_collapse_operators(dim, strength=strength)

        snap_before = capture_dissipative_snapshot(rho)
        rho_after = _lindblad_step(rho, collapse_ops, dt=dt)
        snap_after = capture_dissipative_snapshot(rho_after)

        balance = verify_dissipative_balance(
            snap_before, snap_after, dt=dt, collapse_operators=collapse_ops
        )
        classification = classify_dissipative_regime(balance)

        print(f"\n  Collapse strength = {strength}")
        print(f"    Regime:        {classification['regime']}")
        print(f"    Quality:       {classification['conservation_quality']:.3f}")
        print(f"    Grammar:       {classification['grammar_analog']}")
    print()


# ------------------------------------------------------------------
# 6. Grammar violations as collapse operators
# ------------------------------------------------------------------


def demo_grammar_violations() -> None:
    """Show how grammar U2 violation magnitude maps to dissipation."""
    print("=" * 60)
    print("6. GRAMMAR VIOLATIONS → COLLAPSE OPERATORS")
    print("=" * 60)

    dim = 4
    rho = _make_pure_state(dim)

    print("\n  U2 compliance level  |  After 20 steps")
    print("  --------------------|-------------------")

    for label, strength in [
        ("Full compliance (weak)", 0.001),
        ("Partial violation (moderate)", 0.03),
        ("Strong violation", 0.15),
        ("No stabilizers (critical)", 0.5),
    ]:
        collapse_ops = _make_collapse_operators(dim, strength=strength)
        current = rho.copy()
        for _ in range(20):
            current = _lindblad_step(current, collapse_ops, dt=0.1)

        snap = capture_dissipative_snapshot(current)
        print(f"  {label:35s}  P={snap.purity:.4f}  S={snap.von_neumann_entropy:.4f}")

    print("\n  Interpretation: Stronger grammar violations (U2 destabilizers")
    print("  without stabilizers) map to stronger collapse operators,")
    print("  causing faster purity loss and entropy production.")
    print()


# ------------------------------------------------------------------
# 7. Analytical predictions
# ------------------------------------------------------------------


def demo_analytical_predictions() -> None:
    """Compare Lindblad evolution with analytical predictions."""
    print("=" * 60)
    print("7. ANALYTICAL PREDICTIONS — amplitude damping & dephasing")
    print("=" * 60)

    dim = 4
    gamma = 0.1
    t_values = [0.0, 1.0, 3.0, 5.0, 10.0]

    # Amplitude damping prediction
    print("\n  Amplitude damping (gamma = 0.1):")
    print("    t     |  P_predicted  |  P_actual")
    print("  --------|---------------|----------")

    rho0 = _make_mixed_state(dim, purity_target=0.6)
    snap0 = capture_dissipative_snapshot(rho0)
    P0 = snap0.purity

    # Build amplitude damping collapse operators
    ad_ops: list[np.ndarray] = []
    for k in range(dim - 1):
        L = np.zeros((dim, dim), dtype=np.complex128)
        L[k, k + 1] = np.sqrt(gamma)
        ad_ops.append(L)

    for t in t_values:
        steps = max(1, int(t / 0.05))
        dt = t / steps if steps > 0 else 0.05
        current = rho0.copy()
        for _ in range(steps):
            current = _lindblad_step(current, ad_ops, dt=dt)
        snap = capture_dissipative_snapshot(current)
        predicted = predict_amplitude_damping_purity(P0, gamma, t, dim)
        print(f"  {t:7.1f} | {predicted:13.6f} | {snap.purity:.6f}")

    # Dephasing prediction
    print("\n  Pure dephasing (gamma = 0.1):")
    print("    t     |  P_predicted  |  P_actual")
    print("  --------|---------------|----------")

    deph_ops: list[np.ndarray] = []
    for k in range(dim):
        L = np.zeros((dim, dim), dtype=np.complex128)
        L[k, k] = np.sqrt(gamma)
        deph_ops.append(L)

    for t in t_values:
        steps = max(1, int(t / 0.05))
        dt = t / steps if steps > 0 else 0.05
        current = rho0.copy()
        for _ in range(steps):
            current = _lindblad_step(current, deph_ops, dt=dt)
        snap = capture_dissipative_snapshot(current)
        predicted = predict_dephasing_purity(rho0, gamma, t)
        print(f"  {t:7.1f} | {predicted:13.6f} | {snap.purity:.6f}")
    print()


# ------------------------------------------------------------------
# Main
# ------------------------------------------------------------------


def main() -> None:
    print()
    print("TNFR DISSIPATIVE SYSTEMS — LINDBLAD DECOHERENCE & GRAMMAR")
    print("Grammar violations mapping to Lindblad collapse operators.")
    print("Conservation → Dissipation → Decoherence continuum.")
    print()

    demo_snapshots()
    demo_dissipation_bound()
    demo_purity_tracking()
    demo_dissipative_balance()
    demo_regime_classification()
    demo_grammar_violations()
    demo_analytical_predictions()

    print("=" * 60)
    print("CONCLUSION: Grammar rules U1-U6 ensure conservative dynamics.")
    print("Violations act as Lindblad collapse operators, causing")
    print("purity loss, entropy production, and structural decoherence.")
    print("See: theory/DISSIPATIVE_AND_OPEN_SYSTEMS.md")
    print("=" * 60)


if __name__ == "__main__":
    main()